2,899 results
Search Results
2. Papers from the Australian Biophysical Society Meeting 2000
- Published
- 2002
- Full Text
- View/download PDF
3. A novel assay based on pre-equilibrium titration curves for the determination of enzyme inhibitor binding kinetics
- Author
-
Marc Vanhove, Alan W. Stitt, Bernard Noppen, and Anouk Vanbelle
- Subjects
0301 basic medicine ,Titration curve ,Methods Paper ,Biophysics ,Peptide ,010402 general chemistry ,01 natural sciences ,Dissociation (chemistry) ,03 medical and health sciences ,Enzyme Inhibitors ,chemistry.chemical_classification ,Serine protease ,Tight-binding inhibitors ,Chromatography ,biology ,Serine Endopeptidases ,General Medicine ,Kallikrein ,Receptor–ligand kinetics ,Pre-equilibrium inhibition curves ,0104 chemical sciences ,Kinetics ,030104 developmental biology ,Enzyme ,chemistry ,Enzyme inhibition assay ,Enzyme inhibitor ,biology.protein ,Protein Binding - Abstract
Selection of pharmacological agents based on potency measurements performed at equilibrium fail to incorporate the kinetic aspects of the drug–target interaction. Here we describe a method for screening or characterization of enzyme inhibitors that allows the concomitant determination of the equilibrium inhibition constant in unison with rates of complex formation and dissociation. The assay is distinct from conventional enzymatic assays and is based on the analysis of inhibition curves recorded prior to full equilibration of the system. The methodology is illustrated using bicyclic peptide inhibitors of the serine protease plasma kallikrein.
- Published
- 2021
4. Peptide-based pore formation and cell membrane deformation: European Biophysics Journal Prizes at EBSA 2023.
- Author
-
Gilbert, Robert J. C.
- Subjects
- *
CELL membrane formation , *BIOPHYSICS , *MOLECULAR dynamics , *CELL-penetrating peptides , *ATOMIC force microscopy , *ERYTHROCYTE deformability , *MELITTIN - Abstract
The European Biophysics Journal Prizes awarded at the European Biophysical Societies Association (EBSA) Congress in Stockholm in the Summer of 2023 recognised papers published in 2020 and 2021 which made use of multiple complementing experimental, theoretical and computational approaches. One of the winning papers addressed the specific role of arginine residues within antimicrobial and cell-penetrating peptides, in promoting membrane defect stabilisation and pore formation. The other winning paper described the influence of atomic force microscopy probe geometry on the measurement of surface deformability, assessed for investigation of the differing viscoelastic properties of non-malignant and cancerous cells. These papers showcase biophysical science; the importance of combining different experimental, modelling and molecular dynamics methods; and how researchers need to understand the theoretical basis and the limitations of the techniques they use. EBSA warmly congratulates the authors on their work and its subsequent recognition. Publication of these papers also demonstrates the ongoing commitment of the European Biophysics Journal to molecular scale and to systems biophysics, and to support of the international biophysical community. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission.
- Author
-
Hall, Damien
- Subjects
PRIONS ,SACCHAROMYCES cerevisiae ,LIFE cycles (Biology) ,SCRAPIE ,YEAST ,CELLULAR aging ,CHILDBEARING age - Abstract
The single-celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (Monitoring Induction and Loss of prions in Cells; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
6. Mechanisms of stationary voltage fluctuation in the neuromuscular junction endplate and corresponding denoising paradigms.
- Author
-
Wang, Jia-Zeng, Hu, Pengkun, and Ma, Shu
- Subjects
- *
MYONEURAL junction , *POWER spectra , *VOLTAGE , *ACETYLCHOLINE , *ANATOMY - Abstract
The neuromuscular junction (NMJ) has an elaborate anatomy to ensure agile and accurate signal transmission. Based on our formerly obtained expressions of the thermal and conductance induced voltage fluctuations, in this paper, the mechanisms underlying the conductance-induced voltage fluctuation are characterized from two aspects: the scaling laws with respect to either of the two system-size factors, the number of receptors or the membrane area; and the "seesaw effect" with respect to the intensive parameter, the concentration of acetylcholine. According to these mechanisms, several aspects of the NMJ anatomy are explained from a denoising perspective. Finally, the power spectra of the two types of voltage fluctuations are characterized by their specific scaling laws, based on which we explain why the endplate noise has the low-frequency property that is described by the term "seashell sound". [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
7. Insights into open/closed conformations of the catalytically active human guanylate kinase as investigated by small-angle X-ray scattering
- Author
-
Ivan Rajkovic, Nazimuddin Khan, Manfred Konrad, Rohit Jain, Simone Techert, and Andreas Menzel
- Subjects
Nucleotide kinase ,0301 basic medicine ,Guanylate kinase ,Guanine ,Stereochemistry ,Molecular Sequence Data ,Allosteric regulation ,Biophysics ,Molecular Dynamics Simulation ,03 medical and health sciences ,chemistry.chemical_compound ,X-Ray Diffraction ,Catalytic Domain ,ddc:570 ,Scattering, Small Angle ,Humans ,Amino Acid Sequence ,Protein conformations ,Peptide sequence ,Small-angle X-ray scattering (SAXS) ,chemistry.chemical_classification ,Original Paper ,Guanylate kinase (GMPK) ,Kinase ,Small-angle X-ray scattering ,Chemistry ,General Medicine ,3. Good health ,030104 developmental biology ,Enzyme ,Guanylate Cyclase ,Nucleoside - Abstract
Bio-catalysis is the outcome of a subtle interplay between internal motions in enzymes and chemical kinetics. Small-angle X-ray scattering (SAXS) investigation of an enzyme’s internal motions during catalysis offers an integral view of the protein’s structural plasticity, dynamics, and function, which is useful for understanding allosteric effects and developing novel medicines. Guanylate kinase (GMPK) is an essential enzyme involved in the guanine nucleotide metabolism of unicellular and multicellular organisms. It is also required for the intracellular activation of numerous antiviral and anticancer purine nucleoside analog prodrugs. Catalytically active recombinant human GMPK (hGMPK) was purified for the first time and changes in the size and shape of open/closed hGMPK were tracked by SAXS. The binding of substrates (GMP + AMPPNP or Ap5G or GMP + ADP) resulted in the compaction of size and shape of hGMPK. The structural changes between open and completely closed hGMPK conformation were confirmed by observing differences in the hGMPK secondary structures with circular dichroism spectroscopy. Graphical abstract Electronic supplementary material The online version of this article (doi:10.1007/s00249-015-1079-9) contains supplementary material, which is available to authorized users.
- Published
- 2015
8. Molecular dynamics study on protein–water interplay in the mechanogating of the bacterial mechanosensitive channel MscL
- Author
-
Masahiro Sokabe and Yasuyuki Sawada
- Subjects
Mechano-gating ,Molecular Sequence Data ,Vapor lock ,Biophysics ,Hydration ,Gating ,Molecular Dynamics Simulation ,Mechanotransduction, Cellular ,Ion Channels ,Hydrophobic effect ,Molecular dynamics ,Amino Acid Sequence ,Dewetting ,Ion channel ,Hydrogen bond ,Original Paper ,Molecular dynamics simulations ,Chemistry ,Escherichia coli Proteins ,Hydrogen Bonding ,General Medicine ,MscL ,Crystallography ,Wetting transition ,Helix ,Mechanosensitive channels ,Hydrophobic and Hydrophilic Interactions ,Ion Channel Gating - Abstract
One of the goals of mechanosensitive channel (MSC) studies is to understand the underlying molecular and biophysical mechanisms of the mechano-gating process from force sensing to gate opening. We focus on the latter process and investigate the role of water in the bacterial MSC MscL, which is activated by membrane tension. We analyze the interplay between water and the gate-constituting amino acids, Leu19-Gly26, through molecular dynamics simulations. To highlight the role of water, specifically hydration of the gate, in MscL gating, we restrain lateral movements of the water molecules along the water-vapor interfaces at the top and bottom of the vapor bubble, plugging the closed gate. The gating behaviors in this model and the normal MscL model, in which water movements are unrestrained, are compared. In the normal model, increased membrane tension breaks the hydrogen bond between Leu19 and Val 23 of the inner helix, exposing the backbone carbonyl oxygen of Leu19 to the water-accessible lumen side of the gate. Associated with this activity, water comes to access the vapor region and stably interacts with the carbonyl oxygen to induce a dewetting to wetting transition that facilitates gate expansion toward channel opening. By contrast, in the water-restrained model, carbonyl oxygen is also exposed, but no further conformational changes occur at the gate. This suggests that gate opening relies on a conformational change initiated by wetting. The penetrated water weakens the hydrophobic interaction between neighboring transmembrane inner helices called the "hydrophobic lock" by wedging into the space between their interacting portions.
- Published
- 2015
9. Trace membrane additives affect lipid phases with distinct mechanisms: a modified Ising model
- Author
-
Christopher V. Kelly and Rebecca L. Meerschaert
- Subjects
Phase transition ,Lipid Bilayers ,Biophysics ,Mole fraction ,Miscibility ,Phase Transition ,Lipid membrane ,Phase (matter) ,Membrane fluidity ,Transition Temperature ,Organic chemistry ,Lipid bilayer phase behavior ,Lipid bilayer ,Original Paper ,Chemistry ,Phase partitioning ,General Medicine ,Lipids ,Membrane ,Models, Chemical ,Chemical physics ,Correlation length ,lipids (amino acids, peptides, and proteins) ,Phase transition temperature ,Simulation - Abstract
The addition of trace molecules into membranes can significantly alter the morphology of the co-existing liquid phases and lipid phase transition temperature. Membrane additives may affect lipid phase dynamics through preferentially partitioning to the boundary between lipid phases or preferentially mixing into one lipid phase. The characteristic differences between these mechanisms are demonstrated here in a minimalistic nearest neighbor model to provide a framework for how slight changes to membrane composition may affect lipid-phase-dependent processes, such as lipid-raft formation, immunological signaling, and molecular sorting preceding endocytosis with coexisting liquid phases. Within the low mole fractions explored here (≤3 mol%), increasing the additive concentration linearly changed the phase miscibility temperature. Rotationally asymmetric Janus particles reduced the miscibility transition temperature for all fractions and degree of phase polarization. Rotationally symmetric additives, however, either increased or decreased the phase miscibility temperature depending on the phase preference of the additive. While most experimental molecules may contain aspects of both of these idealized additives, this model provides a broad framework to quantify the effects of membrane additives in regard to lipid phase preference, lipid-raft association, and contribution to lipid phase-dependent molecular sorting. Electronic supplementary material The online version of this article (doi:10.1007/s00249-015-1017-x) contains supplementary material, which is available to authorized users.
- Published
- 2015
10. Peptide-membrane interactions of arginine-tryptophan peptides probed using quartz crystal microbalance with dissipation monitoring
- Author
-
Hanna A. Rydberg, Nils Carlsson, Noomi Altgärde, Angelika Kunze, Sofia Svedhem, and Bengt Nordén
- Subjects
Quartz crystal microbalance with dissipation monitoring ,Molecular Sequence Data ,Antimicrobial peptides ,Biophysics ,Membrane biology ,Peptide ,Arginine ,Protein Structure, Secondary ,Cell membrane ,chemistry.chemical_compound ,medicine ,Amino Acid Sequence ,POPC ,Peptide sequence ,chemistry.chemical_classification ,Original Paper ,Chemistry ,Cell Membrane ,Tryptophan ,Cell-penetrating peptides ,Phosphatidylglycerols ,Peptide-membrane interactions ,General Medicine ,Membrane-active peptides ,Amino acid ,Membrane ,medicine.anatomical_structure ,Biochemistry ,Liposomes ,Phosphatidylcholines ,Quartz Crystal Microbalance Techniques ,Peptides - Abstract
Membrane-active peptides include peptides that can cross cellular membranes and deliver macromolecular cargo as well as peptides that inhibit bacterial growth. Some of these peptides can act as both transporters and antibacterial agents. It is desirable to combine the knowledge from these two different fields of membrane-active peptides into design of new peptides with tailored actions, as transporters of cargo or as antibacterial substances, targeting specific membranes. We have previously shown that the position of the amino acid tryptophan in the peptide sequence of three arginine-tryptophan peptides affects their uptake and intracellular localization in live mammalian cells, as well as their ability to inhibit bacterial growth. Here, we use quartz crystal microbalance with dissipation monitoring to assess the induced changes caused by binding of the three peptides to supported model membranes composed of POPC, POPC/POPG, POPC/POPG/cholesterol or POPC/lactosyl PE. Our results indicate that the tryptophan position in the peptide sequence affects the way these peptides interact with the different model membranes and that the presence of cholesterol in particular seems to affect the membrane interaction of the peptide with an even distribution of tryptophans in the peptide sequence. These results give mechanistic insight into the function of these peptides and may aid in the design of membrane-active peptides with specified cellular targets and actions. Electronic supplementary material The online version of this article (doi:10.1007/s00249-014-0958-9) contains supplementary material, which is available to authorized users.
- Published
- 2014
11. European Biophysics Journal: YOUR Journal.
- Subjects
BIOPHYSICS periodicals ,PUBLISHING ,COPYRIGHT of electronic data ,EDITORS ,MANAGEMENT committees - Published
- 2011
- Full Text
- View/download PDF
12. MultiSig: a new high-precision approach to the analysis of complex biomolecular systems
- Author
-
Melanie Nikolajski, Thomas Heinze, Gary G. Adams, Stephen E. Harding, Arthur J. Rowe, and Richard B. Gillis
- Subjects
Rayleigh interference optics ,Instrument approach ,Biophysics ,Molecular weight histograms ,Signal ,Fitting algorithm ,Optics ,Polysaccharides ,Point average molecular weights ,Histogram ,Sedimentation equilibrium ,Original Paper ,Spatial filtering ,Spatial filter ,Chemistry ,business.industry ,Noise (signal processing) ,Mode (statistics) ,General Medicine ,Molecular Weight ,Orders of magnitude (time) ,Solvents ,Numerical differentiation ,Biological system ,business ,Ultracentrifugation ,Algorithms - Abstract
MultiSig is a newly developed mode of analysis of sedimentation equilibrium (SE) experiments in the analytical ultracentrifuge, having the capability of taking advantage of the remarkable precision (~0.1 % of signal) of the principal optical (fringe) system employed, thus supplanting existing methods of analysis through reducing the ‘noise’ level of certain important parameter estimates by up to orders of magnitude. Long-known limitations of the SE method, arising from lack of knowledge of the true fringe number in fringe optics and from the use of unstable numerical algorithms such as numerical differentiation, have been transcended. An approach to data analysis, akin to ‘spatial filtering’, has been developed, and shown by both simulation and practical application to be a powerful aid to the precision with which near-monodisperse systems can be analysed, potentially yielding information on protein-solvent interaction. For oligo- and poly-disperse systems the information returned includes precise average mass distributions over both cell radial and concentration ranges and mass-frequency histograms at fixed radial positions. The application of MultiSig analysis to various complex heterogenous systems and potentially multiply-interacting carbohydrate oligomers is described.
- Published
- 2013
13. Interaction of formin FH2 with skeletal muscle actin. EPR and DSC studies
- Author
-
Pál Gróf, Miklós Nyitrai, Tünde Kupi, and József Belágyi
- Subjects
Fetal Proteins ,Conformational change ,Hot Temperature ,Maleimido-TEMPO ,Biophysics ,Formins ,macromolecular substances ,Formin ,03 medical and health sciences ,Protein structure ,Animals ,Muscle, Skeletal ,Protein Structure, Quaternary ,Cytoskeleton ,Actin ,030304 developmental biology ,Original Paper ,0303 health sciences ,Calorimetry, Differential Scanning ,biology ,Protein Stability ,Chemistry ,Microfilament Proteins ,fungi ,030302 biochemistry & molecular biology ,Electron Spin Resonance Spectroscopy ,Nuclear Proteins ,Actin remodeling ,General Medicine ,Actin cytoskeleton ,Actins ,Protein Structure, Tertiary ,Cell biology ,Protein conformation ,biology.protein ,MDia1 ,Protein Multimerization ,Electron paramagnetic resonance ,Protein Binding - Abstract
Formins are highly conserved proteins that are essential in the formation and regulation of the actin cytoskeleton. The formin homology 2 (FH2) domain is responsible for actin binding and acts as an important nucleating factor in eukaryotic cells. In this work EPR and DSC were used to investigate the properties of the mDia1-FH2 formin fragment and its interaction with actin. MDia1-FH2 was labeled with a maleimide spin probe (MSL). EPR results suggested that the MSL was attached to a single SH group in the FH2. In DSC and temperature-dependent EPR experiments we observed that mDia1-FH2 has a flexible structure and observed a major temperature-induced conformational change at 41 °C. The results also confirmed the previous observation obtained by fluorescence methods that formin binding can destabilize the structure of actin filaments. In the EPR experiments the intermolecular connection between the monomers of formin dimers proved to be flexible. Considering the complex molecular mechanisms underlying the cellular roles of formins this internal flexibility of the dimers is probably important for manifestation of their biological functions. Electronic supplementary material The online version of this article (doi:10.1007/s00249-013-0922-0) contains supplementary material, which is available to authorized users.
- Published
- 2013
14. Cooperative regulation of myosin-S1 binding to actin filaments by a continuous flexible Tm–Tn chain
- Author
-
Hugh Griffiths, Oliver Kayser-Herold, Xiaochuan Li, Michael A. Geeves, and Srboljub M. Mijailovich
- Subjects
Static Electricity ,Biophysics ,Tropomyosin chain ,Tropomyosin ,macromolecular substances ,Molecular Dynamics Simulation ,Myosins ,Stopped flow ,03 medical and health sciences ,0302 clinical medicine ,Allosteric Regulation ,Myosin ,Troponin I ,Animals ,Actin ,030304 developmental biology ,Original Paper ,0303 health sciences ,Chemistry ,Cooperative binding ,General Medicine ,Striated muscle contraction ,Myosin-S1 binding ,Actin cytoskeleton ,Ca2+ sensitivity ,Troponin ,Actin Cytoskeleton ,Biochemistry ,Myosin binding ,Calcium ,030217 neurology & neurosurgery ,Protein Binding - Abstract
The regulation of striated muscle contraction involves cooperative interactions between actin filaments, myosin-S1 (S1), tropomyosin (Tm), troponin (Tn), and calcium. These interactions are modeled by treating overlapping tropomyosins as a continuous flexible chain (CFC), weakly confined by electrostatic interactions with actin. The CFC is displaced locally in opposite directions on the actin surface by the binding of either S1 or Troponin I (TnI) to actin. The apparent rate constants for myosin and TnI binding to and detachment from actin are then intrinsically coupled via the CFC model to the presence of neighboring bound S1s and TnIs. Monte Carlo simulations at prescribed values of the CFC stiffness, the CFC’s degree of azimuthal confinement, and the angular displacements caused by the bound proteins were able to predict the stopped-flow transients of S1 binding to regulated F-actin. The transients collected over a large range of calcium concentrations could be well described by adjusting a single calcium-dependent parameter, the rate constant of TnI detachment from actin, k−I. The resulting equilibrium constant \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ K_{\text{B}} \equiv 1/K_{\text{I}} $$\end{document} varied sigmoidally with the free calcium, increasing from 0.12 at low calcium (pCa >7) to 12 at high calcium (pCa
- Published
- 2012
15. Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations
- Author
-
Chris Oostenbrink and Gabor Nagy
- Subjects
In silico ,Molecular Sequence Data ,Biophysics ,Mutation, Missense ,Stereoisomerism ,Plasma protein binding ,Molecular Dynamics Simulation ,01 natural sciences ,03 medical and health sciences ,Molecular dynamics ,Computational chemistry ,0103 physical sciences ,Animals ,Amino Acid Sequence ,Binding site ,030304 developmental biology ,0303 health sciences ,Original Paper ,Binding Sites ,010304 chemical physics ,Chemistry ,CYP2D6 ,Wild type ,Stereoselectivity ,General Medicine ,Hamiltonian replica exchange ,Propranolol ,Cytochrome P-450 CYP2D6 ,Thermodynamics ,Free energy calculations ,Improved sampling ,Protein Binding - Abstract
Cytochrome P450 2D6 is a major drug-metabolising enzyme with a wide substrate range. A single-point mutation introduced in this enzyme induces stereoselective binding of R and S-propranolol whereas the wild type has no preference. The system has previously been studied both experimentally and computationally (de Graaf et al. in Eur Biophys J 36:589–599, 2007a). The in silico study reported hysteresis and significant deviations from closure of thermodynamic cycles, probably because of lack of sampling. Here, we focus on the effect of prolonged simulation time and enhanced sampling methods, such as Hamiltonian replica exchange, to reduce these problems and to improve the precision of free energy calculations. Finally we rationalize the results at a molecular level and compare data with experimental findings and previously estimated free energies. Graphical Abstract Propranolol (PPD) binds stereospecifically to cytochrome P450 2D6, if the mutation F483A is introduced, by reducing binding affinity to R-PPD. This observation has previously been studied by molecular dynamics, by use of several different thermodynamic cycles. Previous computational results suffered from internal inconsistencies, probably because of insufficient sampling. Here we use prolonged simulation time and Hamiltonian replica exchange to overcome the inconsistencies, and give a possible rationalization of the phenomenon at a molecular level.
- Published
- 2012
16. On the biophysics of cathodal galvanotaxis in rat prostate cancer cells: Poisson–Nernst–Planck equation approach
- Author
-
Przemysław Borys
- Subjects
Male ,Sodium ,Biophysics ,chemistry.chemical_element ,Calcium ,Cathodal galvanotaxis ,Mat-Ly-Lu ,Models, Biological ,Sodium Channels ,Calcium in biology ,Metastasis ,Membrane Potentials ,Cell Movement ,Myosin ,Tumor Cells, Cultured ,Animals ,Computer Simulation ,Nernst–Planck equation ,Neoplasm Metastasis ,Electrodes ,Membrane potential ,Original Paper ,Prostate cancer ,Sodium channel ,Electric Conductivity ,Prostatic Neoplasms ,Motility ,Depolarization ,General Medicine ,Rats ,Poisson–Nernst–Planck equation ,chemistry - Abstract
Rat prostate cancer cells have been previously investigated using two cell lines: a highly metastatic one (Mat-Ly-Lu) and a nonmetastatic one (AT-2). It turns out that the highly metastatic Mat-Ly-Lu cells exhibit a phenomenon of cathodal galvanotaxis in an electric field which can be blocked by interrupting the voltage-gated sodium channel (VGSC) activity. The VGSC activity is postulated to be characteristic for metastatic cells and seems to be a reasonable driving force for motile behavior. However, the classical theory of cellular motion depends on calcium ions rather than sodium ions. The current research provides a theoretical connection between cellular sodium inflow and cathodal galvanotaxis of Mat-Ly-Lu cells. Electrical repulsion of intracellular calcium ions by entering sodium ions is proposed after depolarization starting from the cathodal side. The disturbance in the calcium distribution may then drive actin polymerization and myosin contraction. The presented modeling is done within a continuous one-dimensional Poisson-Nernst-Planck equation framework.
- Published
- 2012
17. The effect of membrane curvature on the conformation of antimicrobial peptides: implications for binding and the mechanism of action
- Author
-
Rong Chen and Alan E. Mark
- Subjects
Protein Conformation ,Stereochemistry ,Lipid Bilayers ,Antimicrobial peptides ,Biophysics ,Membrane biology ,Molecular Dynamics Simulation ,Biology ,Amphibian Proteins ,Lipid bilayer ,Cell membrane ,GROMOS ,Anti-Infective Agents ,Secondary structure ,medicine ,Original Paper ,Antiinfective agent ,Binding Sites ,Curvature ,Circular Dichroism ,Cell Membrane ,General Medicine ,Transmembrane protein ,Membrane ,medicine.anatomical_structure ,Membrane curvature ,Antimicrobial Cationic Peptides - Abstract
Short cationic antimicrobial peptides (AMPs) are believed to act either by inducing transmembrane pores or disrupting membranes in a detergent-like manner. For example, the antimicrobial peptides aurein 1.2, citropin 1.1, maculatin 1.1 and caerin 1.1, despite being closely related, appear to act by fundamentally different mechanisms depending on their length. Using molecular dynamics simulations, the structural properties of these four peptides have been examined in solution as well as in a variety of membrane environments. It is shown that each of the peptides has a strong preference for binding to regions of high membrane curvature and that the structure of the peptides is dependent on the degree of local curvature. This suggests that the shorter peptides aurein 1.2 and citropin 1.1 act via a detergent-like mechanism because they can induce high local, but not long-range curvature, whereas the longer peptides maculatin 1.1 and caerin 1.1 require longer range curvature to fold and thus bind to and stabilize transmembrane pores.
- Published
- 2011
18. Biophysical properties of Saccharomyces cerevisiae and their relationship with HOG pathway activation
- Author
-
Edda Klipp, Mattias Goksör, Stefan Hohmann, Emma Eriksson, Francesc Posas, Mathias Peter, Jörg Schaber, Serge Pelet, Miquel Àngel Adrover, Dagmara Medrala Klein, and Elzbieta Petelenz-Kurdziel
- Subjects
Glycerol ,0106 biological sciences ,Volumetric elastic modulus ,Osmotic shock ,Turgor pressure ,Intracellular Space ,Biophysics ,Saccharomyces cerevisiae ,Biology ,Cell wall elasticity ,Models, Biological ,Plasmolysis ,010603 evolutionary biology ,01 natural sciences ,Biophysical Phenomena ,Cell wall ,03 medical and health sciences ,Cell Wall ,Osmotic Pressure ,Elastic Modulus ,Turgor ,High osmolarity glycerol (HOG) signaling ,Elasticity (economics) ,Elastic modulus ,030304 developmental biology ,Original Paper ,0303 health sciences ,Osmotic concentration ,Cell Membrane ,Reproducibility of Results ,General Medicine ,Yeast ,Biochemistry ,Thermodynamics ,Saccharomyces cerevisiae -- Metabolisme ,Model discrimination ,Extracellular Space ,Membranes cel·lulars ,Intracellular ,Signal Transduction - Abstract
Parameterized models of biophysical and mechanical cell properties are important for predictive mathematical modeling of cellular processes. The concepts of turgor, cell wall elasticity, osmotically active volume, and intracellular osmolarity have been investigated for decades, but a consistent rigorous parameterization of these concepts is lacking. Here, we subjected several data sets of minimum volume measurements in yeast obtained after hyper-osmotic shock to a thermodynamic modeling framework. We estimated parameters for several relevant biophysical cell properties and tested alternative hypotheses about these concepts using a model discrimination approach. In accordance with previous reports, we estimated an average initial turgor of 0.6 ± 0.2 MPa and found that turgor becomes negligible at a relative volume of 93.3 ± 6.3% corresponding to an osmotic shock of 0.4 ± 0.2 Osm/l. At high stress levels (4 Osm/l), plasmolysis may occur. We found that the volumetric elastic modulus, a measure of cell wall elasticity, is 14.3 ± 10.4 MPa. Our model discrimination analysis suggests that other thermodynamic quantities affecting the intracellular water potential, for example the matrix potential, can be neglected under physiological conditions. The parameterized turgor models showed that activation of the osmosensing high osmolarity glycerol (HOG) signaling pathway correlates with turgor loss in a 1:1 relationship. This finding suggests that mechanical properties of the membrane trigger HOG pathway activation, which can be represented and quantitatively modeled by turgor. This work was supported via several projects funded by the European Commission: QUASI (Contract No. 503230 to SH, EK, FP and MP), CELLCOMPUT (Contract No. 043310 to SH, EK and FP), UNICELLSYS (Contract No. 201142 to SH, EK, FP, MP and MG), SYSTEMSBIOLOGY (Contract No. 514169 to SH and EK), and AMPKIN (Contract No. 518181 to SH and MG). In addition work was funded by grants from the Swedish Foundation for Strategic Research SSF (Bio-X to MG), the Swedish Research Council (project grants to SH and MG), the Carl Trygger Foundation (to MG), the Science Faculty, University of Gothenburg (to SH and MG), and the Swiss systemsX.ch (to MP)
- Published
- 2010
19. Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ
- Author
-
Jozef Hritz, Tilman Läppchen, and Chris Oostenbrink
- Subjects
Ensemble average ,GTP' ,Polymers ,Protein Conformation ,One-step free energy perturbation ,Stereochemistry ,Biophysics ,macromolecular substances ,Dihedral angle ,FtsZ ,01 natural sciences ,03 medical and health sciences ,Heteronuclear coupling constant ,Protein structure ,Bacterial Proteins ,0103 physical sciences ,Computer Simulation ,Glycosides ,Restraining free energy ,Binding site ,Cytoskeleton ,030304 developmental biology ,chemistry.chemical_classification ,Original Paper ,0303 health sciences ,Binding Sites ,010304 chemical physics ,biology ,Chemistry ,Glycosidic bond ,General Medicine ,Ligand (biochemistry) ,Cytoskeletal Proteins ,Conformational selection ,biology.protein ,Thermodynamics ,Guanosine Triphosphate ,GTP analogs ,Algorithms ,Cell Division - Abstract
The FtsZ protein is a self-polymerizing GTPase that plays a central role in bacterial cell division. Several C8-substituted GTP analogs are known to inhibit the polymerization of FtsZ by competing for the same binding site as its endogenous activating ligand GTP. Free energy calculations of the relative binding affinities to FtsZ for a set of five C8-substituted GTP analogs were performed. The calculated values agree well with the available experimental data, and the main contribution to the free energy differences is determined to be the conformational restriction of the ligands. The dihedral angle distributions around the glycosidic bond of these compounds in water are known to vary considerably depending on the physicochemical properties of the substituent at C8. However, within the FtsZ protein, this substitution has a negligible influence on the dihedral angle distributions, which fall within the narrow range of −140° to −90° for all investigated compounds. The corresponding ensemble average of the coupling constants 3 J(C4,H1′) is calculated to be 2.95 ± 0.1 Hz. The contribution of the conformational selection of the GTP analogs upon binding was quantified from the corresponding populations. The obtained restraining free energy values follow the same trend as the relative binding affinities to FtsZ, indicating their dominant contribution.
- Published
- 2010
20. NMR studies of p7 protein from hepatitis C virus
- Author
-
Stanley J. Opella and Gabriel A. Cook
- Subjects
Lipid Bilayers ,Phospholipid ,Biophysics ,Hepacivirus ,Model lipid bilayer ,Biophysics and Biological Physics ,Solid-state NMR ,Antiviral Agents ,Protein Structure, Secondary ,03 medical and health sciences ,chemistry.chemical_compound ,Viral Proteins ,Neurobiology ,Membrane Biology ,p7 ,Amantadine ,Escherichia coli ,Nanotechnology ,Lipid bilayer ,Peptide sequence ,Nuclear Magnetic Resonance, Biomolecular ,Ion channel ,Bicelles ,Micelles ,Phospholipids ,030304 developmental biology ,Hepatitis C virus ,0303 health sciences ,Original Paper ,Nitrogen Isotopes ,Chemistry ,030302 biochemistry & molecular biology ,Life Sciences ,Phospholipid Ethers ,Water ,Cell Biology ,General Medicine ,3. Good health ,Biochemistry, general ,Transmembrane domain ,Biochemistry ,Solid-state nuclear magnetic resonance ,Membrane protein ,Protons - Abstract
The p7 protein of hepatitis C virus (HCV) plays an important role in the viral lifecycle. Like other members of the viroporin family of small membrane proteins, the amino acid sequence of p7 is largely conserved over the entire range of genotypes, and it forms ion channels that can be blocked by a number of established channel-blocking compounds. Its characteristics as a membrane protein make it difficult to study by most structural techniques, since it requires the presence of lipids to fold and function properly. Purified p7 can be incorporated into phospholipid bilayers and micelles. Initial solid-state nuclear magnetic resonance (NMR) studies of p7 in 14-O-PC/6-O-PC bicelles indicate that the protein contains helical segments that are tilted approximately 10 degrees and 25 degrees relative to the bilayer normal. A truncated construct corresponding to the second transmembrane domain of p7 is shown to have properties similar to those of the full-length protein, and was used to determine that the helix segment tilted at 10 degrees is in the C-terminal portion of the protein. The addition of the channel blocker amantadine to the full-length protein resulted in selective chemical shift changes, demonstrating that NMR has a potential role in the development of drugs targeted to p7.
- Published
- 2009
21. Conformational studies of peptides representing a segment of TM7 from H+-VO-ATPase in SDS micelles
- Author
-
Marcus A. Hemminga, Rob B. M. Koehorst, Afonso M.S. Duarte, and Edwin R. de Jong
- Subjects
Circular dichroism ,Vacuolar Proton-Translocating ATPases ,Stereochemistry ,Molecular Sequence Data ,Biophysics ,Peptide ,V-ATPase ,Saccharomyces cerevisiae ,Fluorescence spectroscopy ,Protein Structure, Secondary ,5th transmembrane segment ,nmr ,Residue (chemistry) ,Aggregation ,mimicking ,detergent ,Secondary structure ,Membrane-mimicking solvent ,Amino Acid Sequence ,Peptide sequence ,Protein secondary structure ,major coat protein ,Spectroscopy ,Micelles ,chemistry.chemical_classification ,proton translocation channel ,Original Paper ,EPS-2 ,Protein Stability ,Circular Dichroism ,Cell Membrane ,Tryptophan ,Sodium Dodecyl Sulfate ,General Medicine ,bacteriophage-m13 ,dodecyl-sulfate micelles ,Transmembrane protein ,Peptide Fragments ,Biofysica ,Spectrometry, Fluorescence ,chemistry ,Biochemistry ,Solubility ,membrane-proteins ,escherichia-coli ,SDS micelles ,Protein Binding - Abstract
The conformation of a transmembrane peptide, sMTM7, encompassing the cytoplasmic hemi-channel domain of the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae solubilized in SDS solutions was studied by circular dichroism (CD) spectroscopy and fluorescence spectroscopy of the single tryptophan residue of this peptide. The results show that the peptide adopts an alpha-helical conformation or aggregated beta-sheet depending on the peptide-to-SDS ratio used. The results are compared with published data about a longer version of the peptide (i.e., MTM7). It is concluded that the bulky, positively charged arginine residue located in the center of both peptides has a destabilizing effect on the helical conformation of the SDS-solubilized peptides, leading to beta-sheet formation and subsequent aggregation.
- Published
- 2009
22. Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification
- Author
-
Tobias Knoch, Frank Grosveld, Rudolf Lohner, Anis Abuseiris, Markus Göker, and Cell biology
- Subjects
Sequence analysis ,Arabidopsis ,Biophysics ,Nuclear architecture ,Scaling analysis ,Saccharomyces cerevisiae ,Genome organization ,Genome ,Chromosomes ,Chromosomes, Plant ,Schizosaccharomyces ,Animals ,Chromosomes, Human ,Humans ,Computer Simulation ,Codon ,Genomic organization ,Genetics ,Original Paper ,Models, Genetic ,biology ,DNA ,Sequence Analysis, DNA ,General Medicine ,DNA sequence classification ,biology.organism_classification ,humanities ,Nucleosomes ,Drosophila melanogaster ,Evolutionary biology ,Codon usage bias ,Long-range correlations ,Mutation ,Mutation (genetic algorithm) ,Schizosaccharomyces pombe ,Chromosomes, Fungal ,Algorithms - Abstract
The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 x 10(6) to 3.0 x 10(7) bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens. The local correlation coefficients show a species-specific multi-scaling behaviour: close to random correlations on the scale of a few base pairs, a first maximum from 40 to 3,400 bp (for Arabidopsis thaliana and Drosophila melanogaster divided in two submaxima), and often a region of one or more second maxima from 10(5) to 3 x 10(5) bp. Within this multi-scaling behaviour, an additional fine-structure is present and attributable to codon usage in all except the human sequences, where it is related to nucleosomal binding. Computer-generated random sequences assuming a block organization of genomes, the codon usage, and nucleosomal binding explain these results. Mutation by sequence reshuffling destroyed all correlations. Thus, the stability of correlations seems to be evolutionarily tightly controlled and connected to the spatial genome organization, especially on large scales. In summary, genomes show a complex sequential organization related closely to their three-dimensional organization.
- Published
- 2009
23. An ultrasoft X-ray multi-microbeam irradiation system for studies of DNA damage responses by fixed- and live-cell fluorescence microscopy
- Author
-
Angelo L. Gobbi, Przemek M. Krawczyk, Maria H. O. Piazzetta, A. M. Melo, Jan Stap, Jacob A. Aten, Jan W. Verhoeven, Carel H. van Oven, Henk A. van Veen, Faculteit der Geneeskunde, Other departments, CCA -Cancer Center Amsterdam, and Cell Biology and Histology
- Subjects
DNA Repair ,DNA repair ,DNA damage ,Green Fluorescent Proteins ,Biophysics ,Radiation ,Biology ,chemistry.chemical_compound ,Live-cell microscopy ,Cell Line, Tumor ,Microscopy ,Fluorescence microscope ,DNA double-strand breaks ,Humans ,Original Paper ,X-Rays ,X-ray ,Soft X-rays ,DNA ,General Medicine ,Immunohistochemistry ,Molecular biology ,Microbeam irradiation ,Microscopy, Fluorescence ,chemistry ,Cell culture - Abstract
Localized induction of DNA damage is a valuable tool for studying cellular DNA damage responses. In recent decades, methods have been developed to generate DNA damage using radiation of various types, including photons and charged particles. Here we describe a simple ultrasoft X-ray multi-microbeam system for high dose-rate, localized induction of DNA strand breaks in cells at spatially and geometrically adjustable sites. Our system can be combined with fixed- and live-cell microscopy to study responses of cells to DNA damage.
- Published
- 2009
24. Hydrodynamic properties of cyclodextrin molecules in dilute solutions
- Author
-
N. A. Smolina, Georges M. Pavlov, Ulrich S. Schubert, Evguenia V. Korneeva, and Chemical Engineering and Chemistry
- Subjects
Models, Molecular ,alpha-Cyclodextrins ,Time Factors ,alpha-Cyclodextrin ,Diffusion ,Biophysics ,Thermodynamics ,Beta-Cyclodextrins ,chemistry.chemical_compound ,Molecule ,Organic chemistry ,Computer Simulation ,Dimethyl Sulfoxide ,Physics::Chemical Physics ,chemistry.chemical_classification ,Original Paper ,Cyclodextrin ,Chemistry ,beta-Cyclodextrins ,Water ,Lamm equation ,Dimethylformamide ,Molecular hydrodynamics 2 ,General Medicine ,Solutions ,Solvent ,Sedimentation coefficient ,Toroid 3 ,Models, Chemical ,Solvents ,Cyclodextrins 1 ,Algorithms ,Software ,gamma-Cyclodextrins - Abstract
Three well-known representatives of the cyclodextrin family were completely characterized by molecular hydrodynamics methods in three different solvents. For the first time the possibility of an estimation of velocity sedimentation coefficients s between 0.15 and 0.5 S by the numerical solution of the Lamm equation is shown. Comparison of the experimental hydrodynamic characteristics of the cyclodextrins with theoretical calculations for toroidal molecules allows an estimation of the thickness of the solvent layers on the surface of cyclodextrin molecules.
- Published
- 2009
25. Dynamics of hydration water in deuterated purple membranes explored by neutron scattering
- Author
-
Brigitte Kessler, Giuseppe Zaccai, Martin Weik, Frank Gabel, Kathleen Wood, Dieter Oesterhelt, and Marie Plazanet
- Subjects
Halobacterium salinarum ,Dynamical transition ,Time Factors ,Movement ,Neutron diffraction ,Biophysics ,Analytical chemistry ,Neutron scattering ,Hydration water dynamics ,Neutron spectroscopy ,Kinetic isotope effect ,Lamellar structure ,Original Paper ,Chemistry ,Dynamics (mechanics) ,Temperature ,Membrane Proteins ,Water ,General Medicine ,Deuterium ,Purple membrane ,Neutron Diffraction ,Crystallography ,Membrane - Abstract
The function and dynamics of proteins depend on their direct environment, and much evidence has pointed to a strong coupling between water and protein motions. Recently however, neutron scattering measurements on deuterated and natural-abundance purple membrane (PM), hydrated in H2O and D2O, respectively, revealed that membrane and water motions on the ns–ps time scale are not directly coupled below 260 K (Wood et al. in Proc Natl Acad Sci USA 104:18049–18054, 2007). In the initial study, samples with a high level of hydration were measured. Here, we have measured the dynamics of PM and water separately, at a low-hydration level corresponding to the first layer of hydration water only. As in the case of the higher hydration samples previously studied, the dynamics of PM and water display different temperature dependencies, with a transition in the hydration water at 200 K not triggering a transition in the membrane at the same temperature. Furthermore, neutron diffraction experiments were carried out to monitor the lamellar spacing of a flash-cooled deuterated PM stack hydrated in H2O as a function of temperature. At 200 K, a sudden decrease in lamellar spacing indicated the onset of long-range translational water diffusion in the second hydration layer as has already been observed on flash-cooled natural-abundance PM stacks hydrated in D2O (Weik et al. in J Mol Biol 275:632–634, 2005), excluding thus a notable isotope effect. Our results reinforce the notion that membrane-protein dynamics may be less strongly coupled to hydration water motions than the dynamics of soluble proteins.
- Published
- 2008
26. Dynamics of C-phycocyanin in various deuterated trehalose/water environments measured by quasielastic and elastic neutron scattering
- Author
-
Sophie Combet, Marie-Claire Bellissent-Funel, Ingo Köper, and Winfried Petry
- Subjects
Heavy water ,Models, Molecular ,Quasielastic scattering ,Original Paper ,Transition temperature ,Neutron diffraction ,Biophysics ,Phycocyanin ,Trehalose ,Water ,General Medicine ,Neutron scattering ,Deuterium ,Elasticity ,chemistry.chemical_compound ,Crystallography ,Neutron Diffraction ,chemistry ,Models, Chemical ,Chemical physics ,Computer Simulation ,Protein stabilization - Abstract
The molecular understanding of protein stabilization by the disaccharide trehalose in extreme temperature or hydration conditions is still debated. In the present study, we investigated the role of trehalose on the dynamics of the protein C-phycocyanin (C-PC) by neutron scattering. To single out the motions of C-PC hydrogen (H) atoms in various trehalose/water environments, measurements were performed in deuterated trehalose and heavy water (D2O). We report that trehalose decreases the internal C-PC dynamics, as shown by a reduced diffusion coefficient of protein H atoms. By fitting the Elastic Incoherent Structure Factor--which gives access to the "geometry" of the internal proton motions--with the model of diffusion inside a sphere, we found that the presence of trehalose induces a significantly higher proportion of immobile C-PC hydrogens. We investigated, by elastic neutron scattering, the mean square displacements (MSDs) of deuterated trehalose/D2O-embedded C-PC as a function of temperature in the range of 40-318 K. Between 40 and approximately 225 K, harmonic MSDs of C-PC are slightly smaller in samples containing trehalose. Above a transition temperature of approximately 225 K, we observed anharmonic motions in all trehalose/water-coated C-PC samples. In the hydrated samples, MSDs are not significantly changed by addition of 15% trehalose but are slightly reduced by 30% trehalose. In opposition, no dynamical transition was detected in dry trehalose-embedded C-PC, whose hydrogen motions remain harmonic up to 318 K. These results suggest that a role of trehalose would be to stabilize proteins by inhibiting some fluctuations at the origin of protein unfolding and denaturation.
- Published
- 2008
27. Experimental extraction of Young's modulus of MCF-7 tissue using atomic force microscopy and the spherical contact models.
- Author
-
Mirzaluo, Mahdi, Fereiduni, Fateme, Taheri, Moein, and Modabberifar, Mehdi
- Subjects
YOUNG'S modulus ,ATOMIC absorption spectroscopy ,TISSUE mechanics ,ATOMIC force microscopy ,EARLY detection of cancer ,MODULUS of elasticity ,BREAST ,TISSUE extracts - Abstract
The study of mechanical properties of tissues can be considered as biomarkers for early detection of cancer and help in new treatments. In this study, the Young's modulus of MCF-7 breast cancer tissue was extracted using atomic force microscopy (AFM) by measuring the interaction force of the sample and performing a simulation. The force–indentation depth diagram was plotted by averaging the experimental results. In this paper, the modulus of elasticity of breast cancer tissue has been extracted with complex models such as DMT, MD, BCP, and SUN. By comparing the experimental and theoretical results and by changing the amount of hypothetical Young's modulus in the spherical contact models, the Young's modulus of the cancer tissue is considered to be between 300 and 400 Pa. The geometry of the cell was also assumed to be spherical according to the images obtained by atomic force microscopy. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
28. Protection of liposomes against fusion during drying by oligosaccharides is not predicted by the calorimetric glass transition temperatures of the dry sugars
- Author
-
Petra Rennecke, Dirk K. Hincha, and Ann E. Oliver
- Subjects
Inulin ,Phospholipid ,Biophysics ,Carbohydrates ,Oligosaccharides ,Degree of polymerization ,Calorimetry ,Membrane Fusion ,chemistry.chemical_compound ,Differential scanning calorimetry ,Phosphatidylcholine ,Transition Temperature ,chemistry.chemical_classification ,Liposome ,Original Paper ,Chromatography ,Calorimetry, Differential Scanning ,Temperature ,General Medicine ,Oligosaccharide ,Membrane ,chemistry ,Liposomes ,Phosphatidylcholines ,Glass ,human activities - Abstract
Sugars play an important role in the desiccation tolerance of most anhydrobiotic organisms. It has been shown in previous studies that different structural families of oligosaccharides have different efficacies to interact with phospholipid headgroups and protect membranes from solute leakage during drying. Here, we have compared three families of linear oligosaccharides (fructans (inulins), malto-oligosaccharides, manno-oligosaccharides) for their chain-length dependent protection of egg phosphatidylcholine liposomes against membrane fusion. We found increased protection with chain length up to a degree of polymerization (DP) of 5 for malto-oligosaccharides, and a decrease for inulins and manno-oligosaccharides. Differential scanning calorimetry measurements showed that for all sugars the glass transition temperature (T(g)) increased with DP, although to different degrees for the different oligosaccharide families. Higher T(g) values resulted in reduced membrane fusion only for malto-oligosaccharides below DP5. Contrary to expectation, for inulins, manno-oligosaccharides and malto-oligosaccharides of a DP above five, fusion increased with increasing T(g), indicating that other physical parameters are more important in determining the ability of different sugars to protect membranes against fusion during drying. Further research will be necessary to experimentally define such parameters.
- Published
- 2007
29. Ultraviolet C intensity dependence of decontamination efficiency for pathogens as function of repacked metamaterials with screw channels.
- Author
-
Munteanu, Ion, Starodub, Elena, Bazgan, Sergiu, Turcan, Marina, Paslari, Tatiana, Podoleanu, Diana, and Enaki, Nicolae A.
- Subjects
- *
METAMATERIALS , *SACCHAROMYCES cerevisiae , *SCREWS , *PATHOGENIC microorganisms - Abstract
A new method for repackaging optical metamaterials formed from quartz spheres (fibers) of various diameters is proposed for ultraviolet C disinfection of infected liquids by pathogens (viruses and bacteria). The main idea of the new equipment is connected with the rotation of a contaminated fluid by screw channels within a metamaterial matrix prepared from UVC fibers/spherical optics, to improve the decontamination efficiency. In demonstration of the viability of this approach, dynamic and static inactivation of Baker's yeast via Ultraviolet C radiation regimes are used in this paper to show the efficacy of decontamination within the screw channels. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
30. Editorial.
- Author
-
Watts, Anthony
- Subjects
CONFERENCES & conventions ,BIOPHYSICS ,ASSOCIATIONS, institutions, etc. ,PERIODICALS - Abstract
Focuses on the 5th European Biophysical Societies Association (EBSA) and the 15th International Union of Pure and Applied Biophysics International Biophysics Congress which will be held in Montpellier, France on August 27-September 1, 2005. Significance of the congress; Organizing committee of the congress; Relationship of the "European Biophysics Journal" with EBSA.
- Published
- 2005
- Full Text
- View/download PDF
31. An image-processing method to detect sub-optical features based on understanding noise in intensity measurements.
- Author
-
Bhatia, Tripta
- Subjects
NOISE measurement ,IMAGE processing ,FLUORESCENCE ,PHOSPHOCHOLINE ,OPTICAL resolution - Abstract
Accurate quantitative analysis of image data requires that we distinguish between fluorescence intensity (true signal) and the noise inherent to its measurements to the extent possible. We image multilamellar membrane tubes and beads that grow from defects in the fluid lamellar phase of the lipid 1,2-dioleoyl-sn-glycero-3-phosphocholine dissolved in water and water-glycerol mixtures by using fluorescence confocal polarizing microscope. We quantify image noise and determine the noise statistics. Understanding the nature of image noise also helps in optimizing image processing to detect sub-optical features, which would otherwise remain hidden. We use an image-processing technique “optimum smoothening” to improve the signal-to-noise ratio of features of interest without smearing their structural details. A high SNR renders desired positional accuracy with which it is possible to resolve features of interest with width below optical resolution. Using optimum smoothening, the smallest and the largest core diameter detected is of width 88±23
and 6860±50 nm, respectively, discussed in this paper. The image-processing and analysis techniques and the noise modeling discussed in this paper can be used for detailed morphological analysis of features down to sub-optical length scales that are obtained by any kind of fluorescence intensity imaging in the raster mode. [ABSTRACT FROM AUTHOR] - Published
- 2018
- Full Text
- View/download PDF
32. Editorial.
- Subjects
BIOPHYSICS ,CONFERENCES & conventions ,MEDICAL sciences ,PERIODICALS - Abstract
Editorial. Deals with the European Biophysics Journal and the European Biophysics Societies Association (EBSA) 3rd European Biophysics Congress. Relationship between Biophysics Journal and the EBSA; Development of the journal; Overview of the EBSA Congress.
- Published
- 2003
- Full Text
- View/download PDF
33. Wave propagation through a viscous fluid-filled elastic tube under initial pressure: theoretical and biophysical model.
- Author
-
Žikić, Dejan and Žikić, Katarina
- Subjects
PULSE wave analysis ,NAVIER-Stokes equations ,CARDIOVASCULAR system ,FLUID pressure ,BLOOD vessels ,THEORY of wave motion - Abstract
The velocity of propagation of pulse waves through the arteries is one of the indicators of the health of the cardiovascular system. By measuring the pulse wave velocity, cardiologists estimate the elasticity of the blood vessel walls and the changes that occur with aging. When the Moens–Korteweg equation is used in analysis, it leads to an erroneous assessment. This paper presents the solution of Navier–Stokes equations for propagation of pulse waves through an elastic tube filled with viscous fluid under initial pressure. The equation for pulse wave velocity depending on viscosity, density and initial fluid pressure, density and elasticity of the wall and geometry of the tube is derived. The results of the equation were compared with experimental results measured using a biophysical model of the cardiovascular system. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
34. Special Issue: 18th Congress of the Polish Biophysical Society.
- Author
-
Antosiewicz, Jan M., Gilbert, Robert, and Marszalek, Piotr E.
- Subjects
MOLECULAR dynamics ,BIOPHYSICS ,UNIVERSITY faculty ,HYDRODYNAMICS ,SYSTEM dynamics - Abstract
The 18th Congress of the Polish Biophysical Society took place at the Faculty of Physics of the University of Warsaw in Warsaw, Poland, in September 2022. In total, 111 attendees (Attendance Profile: 107 in-person, 4 remote; Italy 1, Lithuania 1, Poland 104, United Kingdom 1, United States 4) participated in the event. The authors of lectures and posters at the Congress were invited to prepare their presentations in the form of articles in this special issue of the European Biophysics Journal. The 11 articles published in this special issue present a limited sampling of the subjects of the conference presentations. Nevertheless, they showcase excellence in Polish biophysics across a wide range of topics, using both theoretical and experimental approaches: mechanisms of receptor-ligand interactions, medical applications of proteins and nucleic acids, non-linear dynamics/molecular dynamics of protein systems, hydrodynamics and biosensing. We hope to improve on the representation of the international Polish biophysical community after the next Congress in 2025. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
35. DNA translocation through pH-dependent soft nanopores.
- Author
-
Yousefi, Alireza, Ganjizade, Ardalan, and Ashrafizadeh, Seyed Nezameddin
- Subjects
NANOPORES ,DNA ,WALL coverings ,POLYELECTROLYTES ,FUNCTIONAL groups - Abstract
Controlling the translocation velocity of DNA is the main challenge in the process of sequencing by means of nanopores. One of the main methods to overcome this challenge is covering the inner walls of the nanopore with a layer of polyelectrolytes, i.e., using soft nanopores. In this paper the translocation of DNA through soft nanopores, whose inner polyelectrolyte layer (PEL) charge is pH-dependent, is theoretically studied. We considered the polyelectrolyte to be made up of either acidic or basic functional groups. It was observed that the electroosmotic flow (EOF) induced by the PEL charge is in the opposite/same direction of DNA electrophoresis (EPH) when the PEL is made up of acidic/basic groups. It was found that, not only the DNA charge and consequently the EPH, but also the EOF are influenced by the electrolyte acidity. The synergy between the changes in the retardation, EOF and EPH, determines how the intensity and direction of DNA translocation alter with pH. In fact, for both cases, at mild values of pH (as long as E O F < E P H for the case that PEL is of acidic nature), the more the pH, the less the translocation velocity. However, for PELs of acidic nature, higher values of pH increase the intensity of the EOF so much that DNA may experience a change in the translocation direction. Ultimately, conducting the process at a particular range of pH values, and at higher pH values, in the cases of using PELs of acidic nature, and basic nature, respectively, was recommended. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
36. Effect of setting data collection parameters on the reliability of a circular dichroism spectrum.
- Author
-
Sousa, Victor K., Pedro, Jéssica A. F., Kumagai, Patricia S., and Lopes, Jose L. S.
- Subjects
PROTEIN analysis ,PROTEIN structure ,MYOGLOBIN ,QUANTITATIVE research ,CIRCULAR dichroism ,SECONDARY analysis ,ACQUISITION of data - Abstract
Circular dichroism (CD) spectroscopy is a well-established biophysical technique used to investigate the structure of molecules. The analysis of a protein CD spectrum depends on the quality of the original CD data, which can be affected by the sample purity, background absorption of the additives/solvent/buffer, the choice of the parameters used for data collection, etc. In this paper, the CD spectrum of myoglobin was used as a model to exploit how variations on each data collection parameter could affect the final protein CD spectrum and, the subsequent effect of them on the quantitative analysis of protein secondary structure. Bioinformatics analysis carried out with SESCA package and PDBMD2CD server predicted a theoretical myoglobin CD spectrum, and a Monte Carlo-like model was implemented to estimate the uncertainty in secondary structure predictions performed with CDSSTR, Selcon 3 and ContinLL algorithms. An inappropriate choice of data collection parameters can lead to a misinterpretation of the CD data in terms of the protein structural content. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
37. Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation.
- Author
-
De Meutter, Joëlle and Goormaghtigh, Erik
- Subjects
AMINO acids ,PROTEIN microarrays ,IMAGING systems ,SUPPORT vector machines ,PROTEINS - Abstract
Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm
−1 is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I–amide II spectral range. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF2 slides and FTIR spectra were acquired with an imaging system. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
38. Vibrational dynamics of bio- and nano-filaments in viscous solution subjected to ultrasound: implications for microtubules.
- Author
-
Samarbakhsh, Abdorreza and Tuszynski, Jack
- Subjects
VISCOUS flow ,MICROTUBULES ,BEAM dynamics ,ELASTICITY ,ENERGY transfer ,RESONANCE - Abstract
In this paper, using a new analytical method, we solved the beam equation for a uniform bio- and nano-filament in a viscous solution. The filament is assumed to be attached at its two ends and driven by ultrasound plane waves. To obtain analytical solutions, we converted the beam equation to an equation that allows us the use of the method of separation of variables. We then reconstructed the solution of the original beam equation from the solution of the converted equation. Subsequently, we have used the parametric equations derived in this paper to investigate the resonance condition for a microtubule (MT) in an aqueous solution. We show that by using ultrasound plane waves, one cannot satisfy a resonance condition for MTs treated as rigid rods. In order to achieve resonance, a single mode of the MT vibration must be excited with a harmonic number larger than a threshold value found here. Single mode excitation not only helps to transfer a minimum amount of energy to the surrounding medium compared with multi-mode excitation, but it also allows for a simultaneous high amplitude and high mode quality that is impossible using plane waves. In order to overcome this difficulty, we propose to use an ultrasound generation device as a potential technical solution characterized by both frequency control and optimized energy transfer to the MT. Finally, the minimum required intensity of the ultrasound at the location of the MT in order to break it is shown to be on the order of 10 W/m, which corresponds to 170 dB. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
39. Structural studies on serum albumins under green light irradiation.
- Author
-
Comorosan, Sorin, Polosan, Silviu, Popescu, Irinel, Ionescu, Elena, Mitrica, Radu, Cristache, Ligia, and State, Alina Elena
- Subjects
PROTEINS ,DICHROISM ,RYDBERG states ,SERUM albumin ,ELECTROPHORESIS ,FLUORESCENCE spectroscopy - Abstract
This paper presents two new experimental results: the protective effect of green light (GL) on ultraviolet (UV) denaturation of proteins, and the effect of GL on protein macromolecular structures. The protective effect of GL was revealed on two serum albumins, bovine (BSA) and human (HSA), and recorded by electrophoresis, absorption, and circular dichroism spectra. The effect of GL irradiation on protein structure was recorded by using fluorescence spectroscopy and electrophoresis. These new effects were modeled by quantum-chemistry computation using Gaussian 03W, leading to good fit between theoretical and experimental absorption and circular dichroism spectra. A mechanism for these phenomena is suggested, based on a double-photon absorption process. This nonlinear effect may lead to generation of long-lived Rydberg macromolecular systems, capable of long-range interactions. These newly suggested systems, with macroscopic quantum coherence behaviors, may block the UV denaturation processes. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
40. Introduction/Welcome.
- Subjects
SPEECHES, addresses, etc. ,CONFERENCES & conventions ,BIOPHYSICS - Abstract
The article presents the texts of welcome addresses for the 7th EBSA European Biophysics Congress to be held in Genoa, Italy from July 11 to 15, 2009 is presented.
- Published
- 2009
- Full Text
- View/download PDF
41. Low-resolution molecular shape, biochemical characterization and emulsification properties of a halotolerant esterase from Bacillus licheniformis.
- Author
-
Leite, Ana Elisa T., Briganti, Lorenzo, de Araújo, Evandro Ares, Pellegrini, Vanessa de Oliveira Arnoldi, Camilo, Cesar Moyses, and Polikarpov, Igor
- Subjects
MOLECULAR shapes ,BACILLUS licheniformis ,SMALL-angle X-ray scattering ,ORGANIC solvents ,BIOSURFACTANTS ,OLIVE oil ,ESTERASES - Abstract
Bacterial esterases are highly versatile enzymes, currently widely used in detergents, biosurfactants, bioemulsifiers and as biocatalysts in paper and food industries. Present work describes heterologous expression, purification, and biophysical and biochemical characterization of a halotolerant esterase from Bacillus licheniformis (BlEstA). BlEstA preferentially cleaves pNP-octanoate and both activity and stability of the enzyme increased in the presence of 2 M NaCl, and also with several organic solvents (ethanol, methanol and DMSO). Furthermore, BlEstA has considerable emulsifying properties, particularly with olive oil as substrate. Our studies also show that the enzyme is monomeric in solution and its small-angle X-ray scattering low-resolution molecular envelope fits well its high-resolution homology model. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
42. Influence of cholesterol on electroporation in lipid membranes of giant vesicles.
- Author
-
Karal, Mohammad Abu Sayem, Ahamed, Md. Kabir, Mokta, Nadia Akter, Ahmed, Marzuk, and Ahammed, Shareef
- Subjects
MEMBRANE lipids ,STABILITY constants ,ELECTROPORATION ,ACTIVATION energy ,EXPONENTIAL functions - Abstract
Irreversible electroporation (IRE) is primarily a nonthermal ablative technology that uses a series of high-voltage and ultra-short pulses with high-frequency electrical energy to induce cell death. This paper presents the influence of cholesterol on the IRE-induced probability of pore formation and the rate constant of pore formation in giant unilamellar vesicles (GUVs). The GUVs are prepared by a mixture of dioleoylphosphatidylglycerol (DOPG), dioleoylphosphatidylcholine (DOPC) and cholesterol using the natural swelling method. An IRE signal of frequency 1.1 kHz is applied to the membranes of GUVs. The probability of pore formation and the rate constant of pore formation events are obtained using statistical analysis from several single GUVs. The time-dependent fraction of intact GUVs among all those examined is fitted to a single exponential decay function from where the rate constant of pore formation is calculated. The probability of pore formation and the rate constant of pore formation decreases with an increase in cholesterol content in the membranes of GUVs. Theoretical equations are fitted to the tension-dependent rate constant of pore formation and to the probability of pore formation, which allows us to obtain the line tension of membranes. The obtained line tension increases with an increase in cholesterol in the membranes. The increase in the energy barrier of the prepore state, due to the increase of cholesterol in membranes, is the main factor explaining the decrease in the rate constant of pore formation. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
43. Experimental study of the difference in deformation between normal and pathological, renal and bladder, cells induced by acoustic radiation force.
- Author
-
Wang, Haibin, Qiao, Yupei, Liu, Jiehui, Jiang, Bo, Zhang, Gutian, Zhang, Chengwei, and Liu, Xiaozhou
- Subjects
ACOUSTIC radiation force ,CELLULAR mechanics ,BLADDER ,CANCER cells ,MICROSCOPES ,URINARY organ diseases - Abstract
Previous studies have shown that alterations in the mechanical properties of cells may be associated with the onset and progression of some forms of pathology. In this paper, an experimental study of two types of cells, renal (cancer) and bladder (cancer) cells, is described which used acoustic radiation force (ARF) generated by a high-frequency ultrasound focusing transducer and performed on the operating platform of an inverted light microscope. Comparing images of cancer cells with those of normal cells of the same kind, we find that the cancer cells are more prone to deform than normal cells of the same kind under the same ARF. In addition, cancer cells with higher malignancy are more deformable than those with lower malignancy. This means that the deformability of cells may be used to distinguish diseased cells from normal ones, and more aggressive cells from less aggressive ones, which may provide a more rapid and accurate method for clinical diagnosis of urological disease in the future. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
44. Obtaining precise and accurate results by ITC.
- Author
-
Hansen, Lee D. and Quinn, Colette
- Subjects
ISOTHERMAL titration calorimetry ,STOICHIOMETRY ,CARBONIC anhydrase ,LIGAND binding (Biochemistry) ,CARRIER proteins ,BINDING constant - Abstract
Acquisition of precise and accurate results by isothermal titration calorimetry (ITC) can be achieved through thoughtful experimental design and modeling and careful experimental operations. Large reported errors in ITC results in determinations of stoichiometries, equilibrium constants and enthalpy changes for ligand binding to proteins are the consequence of poor experiment design, failure to properly calibrate and test instruments and protocols, lack of controls, errors in solution preparation, and incorrect data analyses. Analysis of a recent report that claimed to have determined the "repeatability, precision, and accuracy of the enthalpies and Gibbs energies of a protein–ligand binding reaction" by ITC is used to illustrate how to improve ITC operations and results. The analysis shows that the reported results are misleading because calorimeters were not calibrated, operating parameters were not optimized, errors were made in solution preparations, and data analysis was not optimized. As a consequence, the results do not provide a valid comparison of the capabilities of the calorimeters included in the study. A proposal that reaction of acetazolamide with carbonic anhydrase II be used as a comparison standard for testing ITCs and procedures is problematic because the binding constant is too large and for several other reasons discussed in the paper. Requirements for obtaining precise and accurate results by ITC are discussed and experimental results are presented to illustrate the precision and accuracy attainable with low volume ITCs. The problem of the blank correction is identified as the limiting factor in obtaining accurate results by ITC. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
45. On the simple random-walk models of ion-channel gate dynamics reflecting long-term memory
- Author
-
Zbigniew J. Grzywna, Krzysztof Pawelek, Agata Wawrzkiewicz, Beata Dworakowska, and Przemysław Borys
- Subjects
Models, Molecular ,BK channel ,Memory, Long-Term ,Patch-Clamp Techniques ,Conformational diffusion ,Biophysics ,Gating ,Models, Biological ,Hurst analysis ,Cell Line ,Membrane Potentials ,Simple (abstract algebra) ,Humans ,Computer Simulation ,Statistical physics ,Large-Conductance Calcium-Activated Potassium Channels ,Ion channel ,Original Paper ,Models, Statistical ,biology ,Chemistry ,Long-term memory ,Random walk process ,Epithelial Cells ,General Medicine ,Random walk ,Electrophysiology ,Kinetics ,Activation gate ,biology.protein ,BK channels ,Ion Channel Gating ,Voltage ,Communication channel - Abstract
Several approaches to ion-channel gating modelling have been proposed. Although many models describe the dwell-time distributions correctly, they are incapable of predicting and explaining the long-term correlations between the lengths of adjacent openings and closings of a channel. In this paper we propose two simple random-walk models of the gating dynamics of voltage and Ca(2+)-activated potassium channels which qualitatively reproduce the dwell-time distributions, and describe the experimentally observed long-term memory quite well. Biological interpretation of both models is presented. In particular, the origin of the correlations is associated with fluctuations of channel mass density. The long-term memory effect, as measured by Hurst R/S analysis of experimental single-channel patch-clamp recordings, is close to the behaviour predicted by our models. The flexibility of the models enables their use as templates for other types of ion channel.
- Full Text
- View/download PDF
46. Laser interferometry analysis of ciprofloxacin and ampicillin diffusion from liposomal solutions to water phase
- Author
-
Michał Arabski, Sławomir Wąsik, Zuzanna Drulis-Kawa, and Jerzy Gubernator
- Subjects
Diffusion ,Analytical chemistry ,Biophysics ,Laser interferometry ,Ciprofloxacin ,Phase (matter) ,Ampicillin ,medicine ,Neutral ph ,Original Paper ,Liposome ,Chemistry ,Lasers ,Water ,General Medicine ,Hydrogen-Ion Concentration ,biochemical phenomena, metabolism, and nutrition ,Anti-Bacterial Agents ,Solutions ,Interferometry ,Membrane ,Liposomes ,medicine.drug - Abstract
The paper presents experimental investigations of diffusion of antibiotics (ciprofloxacin or ampicillin) into the water phase from mixtures of neutral or negatively charged liposomes, and antibiotic–liposome interactions. Using the laser interferometry technique, the amounts and fluxes of released antibiotics, concentration field evolution, and the velocity of the concentration boundary layer’s “growth” were determined. To avoid the limitations of membranes, a measurement system without the artificial boundary of phases with a free water–solution interface has been proposed. It was found that the diffusion of anionic and neutral liposomes into the water phase was insignificant and mainly the diffusion of antibiotics was measured. Differences in the diffusion kinetics of ciprofloxacin and ampicillin from liposomal solutions to the water phase were observed. Ampicillin diffused more efficiently than ciprofloxacin regardless of the liposomal solution type. Moreover, the amount of ampicillin and ciprofloxacin released from the anionic liposomal phase was higher than that from the neutral one. Our results confirm that ciprofloxacin at neutral pH shows little tendency to bind neutral liposomes. Additionally, it was also observed that ciprofloxacin disrupts negatively charged liposomes as a final effect of antibiotic–lipid interactions.
- Full Text
- View/download PDF
47. Computational study on the impact of linkage sequence on the structure and dynamics of lignin.
- Author
-
Vural, Derya
- Subjects
- *
MATERIALS science , *GLASS transition temperature , *MOLECULAR dynamics , *VISCOUS flow , *BIOPOLYMERS , *LIGNIN structure , *LIGNINS , *LIGNANS - Abstract
Lignin, one of the most abundant biopolymers on Earth, is of great research interest due to its industrial applications including biofuel production and materials science. The structural composition of lignin plays an important role in shaping its properties and functionalities. Notably, lignin exhibits substantial compositional diversity, which varies not only between different plant species but even within the same plant. Currently, it is unclear to what extent this compositional diversity plays on the overall structure and dynamics of lignin. To address this question, this paper reports on the development of two models of lignin containing all guaiacyl (G) subunits with varied linkage sequences and makes use of all-atom molecular dynamics simulations to examine the impact of linkage sequence alone on the lignin’s structure and dynamics. This work demonstrates that the structure of the lignin polymer depends on its linkage sequence at temperatures above and below the glass transition temperature (Tg\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$T_\textrm{g}$$\end{document}), but the polymers exhibit similar structural properties as it is approaching the viscous flow state (480 K). At low temperatures, both of lignin models have a local dynamics confined in a cage, but the size of cages varies depending on structural differences. Interestingly, at temperatures higher than Tg\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$T_\textrm{g}$$\end{document}, the different linkage sequence leads to the subtle dynamical difference which diminishes at 480 K. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
48. A mathematical approach to cytoskeletal assembly.
- Author
-
Edelstein-Keshet, Leah
- Subjects
CYTOSKELETON ,THERMODYNAMIC equilibrium ,POLYMERIZATION ,ACTIN - Abstract
Abstract The cytoskeleton is a fundamental and important part of cell's structure, and is known to play a large role in controlling the shape, function, division, and motility of the cell. In recent years, the traditional biological and biophysical experimental work on the cytoskeleton has been enhanced by a variety of theoretical, physical and mathematical approaches. Many of these approaches have been developed in the traditional frameworks of physicochemical and statistical mechanics or equilibrium thermodynamic principles. An alternative is to use kinetic modelling and couch the analysis in terms of differential equations which describe mean field properties of cytoskeletal networks or assemblies. This paper describes two such recent efforts. In the first part of the paper, a summary of work on the kinetics of polymerization, fragmentation, and dynamics of actin and polymers in the presence of gelsolin (which nulceates, fragments, and caps the filaments) is given. In the second part, some of the kinetic models aimed at elucidating the spatio-angular density distribution of actin filaments interacting via crosslinks is described. This model given insight into effects that govern the formation of clusters and bundles of actin filaments, and their spatial distribution. [ABSTRACT FROM AUTHOR]
- Published
- 1998
- Full Text
- View/download PDF
49. Cytoskeletal involvement in neuronal learning: a review.
- Author
-
Dayhoff, Judith, Hameroff, Stuart, Lahoz-Beltra, Rafael, and Swenberg, Charles
- Abstract
This paper introduces the ideas of neural networks in the context of currently recognized cellular structures within neurons. Neural network models and paradigms require adaptation of synapses for learning to occur in the network. Some models of learning paradigms require information to move from axon to dendrite. This motivated us to examine the possibility of intracellular signaling to mediate such signals. The cytoskeleton forms a substrate for intracellular signaling via material transport and other putative mechanisms. Furthermore, many experimental results suggest a link between the cytoskeleton and cognitive processing. In this paper we review research on intracellular signaling in the context of neural network learning. [ABSTRACT FROM AUTHOR]
- Published
- 1994
- Full Text
- View/download PDF
50. Variance reduction by simultaneous multi-exponential analysis of data sets from different experiments.
- Author
-
Müller, K.- and Plesser, Th.
- Abstract
The analysis of experimental data from the photocycle of bacteriorhodopsin (bR) as sums of exponentials has accumulated a large amount of information on its kinetics which is still controversial. One reason for ambiguous results can be found in the inherent instabilities connected with the fitting of noisy data by sums of exponentials. Nevertheless, there are strategies to optimize the experiments and the data analysis by a proper combination of well known techniques. This paper describes an applicable approach based on the correct weighting of the data, a separation of the linear and the non-linear parameters in the process of the least squares approximation, and a statistical analysis applying the correlation matrix, the determinant of Fisher's information matrix, and the variance of the parameters as a measure of the reliability of the results. In addition, the confidence regions for the linear approximation of the non-linear model are compared with confidence regions for the true non-linear model. Evaluation techniques and rules for an optimum experimental design are mainly exemplified by the analysis of numerically generated model data with increasing complexity. The estimation of the number of exponentials significant for the interpretation of a given set of data is demonstrated by using records from eight absorption and photocurrent experiments on the photocycle of bacteriorhodopsin. [ABSTRACT FROM AUTHOR]
- Published
- 1991
- Full Text
- View/download PDF
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.