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Discovering new bacterial signaling pathways offers unique antibiotic strategies. Here, through an unbiased resistance screen of 3,884 gene knockout strains, we uncovered a previously unknown non-lytic bactericidal mechanism that sequentially couples three transporters and downstream transcription to lethally suppress respiration of the highly virulent P. aeruginosa strain PA14 - one of three species on the WHO's 'Priority 1: Critical' list. By targeting outer membrane YaiW, cationic lacritin peptide 'N-104' translocates into the periplasm where it ligates outer loops 4 and 2 of the inner membrane transporters FeoB and PotH, respectively, to suppress both ferrous iron and polyamine uptake. This broadly shuts down transcription of many biofilm-associated genes, including ferrous iron-dependent TauD and ExbB1. The mechanism is innate to the surface of the eye and is enhanced by synergistic coupling with thrombin peptide GKY20. This is the first example of an inhibitor of multiple bacterial transporters., Competing Interests: DECLARATION OF INTERESTS GWL is cofounder and CSO of TearSolutions, Inc; and cofounder and CTO of IsletRegen, LLC. Other authors declare no competing interests.

The production of the biofuel, isobutanol, in E. coli faces limitations due to alcohol toxicity, product inhibition, product recovery, and long-term industrial feasibility. Here we demonstrate an approach of combining both in vivo with in vitro metabolic engineering to produce isobutanol. The in vivo production of α-ketoisovalerate (KIV) was conducted through CRISPR mediated integration of the KIV pathway in bicistronic design (BCD) in E. coli and inhibition of competitive valine pathway using CRISPRi technology. The subsequent in vitro conversion to isobutanol was carried out with engineered enzymes for 2-ketoacid decarboxylase (KIVD) and alcohol dehydrogenase (ADH). For the in vivo production of KIV and subsequent in vitro production of isobutanol, this two-step serial approach resulted in yields of 56% and 93%, productivities of 0.62 and 0.074 g L -1 h -1 , and titers of 5.6 and 1.78 g L -1 , respectively. Thus, this combined biosynthetic system can be used as a modular approach for producing important metabolites, like isobutanol, without the limitations associated with in vivo production using a consolidated bioprocess., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Authors.)

Protein-protein interactions are central to biological processes. In vitro methods to examine protein-protein interactions are generally categorized into two classes: in-solution and surface-based methods. Here, using the multivalent interactions between nucleocytoplasmic transport factors and intrinsically disordered FG repeat containing nuclear pore complex proteins as a model system, we examined the utility of three surface-based methods: atomic force microscopy, quartz crystal microbalance with dissipation, and surface plasmon resonance. Although results were comparable to those of previous reports, the apparent effect of mass transport limitations was demonstrated. Additional experiments with a loss-of-interaction FG repeat mutant variant demonstrated that the binding events that take place on surfaces can be unexpectedly complex, suggesting particular care must be exercised in interpretation of such data., Competing Interests: The authors have declared that no competing interests exist.

Aquaporins (AQPs) feature highly selective water transport through cell membranes, where the dipolar orientation of structured water wires spanning the AQP pore is of considerable importance for the selective translocation of water over ions. We recently discovered that water permeability through artificial water channels formed by stacked imidazole I-quartet superstructures increases when the channel water molecules are highly organized. Correlating water structure with molecular transport is essential for understanding the underlying mechanisms of (fast) water translocation and channel selectivity. Chirality adds another factor enabling unique dipolar oriented water structures. We show that water molecules exhibit a dipolar oriented wire structure within chiral I-quartet water channels both in the solid state and embedded in supported lipid bilayer membranes (SLBs). X-ray single-crystal structures show that crystallographic water wires exhibit dipolar orientation, which is unique for chiral I-quartets. The integration of I-quartets into SLBs was monitored with a quartz crystal microbalance with dissipation, quantizing the amount of channel water molecules. Nonlinear sum-frequency generation vibrational spectroscopy demonstrates the first experimental observation of dipolar oriented water structures within artificial water channels inserted in bilayer membranes. Confirmation of the ordered confined water is obtained via molecular simulations, which provide quantitative measures of hydrogen bond strength, connectivity, and the stability of their dipolar alignment in a membrane environment. Together, uncovering the interplay between the dipolar aligned water structure and water transport through the self-assembled I-quartets is critical to understanding the behavior of natural membrane channels and will accelerate the systematic discovery for developing artificial water channels for water desalting.

As pathogenic bacteria become resistant to traditional antibiotics, alternate approaches such as designing and testing new potent selective antimicrobial peptides (AMP) are increasingly attractive. However, whereas much is known regarding the relationship between the AMP sequence and potency, less research has focused on developing links between AMP properties, such as design and structure, with mechanisms. Here we use four natural AMPs of varying known secondary structures and mechanisms of lipid bilayer disruption as controls to determine the mechanisms of four rationally designed AMPs with similar secondary structures and rearranged amino acid sequences. Using a Quartz Crystal Microbalance with Dissipation, we were able to differentiate between molecular models of AMP actions such as barrel-stave pore formation, toroidal pore formation, and peptide insertion mechanisms by quantifying differential frequencies throughout an oscillating supported lipid bilayer. Barrel-stave pores were identified by uniform frequency modulation, whereas toroidal pores possessed characteristic changes in oscillation frequency throughout the bilayer. The resulting modes of action demonstrate that rearrangement of an amino acid sequence of the AMP resulted in identical overall mechanisms, and that a given secondary structure did not necessarily predict mechanism. Also, increased mass addition to Gram-positive mimetic membranes from AMP disruption corresponded with lower minimum inhibitory concentrations against the Gram-positive Staphylococcus aureus., (© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.)

Inteins, self-splicing protein elements, interrupt genes and proteins in many microbes, including the human pathogen Mycobacterium tuberculosis Using conserved catalytic nucleophiles at their N- and C-terminal splice junctions, inteins are able to excise out of precursor polypeptides. The splicing of the intein in the mycobacterial recombinase RecA is specifically inhibited by the widely used cancer therapeutic cisplatin, cis-[Pt(NH 3 ) 2 Cl 2 ], and this compound inhibits mycobacterial growth. Mass spectrometric and crystallographic studies of Pt(II) binding to the RecA intein revealed a complex in which two platinum atoms bind at N- and C-terminal catalytic cysteine residues. Kinetic analyses of NMR spectroscopic data support a two-step binding mechanism in which a Pt(II) first rapidly interacts reversibly at the N terminus followed by a slower, first order irreversible binding event involving both the N and C termini. Notably, the ligands of Pt(II) compounds that are required for chemotherapeutic efficacy and toxicity are no longer bound to the metal atom in the intein adduct. The lack of ammine ligands and need for phosphine represent a springboard for future design of platinum-based compounds targeting inteins. Because the intein splicing mechanism is conserved across a range of pathogenic microbes, developing these drugs could lead to novel, broad range antimicrobial agents., (© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.)

Although thermal desalination technology provides potable water in arid regions (e.g., Israel and the Gulf), its relatively high cost has limited application to less arid regions with large populations (e.g., California). Energy-intensive distillation is currently being replaced with less costly pressure- and electrically driven membrane-based processes. Reverse osmosis (RO) is a preferred membrane technology owing to process and pre- and posttreatment improvements that have significantly reduced energy requirements and cost. Further technical advances will require a deeper understanding of the fundamental science underlying RO. This includes determining the mechanism for water selectivity; elucidating the behavior of molecular water near polar and apolar surfaces, as well as the advantages and limitations of hydrophobic versus hydrophilic pores; learning the rules of selective water transport from nature; and designing synthetic analogs for selective water transport. Molecular dynamics simulations supporting experiments will play an important role in advancing these efforts. Finally, future improvements in RO are limited by inherent technical mass transfer limitations.

Drug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens is Mycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity against M. tuberculosis using a combination of "database filtering" bioinformatics, protein engineering, and de novo design. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) against M. tuberculosis and also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of the M. tuberculosis membrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Amyloid-beta peptides have long been implicated in the pathology of Alzheimer's disease. Bexarotene, a drug approved by the U.S. Food and Drug Administration for treating a class of non-Hodgkin's lymphoma, has been reported to facilitate the removal of amyloid-beta. We have developed a mathematical model to explore the efficacy of bexarotene treatment in reducing amyloid-beta load, and simulate amyloid-beta production throughout the lifespan of diseased mice. Both aspects of the model are based on and consistent with previous experimental results. Beyond what is known empirically, our model shows that low dosages of bexarotene are unable to reverse symptoms in diseased mice, but dosages at and above an age-dependent critical concentration can recover healthy brain cells. Further, early treatment was shown to have significantly improved efficacy versus treatment in older mice. Relevance with respect to bexarotene-based amyloid-beta-clearance mechanism and direct treatment for Alzheimer's disease is emphasized.

The time-dependent nucleation phase is critical to amyloid fibrillation and related to many pathologies, in which the conversion from natively folded amyloidogenic proteins to oligomers via nucleation is often hypothesized as a possible underlying mechanism. In this work, non-uniform AC-electric fields across two asymmetric electrodes were explored to control and examine the aggregation of insulin, a model amyloid protein, in aqueous buffer solution at constant temperature (20 °C) by fluorescence correlation spectroscopy and fluorescence microscopy. Insulin was rapidly concentrated in a strong AC-field by imposed AC-electroosmosis flow over an optimal frequency range of 0.5-2 kHz. In the presence of an AC-field, direct fibrillation from insulin monomers without the formation of oligomer precursors was observed. Once the insulin concentration had nearly doubled its initial concentration, insulin aggregates were observed in solution. The measured lag time for the onset of insulin aggregation, determined from the abrupt reduction in insulin concentration in solution, was significantly shortened from months or years in the absence of AC-fields to 1 min-3 h under AC-fields. The ability of external fields to alter amyloid nucleation kinetics provides insights into the onset of amyloid fibrillation.

Antimicrobial peptides (AMPs) are renowned for their potent bacteriostatic activity and safety, rendering them invaluable in animal husbandry, food safety, and medicine. Despite their potential, the physiological toxicity of AMPs to host cells significantly hampers their biosynthetic production. This study presents a novel approach for the biosynthesis of the antimicrobial peptide Kiadin by engineering a DAMP4–DPS–Kiadin fusion protein to mitigate host cell toxicity and achieve high-level expression. Leveraging the unique properties of the DAMP4 protein, we developed a non-chromatographic purification method to isolate the DAMP4–DPS–Kiadin fusion protein with high purity. The instability of the D–P peptide bond under acidic conditions, combined with the thermal and saline stability of DAMP4, enabled efficient separation of Kiadin through acid cleavage and isoelectric precipitation, yielding Kiadin with 96% purity and a production yield of 29.3 mg/L. Our optimization of acid cleavage temperature, duration, and isoelectric precipitation conditions proved critical for maximizing the purification efficiency and expression levels of Kiadin. The biosynthesized Kiadin exhibited robust bacteriostatic activity against Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Bacillus cereus and Staphylococcus aureus. Notably, Kiadin demonstrated significant post-antibiotic effects by disrupting bacterial membrane integrity, inducing cytoplasmic leakage, and inhibiting biofilm formation in E. coli K88 and S. aureus Mu50, without cytotoxicity towards mouse macrophages. In vivo studies further confirmed Kiadin's exceptional therapeutic efficacy against abdominal infections caused by E. coli K88. The acid cleavage and non-chromatographic purification techniques developed in this study offer a cost-effective and efficient strategy for the high-purity production of AMPs. [ABSTRACT FROM AUTHOR]

Polymeric membranes have emerged as a versatile and efficient liquid separation technology, addressing the growing demand for sustainable, high-performance separation processes in various industrial sectors. This review offers an in-depth analysis of recent developments in polymeric membrane technology, focusing on materials' advancements, innovative fabrication methods, and strategies for improving performance. We discuss the underlying principles of membrane separation, selecting suitable polymers, and integrating novel materials, such as mixed-matrix and composite membranes, to enhance selectivity, permeability, and antifouling properties. The article also highlights the challenges and limitations associated with polymeric membranes, including stability, fouling, and scalability, and explores potential solutions to overcome these obstacles. This review aims to guide the development of next-generation polymeric membranes for efficient and sustainable liquid separation by offering a detailed analysis of current research and future directions. [ABSTRACT FROM AUTHOR]

Modelling catalytic fixed bed reactors with a small tube-to-particle diameter ratio requires a detailed description of the interactions between fluid flow, intra-particle transport, and the chemical reaction(s) within the catalyst. Particle-resolved computational fluid dynamics (PRCFD) simulations are the most promising approach to predict the behaviour of these reactors accurately, since they take into account the local packed bed structure explicitly. In this work, a conjugated heat and mass transfer model for use in PRCFD simulations is presented in order to couple the fluid flow through the fixed bed with transport and reaction in the porous catalyst, while guaranteeing the no-slip boundary condition at the fluid–solid interface. For this purpose, the solutions of the solid and fluid domain are computed separately and are coupled by calculation and updating the boundary condition at the particle surface. Owing to the consideration of secondary gradients, the developed transfer model is also valid for unstructured calculation meshes containing non-orthogonal cells at the fluid–solid interface. Such meshes are often used to resolve complex geometries, such as a packed bed, in a computationally efficient manner. The coupling approach is validated using cases for which an analytical solution or literature correlations derived from experimental data are available. The simulation results of a short catalytic packed bed with rings catalysing the partial oxidation of n-butane to maleic anhydride exemplify the potential of PRCFD involving reactions to analyse the catalyst performance in great detail. [ABSTRACT FROM AUTHOR]

In this work, reverse osmosis and forward osmosis membranes were prepared using base cellulosic polymers with ZrO2. The prepared membranes were rolled on the spiral-wound configuration module. The modules were tested on a pilot unit to investigate the efficiency of the RO membrane and the hydraulic pressure effect on both sides of the FO membranes. The RO membrane provided a rejection of 99% for the seawater desalination, and the brine was used as a draw solution for the FO system. First, seawater was used as a draw solution to indicate the best hydraulic pressure, where the best one was 3 bar for the draw solution side, and 2 bar for the feed side, where the water flux reached 48.89 L/m2·h (LMH) with a dilution percentage of 80% and a low salt reverse flux of 0.128 g/m2·h (gMH) after 5 h of operation time. The integrated system of RO and forward-assisted osmosis (PAO) was investigated using river water as a feed and RO brine as a draw solute, where the results of PAO indicate a high-water flux of 68.6 LMH with a dilution of 93.2% and a salt reverse flux of 0.18 gMH. Therefore, using PAO improves the performance of the system. [ABSTRACT FROM AUTHOR]

The aggregation of amyloid-β (Aβ) peptides plays a crucial role in the etiology of Alzheimer's disease (AD). Recently, it has been reported that an A2T mutation in Aβ can protect against AD. Interestingly, a nonpolar A2V mutation also has been found to offer protection against AD in the heterozygous state, although it causes early-onset AD in homozygous carriers. Since the conformational landscape of the Aβ monomer is known to directly contribute to the early-stage aggregation mechanism, it is important to characterize the effects of the A2T and A2V mutations on Aβ₁₋₄₂ monomer structure. Here, we have performed extensive atomistic replica-exchange molecular dynamics simulations of the solvated wild-type (WT), A2V, and A2T Aβ₁₋₄₂ monomers. Our simulations reveal that although all three variants remain as collapsed coils in solution, there exist significant structural differences among them at shorter timescales. A2V exhibits an enhanced double-hairpin population in comparison to the WT, similar to those reported in toxic WT Aβ₁₋₄₂ oligomers. Such double-hairpin formation is caused by hydrophobic clustering between the N-terminus and the central and C-terminal hydrophobic patches. In contrast, the A2T mutation causes the N-terminus to engage in unusual electrostatic interactions with distant residues, such as K16 and E22, resulting in a unique population comprising only the C-terminal hairpin. These findings imply that a single A2X (where X = V or T) mutation in the primarily disordered N-terminus of the Aβ₁₋₄₂ monomer can dramatically alter the β-hairpin population and switch the equilibrium toward alternative structures. The atomistically detailed, comparative view of the structural landscapes of A2V and A2T variant monomers obtained in this study can enhance our understanding of the mechanistic differences in their early-stage aggregation., (Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Knowledge of the detailed mechanism by which proteins such as human αB- crystallin and human lysozyme inhibit amyloid beta (Aβ) peptide aggregation is crucial for designing treatment for Alzheimer's disease. Thus, unconstrained, atomistic molecular dynamics simulations in explicit solvent have been performed to characterize the Aβ17-42 assembly in presence of the αB-crystallin core domain and of lysozyme. Simulations reveal that both inhibitor proteins compete with inter-peptide interaction by binding to the peptides during the early stage of aggregation, which is consistent with their inhibitory action reported in experiments. However, the Aβ binding dynamics appear different for each inhibitor. The binding between crystallin and the peptide monomer, dominated by electrostatics, is relatively weak and transient due to the heterogeneous amino acid distribution of the inhibitor surface. The crystallin-bound Aβ oligomers are relatively long-lived, as they form more extensive contact surface with the inhibitor protein. In contrast, a high local density of arginines from lysozyme allows strong binding with Aβ peptide monomers, resulting in stable complexes. Our findings not only illustrate, in atomic detail, how the amyloid inhibitory mechanism of human αB-crystallin, a natural chaperone, is different from that of human lysozyme, but also may aid de novo design of amyloid inhibitors.

Using combinatorial methods, we synthesized a series of new vinyl amide monomers and graft-polymerized them to light-sensitive poly(ether sulfone) (PES) porous films for protein resistance. To increase the discovery rate and statistical confidence, we developed high throughput surface modification methods (HTP) that allow synthesis, screening and selection of desirable monomers from a large library in a relatively short time (days). A series of amide monomers were synthesized by amidation of methacryloyl chloride with amines and grafted onto commercial poly(ether sulfone) (PES) membranes using irradiation from atmospheric pressure plasma (APP). The modified PES membrane surfaces were then tested and screened for static protein adhesion using HTP. Hydroxyl amide monomers N-(3-hydroxypropyl)methacrylamide (A3), N-(4-hydroxybutyl)methacrylamide (A4), and N-(4-hydroxybutyl)methacrylamide (A6), ethylene glycol (EG) monomer N-(3-methoxypropyl)methacrylamide (A7), and N-(2-(dimethylamino)ethyl)-N-methylmethacrylamide (A8), and N-(2-(diethylamino)ethyl)-N-methylmethacrylamide (A9) all terminated with tertiary amines and were shown to have protein resistance. The PES membranes modified with these monomers exhibited both low protein adhesion (i.e. membrane plugging or fouling) and high flux. Their performance is comparable with previously identified best performing PEG and zwitterionic monomers, i.e. the so-called gold-standard for protein resistance. Combining a Hansen solubility parameter (HSP) analysis of the amide monomers and the HTP filtration results, we conclude that monomer solubility in water correlates with protein-resistant surfaces, presumably through its effects on surface-water interactions., (Published by Elsevier Ltd.)

Mucus secretion from the body is ubiquitous, and finding materials that resist mucus adhesion is a major technological challenge. Here, using a high throughput platform with photo-induced graft polymerization, we first rapidly synthesized, screened and tested a library of 55 different surfaces from six functional monomer classes to discover porcine intestinal low mucus adhesion surfaces using a 1h static mucus adsorption protocol. From this preliminary screen, two chemistries, a zwitterionic ([2-(acryloyloxy)ethyl] trimethylammonium chloride) and a multiple hydroxyl (N-[tris(hydroxymethyl)methyl]acrylamide) surface, exhibited significantly low mucus adhesion from a Langmuir-type isotherm when exposed to increasing concentrations of mucus for 24 h. Apolar or hydrophobic interactions were likely the dominant attractive forces during mucus binding since many polar or hydrophilic monomers reduced mucus adhesion. Hansen solubility parameters were used to illustrate the importance of monomer polarity and hydrogen bonding in reducing mucus adsorption. For a series of polyethylene glycol (PEG) monomers with changing molecular weight from 144 g mol⁻¹ to 1100 g mol⁻¹, we observed an excellent linear correlation (R²=0.998) between relative amount adsorbed and the distance from a water point in a specialized Hansen solubility parameter plot, emphasizing the role of surface-water interactions for PEG modified surfaces., (Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.)

Three critical aspects of searching for and understanding how to find highly resistant surfaces to protein adhesion are addressed here with specific application to synthetic membrane filtration. They include the (i) discovery of a series of previously unreported monomers from a large library of monomers with high protein resistance and subsequent low fouling characteristics for membrane ultrafiltration of protein-containing fluids, (ii) development of a new approach to investigate protein-resistant mechanisms from structure-property relationships, and (iii) adaptation of a new surface modification method, called atmospheric pressure plasma-induced graft polymerization (APP), together with a high throughput platform (HTP), for low cost vacuum-free synthesis of anti-fouling membranes. Several new high-performing chemistries comprising two polyethylene glycol (PEG), two amines and one zwitterionic monomers were identified from a library (44 commercial monomers) of five different classes of monomers as strong protein-resistant monomers. Combining our analysis here, using the Hansen solubility parameters (HSP) approach, and data from the literature, we conclude that strong interactions with water (hydrogen bonding) and surface flexibility are necessary for producing the highest protein resistance. Superior protein-resistant surfaces and subsequent anti-fouling performance was obtained with the HTP-APP as compared with our earlier HTP-photo graft-induced polymerization (PGP)., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Amyloid diseases, including Alzheimer's disease, are characterized by aggregation of normally functioning proteins or peptides into ordered, β-sheet rich fibrils. Most of the theories on amyloid toxicity focus on the nuclei or oligomers in the fibril formation process. The nuclei and oligomers are transient species, making their full characterization difficult. We have isolated toxic protein species that act like an oligomer and may provide the first evidence of a stable reactive species created by disaggregation of amyloid fibrils. This reactive species was isolated by dissolving amyloid fibrils at high pH and it has a mass >100 kDa and a diameter of 48 ± 15 nm. It seeds the formation of fibrils in a dose dependent manner, but using circular dichroism and deep ultraviolet resonance Raman spectroscopy, the reactive species was found to not have a β-sheet rich structure. We hypothesize that the reactive species does not decompose at high pH and maintains its structure in solution. The remaining disaggregated insulin, excluding the toxic reactive species that elongated the fibrils, returned to native structured insulin. This is the first time, to our knowledge, that a stable reactive species of an amyloid reaction has been separated and characterized by disaggregation of amyloid fibrils., (Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Protein splicing is an autocatalytic reaction where an intervening element (intein) is excised and the remaining two flanking sequences (exteins) are joined. The reaction requires specific conserved residues, and activity may be affected by both the intein and the extein sequence. Predicting how sequence will affect activity is a challenging task. Based on first-principles density functional theory and multiscale quantum mechanics/molecular mechanics, we report C-terminal cleavage reaction rates for five mutations at the first residue of the C-extein (+1), and describe molecular properties that may be used as predictors for future mutations. Independently, we report on experimental characterization of the same set of mutations at the +1 residue resulting in a wide range of C-terminal cleavage activities. With some exceptions, there is general agreement between computational rates and experimental cleavage, giving molecular insight into previous claims that the +1 extein residue affects intein catalysis. These data suggest utilization of attenuating +1 mutants for intein-mediated protein manipulations because they facilitate precursor accumulation in vivo for standard purification schemes. A more detailed analysis of the "+1 effect" will also help to predict sequence-defined effects on insertion points of the intein into proteins of interest., (Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Background: In spite of our extensive knowledge of the more than 20 proteins associated with different amyloid diseases, we do not know how amyloid toxicity occurs or how to block its action. Recent contradictory reports suggest that the fibrils and/or the oligomer precursors cause toxicity. An estimate of their temporal concentration may broaden understanding of the amyloid aggregation process., Methodology/principal Findings: Assuming that conversion of folded protein to fibril is initiated by a nucleation event, we back-calculate the distribution of nuclei concentration. The temporal in vitro concentration of nuclei for the model hormone, recombinant human insulin, is estimated to be in the picomolar range. This is a conservative estimate since the back-calculation method is likely to overestimate the nuclei concentration because it does not take into consideration fibril fragmentation, which would lower the amount of nuclei, Conclusions: Because of their propensity to form aggregates (non-ordered) and fibrils (ordered), this very low concentration could explain the difficulty in isolating and blocking oligomers or nuclei toxicity and the long onset time for amyloid diseases.

We find evidence for a direct transition of insulin monomers into amyloid fibrils without measurable concentrations of oligomers or protofibrils, suggesting that fibrillogenesis may occur directly from assembly of denaturing insulin monomers rather than by successive transitions through protofibril nuclei. To support our finding, we obtain size distributions using electrospray differential mobility analysis (ES-DMA), which provides excellent resolution to clearly distinguish among small oligomers and rapidly generates statistically significant size distributions. The distributions detect an absence of significant peaks between 6 nm and 17 nm as the monomer reacts into fibers-exactly the size range observed by others for small-angle-neutron-scattering-measured intermediates and for circular supramolecular structures. They report concentrations in the nanomolar range, whereas our limit of detection remains three-orders-of-magnitude lower (<5 pmol/L). This finding, along with the lack of significant increases in the β-sheet content of monomers using circular dichroism, suggests monomers do not first structurally rearrange and accumulate in a β-rich state but react and reorganize at the growing fiber's tip. These results quantitatively inform reaction-based theories of amyloid fiber formation and have implications for neurodegenerative, protein conformation ailments including Alzheimer's disease and bovine spongiform encephalopathy., (Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Inteins comprise a large family of phylogenetically widespread self-splicing protein catalysts that colonize diverse host proteins. The evolutionary and functional relationship between the intein and the split-host protein, the exteins, is largely unknown. To probe an association, we developed an in vivo and in vitro intein assay based on FRET. The FRET assay reports cleavage of the intein from its N-terminal extein. Applying this assay to randomized extein libraries, we show that the nature of the extein substrate bordering the intein can profoundly influence intein activity. Residues proximal to the intein-splicing junction in both N- and C-terminal exteins can accelerate the N-terminal cleavage rate by >4-fold or attenuate cleavage by 1,000-fold, both resulting in compromised self-splicing efficiency. The existence and the magnitude of extein effects require consideration for maximizing the utility of inteins in biotechnological applications, and they predict biases in intein integration sites in nature.

The real-time changes in viscoelasticity of adsorbed poly(L-lysine) (PLL) and adsorbed histone (lysine rich fraction) due to cross-linking by glutaraldehyde and corresponding release of associated water were investigated using a quartz crystal microbalance with dissipation monitoring (QCM-D) and attenuated total reflection Fourier transform infrared spectroscopy (ATR/FTIR). The kinetics of PLL and histone adsorption were measured through changes in mass adsorbed onto a gold-coated quartz surface from changes in frequency and dissipation and using the Voigt viscoelastic model. Prior to cross-linking, the shear viscosity and shear modulus of the adsorbed PLL layer were approximately 3.0 x 10(-3) Pas and approximately 2.5 x 10(5) Pa, respectively, while after cross-linking, they increased to approximately 17.5 x 10(-3) Pas and approximately 2.5 x 10(6) Pa, respectively. For the adsorbed histone layer, shear viscosity and shear modulus increased modestly from approximately 1.3 x 10(-3) to approximately 2.0 x 10(-3) Pas and from approximately 1.2 x 10(4) to approximately 1.6 x 10(4) Pa, respectively. The adsorbed mass estimated from the Sauerbrey equation (perfectly elastic) and the Voigt viscoelastic model differ appreciably prior to cross-linking whereas after cross-linking they converged. This is because trapped water molecules were released during cross-linking. This was confirmed experimentally via ATR/FTIR measurements. The variation in viscoelastic properties increased substantially after cross-linking presumably due to fluctuation of the randomly cross-linked network structure. An increase in fluctuation of the viscoelastic properties and the loss of imbibed water could be used as a signature of the formation of a cross-linked network and the amount of cross-linking, respectively.

Amyloid fibrillation has been intensively studied because of its association with various neurological disorders. While extensive time-dependent fibrillation experimental data are available and appear similar, few mechanistic models have been developed to unify those results. The aim of this work was to interpret these experimental results via a rigorous mathematical model that incorporates the physical chemistry of nucleation and fibril growth dynamics. A three-stage mechanism consisting of protein misfolding, nucleation, and fibril elongation is proposed and supported by the features of homogeneous fibrillation responses. Estimated by nonlinear least-squares algorithms, the rate constants for nucleation were approximately 10,000,000 times smaller than those for fibril growth. These results, coupled with the positive feedback characteristics of the elongation process, account for the typical sigmoidal behavior during fibrillation. In addition, experiments with different proteins, various initial concentrations, seeding versus nonseeding, and several agitation rates were analyzed with respect to fibrillation using our new model. The wide applicability of the model confirms that fibrillation kinetics may be fairly similar among amyloid proteins and for different environmental factors. Recommendations on further experiments and on the possible use of molecular simulations to determine the desired properties of potential fibrillation inhibitors are offered.

Inteins are autocatalytic protein cleavage and splicing elements. A cysteine to alanine mutation at the N-terminal of inteins inhibits splicing and isolates the C-terminal cleavage reaction. Experiments indicate an enhanced C-terminal cleavage reaction rate upon decreasing the solution pH for the cleavage mutant, which cannot be explained by the existing mechanistic framework. We use intein crystal structure data and the information about conserved amino acids to perform semiempirical PM3 calculations followed by high-level density functional theory calculations in both gas phase and implicit solvent environments. Based on these calculations, we propose a detailed "low pH" mechanism for intein C-terminal cleavage. Water plays an important role in the proposed reaction mechanism, acting as an acid as well as a base. The protonation of the scissile peptide bond nitrogen by a hydronium ion is an important first step in the reaction. That step is followed by the attack of the C-terminal asparagine side chain on its carbonyl carbon, causing succinimide formation and simultaneous peptide bond cleavage. The computed reaction energy barrier in the gas phase is approximately 33 kcal/mol and reduces to approximately 25 kcal/mol in solution, close to the 21 kcal/mol experimentally observed at pH 6.0. This mechanism is consistent with the observed increase in C-terminal cleavage activity at low pH for the cleavage mutant of the Mycobacterium tuberculosis RecA mini-intein.

The p53 gene is one of the genes most closely associated with human tumors and has become a popular target for tumor drug design. Currently, p53-based gene therapy techniques have been developed, but these therapies face challenges such as immaturity, high safety hazards, limited efficacy, and low patient acceptance. However, researchers are no less enthusiastic about the treatment because of its theoretical potential to treat cancer. In this paper, the advances in p53-based gene therapy and related nucleic acid delivery technologies were reviewed and prospected in order to support further development in this field. [ABSTRACT FROM AUTHOR]

Cell culture methods are indispensable strategies for studies in biological sciences and for drug discovery and testing. Most cell cultures have been developed using two-dimensional (2D) culture methods, but three-dimensional (3D) culture techniques enable the establishment of in vitro models that replicate various pathogenic conditions and they provide valuable insights into the pathophysiology of various diseases as well as more precise results in tests for drug efficacy. However, one difficulty in the use of 3D cultures is selection of the appropriate 3D cell culture technique for the study purpose among the various techniques ranging from the simplest single cell type-derived spheroid culture to the more sophisticated organoid cultures. In the simplest single cell type-derived spheroid cultures, there are also various scaffold-assisted methods such as hydrogel-assisted cultures, biofilm-assisted cultures, particle-assisted cultures, and magnet particle-assisted cultures, as well as non-assisted methods, such as static suspension cultures, floating cultures, and hanging drop cultures. Since each method can be differently influenced by various factors such as gravity force, buoyant force, centrifugal force, and magnetic force, in addition to non-physiological scaffolds, each method has its own advantages and disadvantages, and the methods have different suitable applications. We have been focusing on the use of a hanging drop culture method for modeling various non-cancerous and cancerous diseases because this technique is affected only by gravity force and buoyant force and is thus the simplest method among the various single cell type-derived spheroid culture methods. We have found that the biological natures of spheroids generated even by the simplest method of hanging drop cultures are completely different from those of 2D cultured cells. In this review, we focus on the biological aspects of single cell type-derived spheroid culture and its applications in in vitro models for various diseases. [ABSTRACT FROM AUTHOR]

During the construction of supramolecular polymers of smaller nanoparticles/nanoclusters bearing hierarchy and homochirality, the mechanism understanding via intuitive visualization and precise cross-scale chirality modulation is still challenging. For this goal, a cooperative self-assembly strategy is here proposed by using ionic complexes with uniform chemical composition comprising polyanionic nanocluster cores and surrounded chiral cationic organic components as monomers for supramolecular polymerization. The single helical polymer chains bearing a core-shell structure at utmost length over 20 μm are demonstrated showing comparable flexibility resembling covalent polymers. A nucleation-elongation growth mechanism that is not dealt with in nanoparticle systems is confirmed to be accompanied by strict chiral self-sorting. A permeable membrane prepared by simple suction of such supramolecular polymers displays high enantioselectivity (e.e. 98% after four runs) for separating histidine derivatives, which discloses a benefiting helical chain structure-induced functionalization for macroscopic supramolecular materials in highly efficient racemate separation. Understanding the mechanism for supramolecular polymer assembly from nanoclusters bearing hierarchy and homochirality is challenging. Here, the authors report a cooperative self-assembly strategy using ionic complexes with chiral surfactants through a nucleation-elongation growth mechanism with chiral self-sorting and prepare a permeable membrane for the separation of histidine derivatives. [ABSTRACT FROM AUTHOR]