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Actin is a highly conserved cytoskeletal protein that is present in all eukaryotes. Polymerization of actin to filamentous actin is essential for numerous cellular processes. Abnormal actin dynamics are directly associated with a variety of diseases, including cancer, immunological and neurological disorders. However, the dynamics of actin are not fully understood. In this work, we study the effects of nucleotides and metal ions on conformation of F/G-actin using molecular dynamics (MD) simulations. Our results show that different nucleotides and metal ions change the conformation of actin. The state of Adenosine Triphosphate (ATP) binding on F-actin conformation is more stable than G-actin. The D-loop has a large fluctuation when Ca 2 + binds to G-ATP-actin than Mg 2 + binds. Adenosine Diphosphate (ADP) binding leads to a stronger residual correlation on F-actin conformation, while it is opposite on G-actin. In addition, the detailed interactions between nucleotides and adjacent residues are discussed on different states of actin. This work provides a structural basis for understanding how the different nucleotides/metal ions binding influences the conformation of actin. Actin is crucial for cellular processes through its polymerization. Abnormal actin dynamics are linked to diseases, including cancer. This study investigates how nucleotides and metal ions impact F/G-actin conformation, providing a structural basis for understanding their influence on actin dynamics. [ABSTRACT FROM AUTHOR]

Lysyl oxidase‐like 2 (LOXL2) is a Cu2+‐dependent amine oxidase that catalyzes the oxidative deamination of lysine residues of elastin and collagen to generate aldehyde groups. In the active state of LOXL2, its conserved catalytic domain has a lysine tyrosylquinone (LTQ) cofactor and a copper ion. LTQ is post‐translationally derived from Lys653 and Tyr689 of LOXL2. In this study, well‐tempered metadynamics simulations are used to investigate the conformation modulation from the inactive state to active state and obtain the free energy landscape. Interestingly, the simulations show that LTQ precursor residues cannot get close in Zn2+−bound LOXL2, whereas the copper ion binding triggers a conformation change to form an optional structure for LTQ biosynthesis. It is found that a prominent loop, consisting of residues 654–658, hinders the formation of LTQ in Zn2+−LOXL2 by preventing Lys653 from moving into active site of LOXL2, whereas this loop is relatively flexible in Cu2+−LOXL2. After the formation of LTQ, it needs to be activated by adjusting its position to be exposed to the solvent, thus allowing it to react with its substrate proteins. The results indicate that this process involves an intermediate state and that the activation of LTQ overcomes an energy barrier of 5.9 kcal mol−1. [ABSTRACT FROM AUTHOR]

A fluorescent method is described for trypsin determination through the strong electrostatic interactions between cationic polyelectrolytes and single-stranded DNA (ssDNA) templated Au nanoclusters (AuNCs). The ssDNA-AuNCs display improved fluorescence emission with excitation/emission maxima at 280/475 nm after being incorporated with poly(diallyldimethylammonium chloride) (PDDA). Fluorescent enhancement is mainly attributed to the electrostatic interactions occurring between PDDA and ssDNA templates. This can make the conformation of the ssDNA templates to change. Thus, it offers a better microenvironment for stabilizing and protecting ssDNA-AuNCs, and results in fluorescence emission enhancement. By using protamine as a model, the method is employed for the determination of trypsin. The assay enables trypsin to be determined with good sensitivity and a linear response ranging from 5 ng⋅mL−1 to 60 ng⋅mL−1 with a 1.5 ng⋅mL−1 limit of detection. It is also extended to determine the trypsin contents in human's serum samples with recoveries between 98.7% and 103.5% with relative standard deviations (RSDs) between 3.5% and 4.8%. A novel fluorescent strategy has been developed for of trypsin determination by using protamine mediated fluorescent enhancement of DNA templated Au nanoclusters. [ABSTRACT FROM AUTHOR]

ABCG2 is an exporter-type ABC protein that can expel numerous chemically unrelated xeno- and endobiotics from cells. When expressed in tumor cells or tumor stem cells, ABCG2 confers multidrug resistance, contributing to the failure of chemotherapy. Molecular details orchestrating substrate translocation and ATP hydrolysis remain elusive. Here, we present methods to concomitantly investigate substrate and nucleotide binding by ABCG2 in cells. Using the conformation-sensitive antibody 5D3, we show that the switch from the inward-facing (IF) to the outward-facing (OF) conformation of ABCG2 is induced by nucleotide binding. IF-OF transition is facilitated by substrates, and hindered by the inhibitor Ko143. Direct measurements of 5D3 and substrate binding to ABCG2 indicate that the high-to-low affinity switch of the drug binding site coincides with the transition from the IF to the OF conformation. Low substrate binding persists in the post-hydrolysis state, supporting that dissociation of the ATP hydrolysis products is required to reset the high substrate affinity IF conformation of ABCG2.

O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) transferase (OGT) is an essential enzyme in many cellular physiological catalytic reactions that regulates protein O-GlcNAcylation. Aberrant O-GlcNAcylation is related to insulin resistance, diabetic complications, cancer and neurodegenerative diseases. Understanding the peptide delivery in OGT is significant in comprehending enzymatic catalytic process, target-protein recognition and pathogenic mechanism. Herein extensive molecular dynamics (MD) simulations combined with various techniques are utilized to study the recognizing and binding mechanism of peptide fragment extracted from casein kinase II by OGT from atomic level. The residues of His496, His558, Thr633, Lys634, and Pro897 are demonstrated to play a dominant role in the peptide stabilization via hydrogen bonds and σ-π interaction, whose van der Waals and non-polar solvent effects provide the main driving force. In addition, two channels are identified. The delivery mode, mechanism together with thermodynamic and dynamic characterizations for the most favorable channel are determined. The peptide is more inclined to be recognized by OGT through the cavity comprised of residues 799–812, 893–899, and 865–871, and Tyr13-terminal is prior recognized to Met26-terminal. The transportation process is accompanied with conformation changes between the “spread” and “V” shapes. The whole process is strong exothermic that is highly dependent on the variation of hydrogen bond interactions between peptide and OGT as well as the performance of different subsections of peptide. Besides that, multiple computational methods combinations may contribute meaningfully to calculation of similar bio-systems with long and flexible substrate.

Liposomes have been attracted attention, because liposomes can mimic the lipid bilayer membrane of cells. Scientists apply liposomes for drug delivery systems (DDSs) and for artificial cells. Hence, the handling of liposomes is very important. In particular, it is difficult to control the adsorption of the liposome onto the target selectively and the release of the drug by its own rupture. Therefore, scientists are looking for the way to carefully monitor the behavior of liposomes from adsorption to rupture in deep.We integrated quartz crystal microbalance dissipation (QCM–D) and localized surface plasmon resonance (LSPR) into a single sensor and monitored the signals from the sensor on the adsorption and rupture of liposome. The integrated sensor detected resonance frequency and dissipation from QCM-D, and wavelength shifts from LSPR simultaneously. The integrated sensor successfully monitored conformational changes of liposomes in real time upon exposure to the surfactant, Triton X-100. The data clearly revealed liposome adsorption and deformation, and disruption of membrane integrity by normalizing three signals, resonance frequency, resonance resistance and wavelength shift. In fact, we found that normalized signals were divided into 5 steps through the experiment: liposome adsorption, liposome deformation slightly, liposome conjugated with micelles of surfactant, liposome disruption and lipid bilayer covered on the surface. These results indicate that our device provides a powerful tool to gain deeper insights into biomolecular interactions, expanding numerous applications such as monitoring of conformational changes in proteins, oligonucleotides, viruses, bacteria, vesicles, and cells.

Gluten protein as one of the plant resources is affected by redox agent. Chemical modifications by redox agent have myriad advantages mainly short reaction times, no requirement for specialized equipment, low cost, and highly clear modification impacts. The gluten network properties could be influenced through redox agents (oxidative and reducing agents) which are able to alter the strength of dough via different mechanisms for various purposes. The present review examined the impact of different redox compounds on gluten and its subunits based on their effects on their bonds and conformations and thus with their impacts on the physico‐chemical, morphological, and rheological properties of gluten and their subunits. This allows for the use of gluten for different of purposes in the food and nonfood industry. [ABSTRACT FROM AUTHOR]

A selenium-chelating pea oligopeptide (Se-POP) was prepared from pea oligopeptide (POP) and sodium selenite (SS) via chelation. Se-POP is rich in organic selenium as 57.23% ± 0.36%. The chelation reaction was spontaneous and endothermic, with a binding constant Ka = 2.64 × 104 ± 1.60 × 103 M−1 and binding site number n = 0.27 ± 0.01. Spectral analysis indicated protein conformational changes consistent with chelation, that the peptide chain to fold and curl, causing random coil and β-turn decreasing and the peptide side-chain radicals folding and burying. The antioxidant capacity of Se-POP was increased relative to that of POP. One novel antioxidant peptide fragment was obtained from Se-POP and identified as PPKIYP, presenting at a concentration of 29.47 ng/mg. The results indicated that Se-POP might be a new organic Se supplement with antioxidant capacity, which may be easily absorbed due to its low molecular weight.

Two‐photon‐excited fluorescent probes are important for two‐photon microscopy for biomedical studies. In contrast to the many examples of probes for cationic species, such as metal ions, there have been fewer reports on the control of two‐photon optical properties by anions because in such systems it is difficult to control the associated π‐electronic states. This Minireview summarizes anion‐responsive molecules that exhibit changes in two‐photon optical properties and describes their molecular design and anion‐response mechanisms, which are driven by changes in covalent bonds and noncovalent interactions. Results from a recent study of two‐photon systems, where geometries and optical properties are modulated by anion binding, are also discussed. [ABSTRACT FROM AUTHOR]

Two‐photon absorption (TPA) dyes with intense fluorescence can be used to detect small chemical species and as sensors and bioimaging probes for specific analytes. Various TPA dyes responding to a number of external stimuli have been reported. Among them, biologically important anionic species have not been used as agents to control TPA properties because their direct electronic influences on the transition dipole moments of dyes are typically small. In this study, dipyrrolyldiketone BF2 complexes substituted with π‐extended units exhibited efficient TPA properties that could be regulated by conformation changes induced by anion binding. The TPA intensity decreased to 1/5 of the original intensity upon anion binding, which was much larger than that observed for one‐photon absorption. Anion detection was achieved by a change in the emission intensity of spatially resolved spots of two‐photon‐excited fluorescence (TPEF) in the sample. Experimental and theoretical studies were performed to understand the mechanism of the TPA property control and showed that the drastic changes in the transition dipole moments upon conformation changes between the straight and bending forms of the π‐electronic systems caused the TPA and TPEF intensities drop. [ABSTRACT FROM AUTHOR]

Oyster peptide-zinc nanoparticles (OPZNPs) (28–108 nm) were prepared in the presence of 0.5%–0.9% zinc sulfate at pH 6.0–11.0. The obtained nanoparticles exhibited uniform size distribution and spherical shapes. Nanoparticle characteristics, such as size, surface charge, and hydrophobicity, could be adjusted by controlling zinc sulfate concentration and environmental pH. Increasing pH value or decreasing zinc sulfate concentration tended to reduce nanoparticle size and increase nanoparticle surface charge and hydrophobicity. OPZNPs presented good stability at near-neutral pH and could be stored for at least 20 days at 4°C. The results of the peptide conformation study and nanoparticle dissociation test proved that zinc ions and carboxyl groups are the key factors that affect OPZNP formation. The intermolecular combinations of carboxyl groups via zinc bridging facilitated the aggregation of oyster peptides. Nanoparticle formation was accompanied by aggregate association and conformational changes. These changes included increments in β-sheets, especially intermolecular β-sheets, at the expense of α-helixes. Overall, this work provided a green alternative route for the synthesis of OPZNPs. [ABSTRACT FROM AUTHOR]

Abstract: Surface-enhanced Raman scattering (SERS) has gained a reputation as one of the most sensitive spectroscopic methods for biosensing. However, to design a SERS-based biosensor, almost all currently used methods involve the time-consuming and complicated modification of the metallic nanoparticles, which restricts their wide spread applications. Herein, a facile and sensitive SERS-based aptasensor for colorimetric detection of acetamiprid (AC) was demonstrated. The prepared crystal violet (CV)-aptamer decorated gold nanoparticles (GNPs) tended to aggregate in a solution with high concentrations of salt, and displayed a purple color. In the presence of AC, the specific binding of the target with the aptamer generated conformation changes of aptamer (confirmed by the circular dichroism spectrum), which made the stable GNPs aggregation in the salt solution, thus resulting the SERS signal enhanced. Sequel, the SERS intensity was increased linearly with the concentration of AC ranging from 3.0 × 10−8 to 4.0 × 10−6 M, with a relatively low limit of 1.76 × 10−8 M. The detection ability of AC by this biosensor was also confirmed with different adulterated tea. This approach is not only straightforward in fabrication but also cost-effective in operation, and can be used for diverse bio-molecules detection by changing the aptamer.Graphical abstract: [ABSTRACT FROM AUTHOR]

Investigation of fundamental properties of colloidal systems of cationic surfactants is important for practical and theoretical reasons. In this work, the nonideal behavior in cetyltrimethylammonium bromide and Triton X-100 mixtures was studied, during the mixed micelle formation. In order to study the aggregation behavior, excess Gibbs energy ( G E ), excess enthalpy ( H E ) and excess entropy ( S E ) were determined. The thermodynamic parameters were monitored as a function of the molar ratio, at different temperatures (283.15–328.15 K). G E , H E and S E were obtained based on the critical micelle concentration values of investigated mixtures. The results of the study indicate existence of synergism in the surfactant mixtures. The increase of the stability of the mixed micelles ( G E  < 0) is explained as the result of enthalpic interactions and/or entropy changes during the formation of the aggregates. [ABSTRACT FROM AUTHOR]

• Heating and glycation affected the Nε-carboxymethyllysine level in duck meat. • The degree of glycation changed the myofibrillar proteins aggregates conformation. • Thermal treatment influenced the subsequent glycation process. • Thermal treatment and glycation changed the fibrillation kinetics of myofibrillar proteins. Nε-carboxymethyllysine (CML), a frequently used marker of advanced glycation end products (AGEs) in food, was generated in food processing easily and caused changes in myofibrillar proteins (MPs) characterization. The relevance between glycosylated MPs structure alternation and CML formation under thermal conditions have been reported. However, the correlation mechanism was not clear yet. In this work, the influence of gradient heating (50℃, 60℃, 70℃, 80℃, and 90℃) on the different degrees of glycated MPs, which determined the correlation with CML formation in protein structural changes of MPs. In the rising stage of the CML level, glycation accelerated the fibrillation and aggregation behavior of MPs during heating and increased surface hydrophobicity and particle size. The protein cross-linking affected the protein modification caused by heating and glycation. This work highlights the substantial influences of glycosylation and thermal treatments on MPs, which transformed the MPs structural characteristics and CML level. [ABSTRACT FROM AUTHOR]

Bisphosphonate (BP) has been widely used as a bone-targeting group, and the BP-modified platinum(II) complexes have shown potential to as anticancer drugs against bone-related diseases, such as osteosarcoma. DNA conformation changes induced by the BP-modified dinuclear platinum(II) complexes have been investigated using molecular dynamics simulations. The results indicated that the BP-modified dinuclear platinum(II) complexes coordinated to DNA results in DNA structural distortions, including twisting, unwinding and bending. Furthermore, the rigidity of the bridging linkers in the BP-modified platinum(II) complex may induce more significant DNA structural distortions with same spans. The results provide the detail information of DNA conformational changes induced by the BP-modified platinum(II) complexes with different flexibility of bridging linkers, and are helpful for exploring novel platinum-based antitumor drugs. Molecular dynamics simulation of binding of dinuclear platinum(II) complexes with the bisphosphonate group to DNA is shown to cause DNA structural distortions. [Display omitted] • Molecular dynamics simulation of three dinuclear platinum(II) complexes bound to DNA are reported • Major changes to sugar pucker, groove parameter, conformation dynamics of DNA are observed • More significant DNA structural distortions are caused by the Pt(II) complexes with rigid linker [ABSTRACT FROM AUTHOR]

Dense-phase carbon dioxide (DPCD) can induce myosin denaturation and aggregation and result in the formation of a gel. To explore the mechanism that DPCD induce myosin the formation of gels, molecular dynamics simulations were used to investigate the effects of DPCD on the structural properties of the myosin heavy chain (MHC, GenBank Accession No: BAM65721.1 ) from Litopenaeus vannamei. In addition, the interaction between the MHC and CO 2 was explored under the coupling of pressure and temperature. To facilitate a better understanding and comparison, the structure of MHC was simulated in water at 0.1 MPa and 50 °C (called the myosin-water system, MWS) and in water and DPCD at 25 MPa and 50 °C (called the myosin-water-DPCD system, MWDS). The analysis of the root-mean-square deviation ( RMSD ) and root-mean-square fluctuation ( RMSF ) revealed that the conformation of the MHC in both MWDS and MWS changed significantly relative to its initial structure. Moreover, the results of the solvent-accessible surface area demonstrated that the MHC structure changes from a compact arrangement to a looser arrangement in both MWDS and MWS. Finally, the results from investigations into the secondary structures showed that the α-helix content of the MHC decreased, whereas the β-turn and random coil content increased. Greater overall structural variations of the MHC were observed in MWDS than those observed in MWS. DPCD exerts a substantial effect on the MHC structure because of its hydrogen bonding, electrostatic repulsion and hydrophobic interactions with the MHC. [ABSTRACT FROM AUTHOR]

• Lubricant conformation changes and energy transfer of confined lubricant thin films are studied by molecular dynamics simulations. • The thickness of lubricant thin film shows a power exponential relationship with pressure loads. • The lubricant thin film behaves like the Couette flow under low pressure loads, while boundary slip and temperature jump occur when high pressure loads is used. • Polymers adjusted the film conformation through a "one-step" or "two-step" mode under different loads. The lubrication system plays an important role in the reliability of moving links for spacecrafts while lubrication failure has emerged as one of the challenges in developing advanced spacecrafts with long life and high reliability. However, the process and mechanism of lubrication in space are still unclear due to a complex environment. In this study, the lubrication behavior under various pressure loads was studied by analyzing the lubricant conformation changes and energy transfer through molecular dynamics simulations. Results indicated that a "one-step" or "two-step" adjustment in the polymer conformations occurred, and the film exhibited different motion modes and temperature fields under different pressure loads. This work studied polymer thin film lubricant via energy transfer and molecular motion at a molecular level and gave a fundamental understanding on the lubrication behavior and lubrication failure of polymer thin film in space, providing theoretical guidance in developing advanced space lubrication technology. [ABSTRACT FROM AUTHOR]

ABCG2 is an exporter-type ABC protein that can expel numerous chemically unrelated xeno- and endobiotics from cells. When expressed in tumor cells or tumor stem cells, ABCG2 confers multidrug resistance, contributing to the failure of chemotherapy. Molecular details orchestrating substrate translocation and ATP hydrolysis remain elusive. Here, we present methods to concomitantly investigate substrate and nucleotide binding by ABCG2 in cells. Using the conformation-sensitive antibody 5D3, we show that the switch from the inward-facing (IF) to the outward-facing (OF) conformation of ABCG2 is induced by nucleotide binding. IF-OF transition is facilitated by substrates, and hindered by the inhibitor Ko143. Direct measurements of 5D3 and substrate binding to ABCG2 indicate that the high-to-low affinity switch of the drug binding site coincides with the transition from the IF to the OF conformation. Low substrate binding persists in the post-hydrolysis state, supporting that dissociation of the ATP hydrolysis products is required to reset the high substrate affinity IF conformation of ABCG2., Competing Interests: ZG, GM, ÉH, TS, ZR, LH, AS, TO, JR, GS, KG No competing interests declared, (© 2023, Gyöngy et al.)

The conformation of calmodulin (CaM) changes from closed configuration to open one, converting to a claviform dumbbell-shaped biomolecule upon Ca2+-binding. A hybrid probe of graphene oxide (GO) cationic conjugated polymer for detection of the conformation transition of CaM by using FRET technique is demonstrated. The stronger hydrophobic interaction and weaker electrostatic repulsion leads to more CaM adsorption to the surface of GO upon binding with Ca2+ than that of CaM in the absence of Ca2+ (apoCaM), resulting in much farther proximity between poly[(9,9-bis(6′- N, N, N-trimethy­lammonium)hexyl)-fluorenylene phenylene dibromide] (PFP) and green fluorescent protein labeled at the N-terminus of CaM and therefore much weaker FRET efficiency for PFP/Ca2+/CaM in comparison with that of PFP/apoCaM in the presence of GO. Notably, the assembly of CaM with GO is quantitatively and reversibly controlled by Ca2+ ions. [ABSTRACT FROM AUTHOR]

This study investigated the influence of camellia saponin (CS) on the physicochemical and lipid oxidative stability of camellia oil body-based emulsions (COBE) at pH 3.0 and 7.0 as well as proposed the underlying action mechanism. At pH 3.0, CS could not enhance the physicochemical stability of COBE with intensified aggregation and increased particle size because of the electrostatic neutralization effect of CS on oil body interfacial proteins (OBIP). By contrast, decreased particle size and improved long-term stability of COBE were observed at pH 7.0, which was due to the hydrophobic interaction between OBIP and CS molecules. Furthermore, COBE lipid oxidation was effectively retarded with CS incorporation, which was mainly attributable to the CS-OBIP interaction on the oil body surface, resulting in dramatic changes in OBIP conformation and structure (fluorescence quenching and increased α-helix structure) and the formation of composite interfaces. • Camellia saponin (CS) improves the lipid oxidation stability of oil-body emulsion. • The influence of CS on oil body emulsion physicochemical stability is pH-dependent. • CS induces oil body interfacial protein (OBIP) conformational and structural changes. • The CS-OBIP interaction induces a multi-layer mixed elastic interfaces formation. [ABSTRACT FROM AUTHOR]

How DNA governs transcription is a central question to all who study gene expression. In the conventional mode of DNA with two states, ON and OFF, the switching of DNA states either causes the cell population to form a bimodal distribution or manipulates the noise intensity of a unimodal distribution. Besides, the change of switching rate constants has little effect on the position of peaks in a bimodal distribution. By stochastic simulation algorithm, SSA, we investigated the role of DNA switching between four states, on way to managing the distribution of downstream proteins. We discovered that the system of DNA with four states allows cells to freely adjust the noise intensity of both peaks in the bimodal distribution. We also found that the change of switching frequency may alter the position of peaks in a bimodal distribution. [ABSTRACT FROM AUTHOR]

The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3% greater than in their unbound state, and the BSA, 7% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy. [ABSTRACT FROM AUTHOR]

Cation-induced conformational changes of peptide as a guide to developing insights into human diseases-related proteins have received a lot of attention. The interactions between poly-l-glutamate (PGA) and different cations, including Na+, K+and Mg2+, respectively, are studied in solvent at a concentration of 1 M, and the behaviours of peptide with different cations are investigated. For Na+, an oscillatory stabilising process to α-helix PGA is found, in accordance with the uniform free-energy landscape, whereas for K+, an extended α-helix structure is formed by the terminal turns, suggesting a weaker attraction to charged head groups. For Mg2+, the bridged charged side chains are responsible for the maximum probability of helix state. These distinct structural changes can be attributed to the different interactions between charged head groups and cations. Both Na+and K+are mainly attracted around head groups by direct ion binding while Mg2+is centrally trapped among adjacent charged head groups. In addition, a surprising shift of the backbone hydrogen bond, from intact state to intermediate state, is observed. This is opposite to the stabilising effect of Na+around negatively charged head groups. [ABSTRACT FROM AUTHOR]

Cytochrome P450 reductase (CYPOR) undergoes a large conformational change to allow for an electron transfer to a redox partner to take place. After an internal electron transfer over its cofactors, it opens up to facilitate the interaction and electron transfer with a cytochrome P450. The open conformation appears difficult to crystallize. Therefore, a model of a human CYPOR in the open conformation was constructed to be able to investigate the stability and conformational change of this protein by means of molecular dynamics simulations. Since the role of the protein is to provide electrons to a redox partner, the interactions with cytochrome P450 2D6 (2D6) were investigated and a possible complex structure is suggested. Additionally, electron pathway calculations with a newly written program were performed to investigate which amino acids relay the electrons from the FMN cofactor of CYPOR to the HEME of 2D6. Several possible interacting amino acids in the complex, as well as a possible electron transfer pathway were identified and open the way for further investigation by site directed mutagenesis studies. [ABSTRACT FROM AUTHOR]

A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped Paramecium bursaria chlorella virus was used to interpret structures of the virus at initial stages of cell infection. A fivefold averaged map demonstrated that two minor capsid proteins involved in stabilizing the capsid are missing in the vicinity of the unique vertex. Reconstruction of the virus in the presence of host chlorella cell walls established that the spike at the unique vertex initiates binding to the cell wall, which results in the enveloped nucleocapsid moving closer to the cell. This process is concurrent with the release of the internal viral membrane that was linked to the capsid by many copies of a viral membrane protein in the mature infectous virus. Simultaneously, part of the trisymmetrons around the unique vertex disassemble, probably in part because two minor capsid proteins are absent, causing Paramecium bursaria chlorella virus and the cellular contents to merge, possibly as a result of enzyme(s) within the spike assembly. This may be one of only a few recordings of successive stages of a virus while infecting a eukaryotic host in pseudoatomic detail in three dimensions. [ABSTRACT FROM AUTHOR]

Abstract: We used an in silico computational method to theoretically analyze important residue-ligand interactions as well as ligand conformation changes in the vitamin D receptor (VDR). The ligand used for analysis was 1α,25-dihydroxy-19-nor-vitamin D3 [1α,25-19-nor-(OH)2D3] , whose crystal structure has not been solved. To estimate amino acid residue-ligand interactions with chemical accuracy, we adopted the fragment molecular orbital (FMO) method , which is based on the nonempirical total electronic quantum calculation. The docking of the ligand to the VDR was controlled by hydrophilic and hydrophobic interactions between amino acid residues and the ligand in the ligand binding pocket (LBP) . These molecular interactions changed when the conformation of the ligand in the VDR was changed . This conformation change is important to consider in computational, in silico, approaches for analyzing the mechanism of ligand-docking to the VDR. The position of the 1α,25-19-nor-(OH)2D3 ligand in the VDR-LBP was related to the hydrophobic interaction that occurred between the Ile271 residue of the VDR-LBP and the ligand. The interaction between Ile271 and 1α,25-19-nor-(OH)2D3 was repulsive, whereas, that between Ile271 and the natural ligand, 1α,25-(OH)2D3, is stable. The orientation change in the isopropyl group of Ile271 affected the residue''s interaction with 1α,25-19-nor-(OH)2D3. We also found that conformation changes in the A-ring affected electrostatic (hydrophilic) interactions between the VDR and the ligand. [Copyright &y& Elsevier]

Changes in protein conformation play key roles in facilitating various biochemical processes, ranging from signaling and phosphorylation to transport and catalysis. While various factors that drive these motions such as environmental changes and binding of small molecules are well understood, specific causative effects on the structural features of the protein due to these conformational changes have not been studied on a large scale. Here, we study protein conformational changes in relation to two key structural metrics: packing efficiency and disorder. Packing has been shown to be crucial for protein stability and function by many protein design and engineering studies. We study changes in packing efficiency during conformational changes, thus extending the analysis from a static context to a dynamic perspective and report some interesting observations. First, we study various proteins that adopt alternate conformations and find that tendencies to show motion and change in packing efficiency are correlated: residues that change their packing efficiency show larger motions. Second, our results suggest that residues that show higher changes in packing during motion are located on the changing interfaces which are formed during these conformational changes. These changing interfaces are slightly different from shear or static interfaces that have been analyzed in previous studies. Third, analysis of packing efficiency changes in the context of secondary structure shows that, as expected, residues buried in helices show the least change in packing efficiency, whereas those embedded in bends are most likely to change packing. Finally, by relating protein disorder to motions, we show that marginally disordered residues which are ordered enough to be crystallized but have sequence patterns indicative of disorder show higher dislocation and a higher change in packing than ordered ones and are located mostly on the changing interfaces. Overall, our results demonstrate that between the two conformations, the cores of the proteins remain mostly intact, whereas the interfaces display the most elasticity, both in terms of disorder and change in packing efficiency. By doing a variety of tests, we also show that our observations are robust to the solvation state of the proteins. [ABSTRACT FROM AUTHOR]

Abstract: The use of a flow injection surface plasmon resonance (FI-SPR) spectrometer equipped with a bicell detector or a position-sensitive device for determining coordination of heavy metal ions (Cd2+ and Hg2+) by surface-confined apo-metallothionein (apo-MT) molecules is described. To facilitate the formation of a compact MT adsorbate layer with a uniform surface orientation, MT molecules were attached onto a preformed alkanethiol self-assembled monolayer. The method resorts to the generation of apo-MT at the surface by treating the MT-covered sensor chip with glycine–HCl and the measurement of the apo-MT conformation changes upon metal ion incorporation. Domain-specific metal ion binding processes by the apo-MT molecules were observed. Competitive replacement of one metal ion by another can be monitored in real time by FI-SPR. The tandem use of an immobilization scheme for forming a sub-monolayer of MT molecules at the sensor surface and the highly sensitive FI-SPR instrument affords a low concentration detection level. The detection level for Cd2+ (0.1μM or 15ppb) compares favorably with similar studies and the methodology complements to other well-established sensitive analytical techniques. The extent of metal incorporation by apo-MT molecules was also determined. [Copyright &y& Elsevier]

Abstract: The structural and functional properties of arginine kinase (AK) in alkaline conditions in the absence or presence of salt have been investigated. The conformational changes of AK during alkaline unfolding and salt-induced folding at alkaline pH were monitored using intrinsic fluorescence emission, binding of the fluorescence probe 1-anilino-8-naphthalenesulfonate and circular dichroism. The results for the alkaline unfolded enzyme showed that much lower pH (11.0) was required to cause the complete loss of AK activity than was required to cause an obvious conformational change of the enzyme. Compared with the completely unfolded state in 5M urea, the high pH denatured enzyme had some residual secondary and tertiary structure even at pH 13.0. Increasing the ionic strength by adding salt at pH 12.75 resulted in the formation of a relatively compact tertiary structure and a little new secondary structure with hydrophobic surface enhancement. These results indicate that the partially folded state formed under alkaline conditions may have similarities to the molten globule state which is compact, but it has a poorly defined tertiary structure and a native-like secondary structure. [Copyright &y& Elsevier]

Measurement of the temperature-dependence of thrombin-catalyzed cleavage of the Arg155–Ser156 and Arg284–Thr285 peptide bonds in prothrombin and prothrombin-derived substrates has yielded Arrhenius parameters that are far too large for classical mechanistic interpretation in terms of a simple hydrolytic reaction. Such a difference from the kinetic behavior exhibited in trypsin- and chymotrypsin-catalyzed proteolysis of peptide bonds is attributed to contributions by enzyme exosite interactions as well as enzyme conformational equilibria to the magnitudes of the experimentally determined Arrhenius parameters. Although the pre-exponential factor and the energy of activation deduced from the temperature-dependence of rate constants for proteolysis by thrombin cannot be accorded the usual mechanistic significance, their evaluation serves a valuable role by highlighting the existence of contributions other than those emanating from simple peptide hydrolysis to the kinetics of proteolysis by thrombin and presumably other enzymes of the blood coagulation system. [Copyright &y& Elsevier]

Cyt1A is a cytolytic toxin produced by Bacillus thuringiensis var. israelensis. Due to its toxicity in vivo against mosquitoes and black flies, it is used as an environmentally friendly insecticide, although its mode of action is not completely understood. The toxin is membrane-active, but its membrane-bound conformation is unknown. In the absence of direct structural data, fluorescence spectroscopy was used to obtain indirect information on Cyt1A conformation changes in the environment mimicking the vicinity of the lipid membrane (lower pH and increased ionic strength). With decreasing pH, Cyt1A''s surface hydrophobicity increased, which is consistent with an increased interaction with model membranes at low pH values, as observed previously. The pKa value of this conformation change is 4.4±0.1. Intrinsic tryptophan fluorescence decreased with decreasing pH, and the pKa value was the same as the one determined with synthetic probes. The protein has two types of hydrophobic binding sites, and at low pH these sites bind more probe molecules (bis-ANS) with a higher affinity than at pH 7.4. When bound to the lipid, the toxin exhibited conformation similar to the molten-globule state and showed some characteristics also observed at low pH. However, the conformation of the lipid-bound toxin did not depend on pH. Neutral salts like NaCl and KCl induced conformational changes at neutral pH, but not at low pH. These changes were most probably due to specific interactions of the salt ions with the charged amino acids on the protein surface rather than due to general effects such as Hofmeister and Debye–Hückel. Our results might contribute to elucidating the mode of action of Cyt1A, and perhaps also to improving the formulation of the insecticidal preparations. [Copyright &y& Elsevier]

Background: Changes of albumin conformation flexibility and binding characteristics in plasma products can be determined by electron spin resonance spectroscopy (ESR) with spin probes as reporter molecules.Methods: Quality of albumin transport was analyzed in different processed plasma units using a new ESR method which provides estimation of albumin properties by examination of albumin molecular structure changes.Results: In serum of healthy donors could not be obtained any abnormalities. Transport function of albumin in plasma products can be influenced by various methods of plasma collection, preparation, and filtration. Evident are changes in capacity of fatty acid binding sites and ordering changes of bound substrates. Transport respiratory detoxification efficiency is decreased between 30% and 70% in all FFP compared to control values.Conclusions: ESR spectroscopy can be used as a quality test for plasma. The ESR technique has a big potential for determination of conformation changes of macromolecules and as a global tumor marker test for donor screening. [Copyright &y& Elsevier]

Using the methods of spectrophotometry, luminescent analysis, and fluorescent probes, we have investigated the structural changes in bull serum albumin (BSA) molecules induced by the action of vacuum UV (VUV) radiation (λ = 131161 nm, dose — 6300 kJ/m2). It has been found that the change in the spectral fluorescent properties of BSA molecules after irradiation under the conditions of different microsurroundings is caused by the “unrolling” of the protein globule due to the weakening and rupture of weak intramolecular bonds as well as by the photomodification of the aromatic amino acid residues in the composition of the protein macromolecule. A scheme of the phototransformation processes in the BSA molecules under the action of vacuum ultraviolet has been drawn. In accordance with this scheme the VUV light in the region of absorption of peptide bonds of protein molecules induces a disturbance in their third order structure, which leads to a modification of the state of aromatic amino acid residues and a change in the functional properties of protein macromolecules. [ABSTRACT FROM AUTHOR]

Fig. A. ITC of POP and SS interaction at 298 K. The upper panel shows the isothermal titration plot of POP (in cell) with SS (in syringe), and the lower panel shows the integrated heat profile for the calorimetric titration plot shown in the upper panel. Fig. B. DPPH scavenging capacity comparison (A), OH scavenging capacity comparison (B), reducing power comparison (C) of SS, POP, and Se-POP. The data are average values of triplicate experiments. Error bars indicate the standard deviation. • A new small molecular weight supplement was prepared that is rich in organic selenium. • The chelation mechanism was explored and protein conformational changes were identified. • Novel antioxidant peptide fragments were detected and quantified. A selenium-chelating pea oligopeptide (Se-POP) was prepared from pea oligopeptide (POP) and sodium selenite (SS) via chelation. Se-POP is rich in organic selenium as 57.23% ± 0.36%. The chelation reaction was spontaneous and endothermic, with a binding constant Ka = 2.64 × 104 ± 1.60 × 103 M−1 and binding site number n = 0.27 ± 0.01. Spectral analysis indicated protein conformational changes consistent with chelation, that the peptide chain to fold and curl, causing random coil and β-turn decreasing and the peptide side-chain radicals folding and burying. The antioxidant capacity of Se-POP was increased relative to that of POP. One novel antioxidant peptide fragment was obtained from Se-POP and identified as PPKIYP, presenting at a concentration of 29.47 ng/mg. The results indicated that Se-POP might be a new organic Se supplement with antioxidant capacity, which may be easily absorbed due to its low molecular weight. [ABSTRACT FROM AUTHOR]

O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) transferase (OGT) is an essential enzyme in many cellular physiological catalytic reactions that regulates protein O-GlcNAcylation. Aberrant O-GlcNAcylation is related to insulin resistance, diabetic complications, cancer and neurodegenerative diseases. Understanding the peptide delivery in OGT is significant in comprehending enzymatic catalytic process, target-protein recognition and pathogenic mechanism. Herein extensive molecular dynamics (MD) simulations combined with various techniques are utilized to study the recognizing and binding mechanism of peptide fragment extracted from casein kinase II by OGT from atomic level. The residues of His496, His558, Thr633, Lys634, and Pro897 are demonstrated to play a dominant role in the peptide stabilization via hydrogen bonds and σ-π interaction, whose van der Waals and non-polar solvent effects provide the main driving force. In addition, two channels are identified. The delivery mode, mechanism together with thermodynamic and dynamic characterizations for the most favorable channel are determined. The peptide is more inclined to be recognized by OGT through the cavity comprised of residues 799-812, 893-899, and 865-871, and Tyr13-terminal is prior recognized to Met26-terminal. The transportation process is accompanied with conformation changes between the "spread" and "V" shapes. The whole process is strong exothermic that is highly dependent on the variation of hydrogen bond interactions between peptide and OGT as well as the performance of different subsections of peptide. Besides that, multiple computational methods combinations may contribute meaningfully to calculation of similar bio-systems with long and flexible substrate., 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., (© 2021 The Author(s).)

An efficient technique using citric acid and glucose based natural deep eutectic solvent (G-C-NADES) was developed to obtain ultrahigh deamidated wheat gluten (UDWG) (deamidation degree (DD) > 90%). FTIR and 1 H NMR indicated intensive hydrogen bonds (HBs) in G-C-NADES supermolecules. Quantum chemical calculations and molecular dynamic simulations demonstrated that 10 wt % diluted G-C-NADES still had a myriad of HBs. Physicochemical results showed UDWG had DD up to 92.45% after G-C-NADES deamidation, that is, 22% higher than citric-acid-DWG with a weak degree of hydrolysis (1.75%). Conformational characterization demonstrated the obvious conversion from α-helix to β-sheet via FTIR, the least amount of disulfide bonds by Raman spectra, and more exposure of tryptophan residues by fluorescence measurement for UDWG. It is proven that enhanced accessible conformation of WG reached with HBs of G-C-NADESs could contribute to the improvement on nucleophilic attack of deamidation, declaring that G-C-NADES might be a potential solvent for obtaining an ultrahigh deamidation for WG to successfully guarantee the safety of wheat gluten based cereal food regarding to lowering its allergy.