Number Of H-bonds Research Articles

Radical Formation Initiates Solvent-Dependent Unfolding and β-sheet Formation in a Model Helical Peptide

We examined the effects of Cα-centered radical formation on the stability of a model helical peptide, N-Ac-KK(AL)10KK-NH2. Three, 100 ns molecular dynamics simulations using the OPLS-AA force field were carried out on each α-helical peptide in six distinct binary TIP4P water/2,2,2-trifluoroethanol (TFE) mixtures. The α-helicity was at a maximum in 20% TFE, which was inversely proportional to the number of H-bonds between water molecules and the peptide backbone. The radial distribution of TFE around the peptide backbone was highest in 20% TFE, which enhanced helix stability. The Cα-centered radical initiated the formation of a turn within 5 ns, which was a smaller kink at high TFE concentrations, and a loop at lower TFE concentrations. The highest helicity of the peptide radical was measured in 100% TFE. The formation of hydrogen bonds between the peptide backbone and water destabilized the helix, whereas the clustering of TFE molecules around the radical center stabilized the helix. Following radical termination, the once helical structure converted to a β-sheet rich state in 100% water only, and this transition did not occur in the nonradical control peptide. This study gives evidence on how the formation of peptide radicals can initiate α-helical to β-sheet transitions under oxidative stress conditions.

Microstructure Changes in Polyester Polyurethane upon Thermal and Humid Aging.

The microstructure of compression molded Estane 5703 films exposed to 11%, 45%, and 80% relative humidity and 70 °C for 1 and 2 months has been studied by small-angle neutron scattering (SANS), Fourier transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), and differential scanning calorimetry (DSC). Scattering data indicated increase of the interdomain distance and domain size with a higher humidity and longer aging time. GPC data showed a progressive shortening of polyurethane chains with increasing humidity and aging time. The shortening of the polyurethane chains caused a drop of the glass transition temperature of soft segments, and promoted crystallization of the soft segments during long-time storage of the aged samples at room temperature. FTIR showed a substantial increase in the number of inter-urethane H-bonds in the aged samples. This correlates with the increase of the hard domain size and the degree of phase separation as measured by SANS. The data collected reveals that the reduced steric hindrance caused by hydrolysis of ester links in polybutylene adipate residues promotes the organization of hard segments into domains, leading to the increase of domain size and distance, as well as phase segregation in aged Estane. These findings provide insight into the effects of humidity and thermal aging on the microstructure of aged polyester urethane from molecular to nanoscale level.

Structural anomaly and dynamic heterogeneity in cycloether/water binary mixtures: Signatures from composition dependent dynamic fluorescence measurements and computer simulations

We have performed steady state UV-visible absorption and time-resolved fluorescence measurements and computer simulations to explore the cosolvent mole fraction induced changes in structural and dynamical properties of water/dioxane (Diox) and water/tetrahydrofuran (THF) binary mixtures. Diox is a quadrupolar solvent whereas THF is a dipolar one although both are cyclic molecules and represent cycloethers. The focus here is on whether these cycloethers can induce stiffening and transition of water H-bond network structure and, if they do, whether such structural modification differentiates the chemical nature (dipolar or quadrupolar) of the cosolvent molecules. Composition dependent measured fluorescence lifetimes and rotation times of a dissolved dipolar solute (Coumarin 153, C153) suggest cycloether mole-fraction (X(THF)/Diox) induced structural transition for both of these aqueous binary mixtures in the 0.1 ≤ X(THF)/Diox ≤ 0.2 regime with no specific dependence on the chemical nature. Interestingly, absorption measurements reveal stiffening of water H-bond structure in the presence of both the cycloethers at a nearly equal mole-fraction, X(THF)/Diox ∼ 0.05. Measurements near the critical solution temperature or concentration indicate no role for the solution criticality on the anomalous structural changes. Evidences for cycloether aggregation at very dilute concentrations have been found. Simulated radial distribution functions reflect abrupt changes in respective peak heights at those mixture compositions around which fluorescence measurements revealed structural transition. Simulated water coordination numbers (for a dissolved C153) and number of H-bonds also exhibit minima around these cosolvent concentrations. In addition, several dynamic heterogeneity parameters have been simulated for both the mixtures to explore the effects of structural transition and chemical nature of cosolvent on heterogeneous dynamics of these systems. Simulated four-point dynamic susceptibility suggests formation of clusters inducing local heterogeneity in the solution structure.

Structural Study of Cell Attachment Peptide Derived from Laminin by Molecular Dynamics Simulation

Peptides with cell attachment activity are beneficial component of biomaterials for tissue engineering. Conformational structure is one of the important factors for the biological activities. The EF1 peptide (DYATLQLQEGRLHFMFDLG) derived from laminin promotes cell spreading and cell attachment activity mediated by α2β1 integrin. Although the sequence of the EF2 peptide (DFATVQLRNGFPYFSYDLG) is homologous sequence to that of EF1, EF2 does not promote cell attachment activity. To determine whether there are structural differences between EF1 and EF2, we performed replica exchange molecular dynamics (REMD) simulations and conventional molecular dynamics (MD) simulations. We found that EF1 and EF2 had β-sheet structure as a secondary structure around the global minimum. However, EF2 had variety of structures around the global minimum compared with EF1 and has easily escaped from the bottom of free energy. The structural fluctuation of the EF1 is smaller than that of the EF2. The structural variation of EF2 is related to these differences in the structural fluctuation and the number of the hydrogen bonds (H-bonds). From the analysis of H-bonds in the β-sheet, the number of H-bonds in EF1 is larger than that in EF2 in the time scale of the conventional MD simulation, suggesting that the formation of H-bonds is related to the differences in the structural fluctuation between EF1 and EF2. From the analysis of other non-covalent interactions in the amino acid sequences of EF1 and EF2, EF1 has three pairs of residues with hydrophobic interaction, and EF2 has two pairs. These results indicate that several non-covalent interactions are important for structural stabilization. Consequently, the structure of EF1 is stabilized by H-bonds and pairs of hydrophobic amino acids in the terminals. Hence, we propose that non-covalent interactions around N-terminal and C-terminal of the peptides are crucial for maintaining the β-sheet structure of the peptides.

Functional Cooperativity among the Subunits of the Homotetrameric Aquaglyceroprotein GlpF

Aquaporins are conserved throughout all kingdoms of life. Each aquaporin monomer possesses a channel that facilitates the transport of water across the membrane, and yet the protein assembles into a tetramer. We investigated the physiological function of the tetrameric assembly by introducing destabilizing point mutations. Therefore, we overexpressed the GlpF variants in E.coli, purified them and reconstituted them into large unilamellar vesicles (LUVs) or giant (GUV) unilamellar vesicles. Subsequently, we osmotically deflated the vesicles. Our new adaptation of the Rayleigh-Gans-Debye equation served to calculate the water efflux from proteoliposomes (PL) based on the accompanying increase in scattered light intensity (Horner et al., 2015). We adopted the micropipette aspiration technique to quantify water efflux from GUVs. Reconstituted GUVs allowed direct determination of GlpF membrane concentration by fluorescence correlation spectroscopy. In order to obtain the channel abundance in LUVs, we exploited fluorescence correlation spectroscopy to count the number of particles before and after detergent-mediated vesicle solubilization (Knyazev et al., 2013). Depending on the total GlpF concentration, we found functional GlpF monomers, dimers, trimers, and tetramers. Spreading the vesicles on mica enabled us to acquire high-speed AFM imaging of the different oligomeric states. Destabilization of the tetrameric assembly was accompanied by looser packing and changes in unitary permeability. The observation suggests that tetramerization serves to control the functional state of each monomer.1. Horner et al. (2015). The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues. Science Advances 1, e1400083.2. Knyazev et al. (2013). The Bacterial Translocon SecYEG Opens upon Ribosome Binding. J. Biol. Chem. 288, 17941-17946.

Molecular Insights for the Role of Key Residues of Calreticulin in its Binding Activities

Calreticulin (CRT) is localized to and has functions in multiple cellular compartments, including cell surface, endoplasmic reticulum, and extracellular matrix (FASEB J. 24: 665- 683, 2010). Mutagenesis studies have identified several residues on a concave β-sheet surface of CRT critical for CRT binding to carbohydrate and other proteins/peptides (J. Biol. Chem. 285: 38612-20, 2010). How the mutations of these key residues in CRT affect the conformation and dynamical motion of CRT, further influencing CRT binding activities remain unknown. In this study, we investigated the effect of several key point mutations on the conformational and dynamical motion changes of CRT via atomistic molecular dynamics simulations. The CRT structure is obtained based on the crystal structure of the globular lectin domain and partial P-domain of CRT, and the NMR structure of P-domain (flexible arm domain). Results from this study show that the mutations of the key residues of CRT result in the changes in the protein's local backbone flexibility and some of the point mutations cause significant changes of the relatively position and orientation between the CRT lectin and P-domains. Within the β-strands in CRT's lection domain, mutant-induced secondary structural changes, including the changes in the residues of β-strand occupancy, number of H-bonds and hydrophobic contacts, are observed. The mutations of the key residues on the concave β-sheet surface of CRT also result in the changes of the solvent accessible surface area, side-chain relative positions and dynamical correlated motions, which could directly affect CRT binding activities. Results from this study provided molecular insight into the effect of the mutations of key residues of CRT on CRT conformational and dynamical motion changes, further influencing CRT binding to carbohydrates and other proteins to signal the important cellular activities.

Water Transport by the Sodium Glucose Cotransporter SGLT1

The small intestine reabsorbs about 8L of fluid daily by a yet unknown mechanism. In contrast to vectorial water transport in the kidney, intestinal water reabsorption is not mediated by aquaporins. The sodium-glucose cotransporter SGLT1 was implicated to play a crucial role because it (i) functions as a molecular water pump or (ii) provides a water channel. Here we tested both hypotheses by overexpressing SGLT1 in MDCK cell monolayers. Fluorescence correlation spectroscopy served to assess the unitary water channel permeability pf of SGLT1 in life cells by measuring (i) the dilution of an aqueous dye in the immediate monolayer vicinity and (ii) SGLT1 plasma membrane abundance1. pf agreed well the one obtained from deflation kinetics of proteoliposomes. We derived vesicle volume from the intensity of scattered light via our new adaptation of the Rayleigh-Gans-Debye equation2 and the number of the reconstituted SGLT1 molecules per vesicle via fluorescence correlation spectroscopy3. SGLT1's pf is comparable to the pf of aquaporins rendering (i) an intracellular pathway plausible and (ii) water pumping against the osmotic gradient physiologically meaningless as the passive backflux would be orders of magnitude larger.Funding: This work was supported by grant P23574 of the Austrian Science Fund to P.P.1. Erokhova, L., Horner, A., Kugler, P., and Pohl, P. (2011). Monitoring single-channel water permeability in polarized cells. J. Biol. Chem. 286, 39926-39932.2. Hoomann, T., Jahnke, N., Horner, A., Keller, S., and Pohl, P. (2013). Filter gate closure inhibits ion but not water transport through potassium channels. PNAS 110, 10842-10847.3. Horner, A., Zocher, F., Preiner, J., Ollinger, N., Siligan, C., Akimov, S.A., and Pohl, P. (2015). The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues. Science Advances 1, e1400083.

Urea hydration from dielectric relaxation spectroscopy: old findings confirmed, new insights gained.

We report results on urea hydration obtained by dielectric relaxation spectroscopy (DRS) in a broad range of concentrations and temperatures. In particular, the effective hydration number and dipole moment of urea have been determined. The observed changes with composition and temperature were found to be insignificant and mainly caused by the changing number density of urea. Similarly, solute reorientation scaled simply with viscosity. In contrast, we find that water reorientation undergoes substantial changes in the presence of urea, resulting in two water fractions. The first corresponds to water molecules strongly bound to urea. These solvent molecules follow the reorientational dynamics of the solute. The second fraction exhibits only a minor increase of its relaxation time (in comparison with pure water) which is not linked to solution viscosity. Its activation energy decreases significantly with urea concentration, indicating a marked decrease of the number of H-bonds among the H2O molecules belonging to this fraction. Noncovalent interactions (NCI) analysis, capable to estimate the strength of the interactions within a cluster, shows that bound water molecules are most probably double-hydrogen bonded to urea via the oxygen atom of the carbonyl group and a cis-hydrogen atom. Due to the increased H-bond strength compared to the water dimer and the rigid position in the formed complex the reorientation of these bound H2O molecules is strongly impeded.

The molecular simulation of the miscibility, mechanical properties and physical cross-linking behavior of the poly(vinyl alcohol)/poly(acrylic acid) composited membranes

The miscibility and mechanical properties of poly vinyl alcohol (PVA) and poly acrylic acid (PAA)-composited membranes were studied with molecular simulation. The Flory–Huggins parameters (δ) were calculated to prove the good miscibility of PVA and PAA. The radial distribution functions of hydroxyl and carboxyl atoms and the average number of H-bonds were observed to indicate the degree of physical cross-linking between PVA and PAA. The influences of intermolecular physical cross-linking on the glass transition temperature and mechanical properties were estimated. The results revealed that the PVA/PAA membrane with a composition of 2:3 has the best plastic properties, which exhibits a good application value. All of the simulated results showed good agreement with the experimental data. It indicates that the method presented in this work has a promising application prospect.

Near-Surface Motion and Dynamic Adhesion during Silica Microparticle Capture on a Polymer (Solvated PEG) Brush via Hydrogen Bonding

Surface modification by “polymer brushes” (dense end-tethered chains) is a strategy to create a steric barrier against colloidal aggregation or bioadhesion or to facilitate lubrication. The approach requires good brush solvation; however, even in a good solvent, brush chains can adhere certain objects. An important example is the hydrogen bonding of silica to PEG (poly(ethylene glycol)) chains in water. To probe how hydrogen bonding at the brush periphery facilitates adhesive capture of flowing particles, we employ a model system comprising silica microspheres on biorepellant PEG brushes sufficiently thick to screen interactions with the underlying substrate. We find that capture of silica spheres on PEG brushes is slower and less efficient than the transport-limited rate and can be hindered by the addition of salt and by flow, up to wall shears at least 500 s–1. Individual flowing silica microparticles adhere gradually to the PEG brush (presumably by increasing the numbers of H-bonds), so that the partic...

Molecular Dynamics Simulation Approach to Understand Lamivudine Resistance in Hepatitis B Virus Polymerase

Hepatitis B virus (HBV) is a global threat that killed many human lives. HBV DNA polymerase (HDP) is the key target for antiviral drug treatment. The widely used drug against HBV infection is lamivudine which targets the reverse transcriptase activity of HDP and inhibits the replication of HBV. However, available evidence demonstrated that tyrosine (Y)-methionine (M)-aspartic acid (D)-aspartic acid (D) motif mutations significantly affected the efficacy of lamivudine binding. In particular, M204I mutations affect the drug binding mechanism and cause resistance to lamivudine. Therefore, in the present study we made an attempt to understand the mechanism of lamivudine resistance with the aid of molecular docking and molecular dynamics (MD) approach. The molecular docking results suggest that lamivudine adopts the most promising conformations to the native type HDP by identifying M-204 and Y-203 as a prospective partner for making polar contacts as compared to the mutant type HDP. The MD results showed that the average movements of atoms, especially atoms of the native type HDP– lamivudine complex, were small and displayed fast convergence of energy and charges in geometry. This highlights the stable binding of lamivudine with native type HDP as compared to mutant type HDP. The R2 and RMSF analysis certainly indicates conformational changes in the HDP structure due to M204I mutation. Furthermore the hydrogen bond (H-bond) analysis from the MD study showed that there is decreased number of intermolecular H-bonds in mutant HDP – lamivudine complex as compared to that in native type HDP – lamivudine complex. Overall, our study certainly will pave way to develop new drugs against the drug resistant mutations (M204I) of HBV.

Bio-Inspired Hydrogen-Bond Cross-Link Strategy toward Strong and Tough Polymeric Materials

It remains a huge challenge to create advanced polymeric materials combining high strength, great toughness, and biodegradability so far. Despite enhanced strength and stiffness, biomimetic materials and polymer nanocomposites suffer notably reduced extensibility and toughness when compared to polymer bulk. Silk displays superior strength and toughness via hydrogen bonds (H-bonds) assembly, while cuticles of mussels gain high hardness and toughness via metal complexation cross-linking. Here, we propose a H-bonds cross-linking strategy that can simultaneously strikingly enhance strength, modulus, toughness, and hardness relative to polymer bulk. The H-bond cross-linked poly(vinyl alcohol) exhibits high yield strength (140 MPa), reduced modulus (22.5 GPa) in nanoindention tests, hardness (0.5 GPa), and great extensibility (40%). More importantly, there exist semiquantitive linear relationships between the number of effective H-bond and macroscale properties. This work suggests a promising methodology of designing advanced materials with exceptional mechanical by adding low amounts (1.0 wt %) of small molecules multiamines serving as H-bond cross-linkers.

Molecular Dynamics Simulations of CO2/Water/Quartz Interfacial Properties: Impact of CO2 Dissolution in Water.

The safe trapping of carbon dioxide (CO2) in deep saline aquifers is one of the major concerns of CO2 sequestration. The amount of capillary trapping is dominated by the capillary pressure of water and CO2 inside the reservoir, which in turn is controlled by the interfacial tension (IFT) and the contact angle (CA) of CO2/water/rock systems. The measurement of IFT and CA could be very challenging at reservoir conditions, especially in the presence of toxic cocontaminants. Thus, the ability to accurately predict these interfacial properties at reservoir conditions is very advantageous. Although the majority of existing molecular dynamics (MD) studies of CO2/water/mineral systems were able to capture the trends in IFT and CA variations with pressure and temperature, their predictions often deviated from experimental data, possibly due to erroneous models and/or overlooked chemical reactions. The objective of this study was to improve the MD predictions of IFT and CA of CO2/water/quartz systems at various pressure and temperature conditions by (i) considering the chemical reactions between CO2 and water and (ii) using a new molecular model for α-quartz surface. The results showed that the presence of carbonic acid at the CO2/water interface improved the predictions of IFT, especially at low temperature and high pressure where more CO2 dissolution occurs. On the other hand, the effect on CA was minor. The slight decrease in CA observed across the pressure range investigated could be attributed to an increase in the total number of H-bonds between fluid molecules and quartz surface.

The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues.

Channel geometry governs the unitary osmotic water channel permeability, pf, according to classical hydrodynamics. Yet, pf varies by several orders of magnitude for membrane channels with a constriction zone that is one water molecule in width and four to eight molecules in length. We show that both the pf of those channels and the diffusion coefficient of the single-file waters within them are determined by the number NH of residues in the channel wall that may form a hydrogen bond with the single-file waters. The logarithmic dependence of water diffusivity on NH is in line with the multiplicity of binding options at higher NH densities. We obtained high-precision pf values by (i) having measured the abundance of the reconstituted aquaporins in the vesicular membrane via fluorescence correlation spectroscopy and via high-speed atomic force microscopy, and (ii) having acquired the vesicular water efflux from scattered light intensities via our new adaptation of the Rayleigh-Gans-Debye equation.

Mucoadhesive Polymer Hyaluronan as Biodegradable Cationic/Zwitterionic-Drug Delivery Vehicle

Mucoadhesive polymers in pharmaceutical formulations release drugs in mucosal areas. They interact and fix to mucus via molecular interpenetration, etc ., which increase drug bioavailability. Polymers physicochemical properties affect formulation mucoadhesion, rheological behaviour and drug absorption. Hyaluronan (HA) is selected as a mucoadhesive and biodegradable polymer. Geometric, topological and fractal analyses are carried out with program TOPO. Reference calculations are performed with algorithm GEPOL. Procedure TOPO underestimates molecular volume by 0.7%. Error results 5% in surface area and derived topological indices. Solvent-accessible surface is undercalculated by 3%: from hexamer HA to HA·3Ca and hydrate, the hydrophobic term rises by 42% and decays by 26%, and hydrophilic part drops by 14% and rises by 58% in agreement with the number of H-bonds. Accessibility rises by 9% and decays by 8%. Fractal dimension is underevaluated by 1% and for HA it results 1.566; on going to HA·3Ca and hydrate it rises by 2% and 1%. External-atoms dimension increases by 11%: for HA it results 1.725. When going to HA·3Ca and hydrate, it augments by 4% and 0.3%. On going from HA to HA·3Ca and hydrate, nonburied minus molecular dimension enlarges by 20% and decays by 9%. The hydrate globularity is lower than for water, Ca 2+ and averages of O-atoms in HA. Ca 2+ rugosity is smaller than for hydrate, averages of O-atoms in HA and water. Ca 2+ and water accessibilities are greater than for hydrate. As cations exchange in HA·3Ca requires Ca 2+ alteration, rises of drug zwitterionic character and acidic p H increase absorption.

Molecular Dynamics Study on Configuration Energy and Radial Distribution Functions of Ammonium Dihydrogen Phosphates Solution

Molecular dynamics simulations were carried out to study the configuration energy and radial distribution functions of mmonium dihydrogen phosphate solution at different temperatures. The dihydrogen phosphate ion was treated as a seven-site model and the ammonium ion was regarded as a five-site model, while a simple-point-charge model for water molecule. An unusually local particle number density fluctuation was observed in the system at saturation temperature. It can be found that the potential energy increases slowly with the temperature from 373 K to 404 K, which indicates that the ammonium dihydrogen phosphate has partly decomposed. The radial distribution function between the hydrogen atom of ammonium cation and the oxygen atom of dihydrogen phosphate ion at three different temperatures shows obvious difference, which indicates that the average H-bond number changes obviously with the temperature. The temperature has an influence on the combination between hydrogen atoms and phosphorus atoms of dihydrogen phosphate ion and there are much more growth units at saturated solutions.

Hydration of protein-RNA recognition sites.

We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less than protein–DNA interfaces, but more than protein–protein interfaces. Majority of the waters at protein–RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein–DNA interfaces, mainly due to the presence of the 2′OH, the ribose in protein–RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein–RNA interfaces is hydrated more than the major groove, while in protein–DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein–RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein–RNA recognition and should be carefully treated while engineering protein–RNA interfaces.

Theoretical study of the temperature dependence of the vibrational relaxation of the H2O bend fundamental in liquid water and the subsequent distortion of the hydrogen bond network.

The molecular dynamics with quantum transitions method is used to study the temperature dependence of the relaxation dynamics of the H2O bend fundamental in liquid water in the range from 277 to 348 K and the subsequent variation of the hydrogen bonds network in the liquid. The vibrational bending degrees of freedom of the water molecules are all described by quantum mechanics while the remaining translational and rotational motions are described classically. The participation of the H-bonds in the relaxation process is studied taking into account the dependence of the relaxation lifetimes on the number of H-bonds formed by the initially excited water molecule and the amount of energy transferred into the hindered rotational motions. It is found that the intermolecular vibrational energy transfer plays an important role in the relaxation mechanism, with almost no temperature dependence, and that the energy transfer into the rotational degrees of freedom is favored over the energy transfer into the translational motions. The thermalization of the system after relaxation is completed in a time scale shorter than the time taken for the H-bond network to recover. The relaxation and equilibration times calculated compare well with experimental and previous theoretical results.

The Mathematical Aspects of our Published Cooperative Specificity Theory: The Entropy Change, (ΔS), Potentiates Protein – Protein Interaction

The Co-operative Specificity Theory explains the reciprocal recognition between specific MHC DR/DQ molecules in a haplotype resulting in a co-operation that precipitates susceptibility to T1D. Co-operativity between protein molecules is the probable formation of one H-bond which seduces the formation of a greater number of H-bonds leading to a strong association between the two molecules. In co-operative specificity the binding between positively and negatively charged aa residues on the specific DR- and DQ-molecules occurs in a procedure that is rapid, exact and in an all-or-none fashion resulting in only one achieved maximal extremum. We theorize that protein molecules in the proteome sense each other’s level of entropy ΔS in search of partner parity, with lowest ΔS existing between two molecules spelling co-operativity with resulting expansion of ΔS.

Hydrogen bonding analysis of phosphoric acid-N,N-dimethylformamide mixtures.

An analysis of H-bonding in phosphoric acid (H3PO4)-N,N-dimethylformamide (DMF) mixtures was performed across the full range of mixture compositions using the results from molecular dynamics simulations. The distribution of molecules according to the number of H-bonds they formed with OH groups or О(=Р) atoms of acid molecules and О(=С) atoms of DMF molecules was calculated. The dependence of the average number of H-bonds per acid molecule on the concentration when the acid molecule acted as a proton acceptor was discerned, as were the corresponding dependences when the acid molecule acted as a proton donor towards H3PO4 and/or DMF. The dependence of the average number of H-bonds per DMF molecule (which always acted as a proton acceptor) on the concentration was also determined.