Loss Of Configurational Entropy Research Articles

Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation.

The sulfation patterns and degree of sulfation of chondroitin sulfate (CS), an important class of glycosaminoglycans (GAG), and their interactions with chemokines are accountable for various diseases. To realize the underlying mechanism of such complex biological phenomena at a molecular level and their application in rational drug design, a study on conformations and dynamics of CSs is necessary. To explore this, in this study, we performed a series of atomistic molecular dynamics (MD) simulations with different sulfated variants of octadecasaccharide CS, like CS-C, CS-E, and CS-T, in their free forms and when bound to the protein chemokine CXCL8 dimer in an aqueous medium. The calculated binding free energy of CSs with the CXCL8 dimer is favorable, and the degree of sulfation favors the complexation process further with prominent hydrophobic and hydrogen-bonded interactions. We find that the recognition is associated with the configurational entropy loss of the CS molecules as calculated from the Gaussian mixture approach, which supports that the degree of sulfation regulates the process. Cluster analysis through the k-means algorithm and end-to-end distance measurement revealed that although the free CS molecules adopted linear conformations, the nonlinear conformations during binding with protein were noted. Adaptation of nonlinear forms in the bound forms is noteworthy for the less-sulfated CS-C and CS-E. Apart from favorable 4C1 conformations, the occasional appearance of skew-boat forms from the free-energy map of ring pucker for the GlcUA unit was observed, which remains unaffected by the sulfation. We find that during recognition, the average relaxation time of intra-CS and inter-CS-CXCL8 hydrogen bonds (HBs) is about a magnitude lesser than that of CS-water HBs, most prominent on the involvement of higher sulfated CS-T analogues. The translational motion of surrounded water molecules in CSs exhibited sublinear diffusion, and the degree of sublinearity increases around the heavily sulfated molecules due to the hindrance created by them as well as the presence of the chemokine and exhibited markedly slow heterogeneous diffusion.

Exploring Pyrrolo-Fused Heterocycles as Promising Anticancer Agents: An Integrated Synthetic, Biological, and Computational Approach.

Five new series of pyrrolo-fused heterocycles were designed through a scaffold hybridization strategy as analogs of the well-known microtubule inhibitor phenstatin. Compounds were synthesized using the 1,3-dipolar cycloaddition of cycloimmonium N-ylides to ethyl propiolate as a key step. Selected compounds were then evaluated for anticancer activity and ability to inhibit tubulin polymerization in vitro. Notably, pyrrolo[1,2-a]quinoline 10a was active on most tested cell lines, performing better than control phenstatin in several cases, most notably on renal cancer cell line A498 (GI50 27 nM), while inhibiting tubulin polymerization in vitro. In addition, this compound was predicted to have a promising ADMET profile. The molecular details of the interaction between compound 10a and tubulin were investigated through in silico docking experiments, followed by molecular dynamics simulations and configurational entropy calculations. Of note, we found that some of the initially predicted interactions from docking experiments were not stable during molecular dynamics simulations, but that configurational entropy loss was similar in all three cases. Our results suggest that for compound 10a, docking experiments alone are not sufficient for the adequate description of interaction details in terms of target binding, which makes subsequent scaffold optimization more difficult and ultimately hinders drug design. Taken together, these results could help shape novel potent antiproliferative compounds with pyrrolo-fused heterocyclic cores, especially from an in silico methodological perspective.

Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases

Synapsed cells can communicate using exocytosed nucleotides like adenosine triphosphate (ATP). Ectonucleotidases localized to synaptic junctions degrade nucleotides into metabolites like adenosine monophosphate (AMP) or adenosine. Oftentimes nucleotide degradation occurs in a sequential manner, of which ATP degradation by CD39 and CD73 is a representative example. Here, CD39 first converts ATP and adenosine diphosphate (ADP) into AMP, after which AMP is dephosphorylated into adenosine by CD73. Hence, the concerted activity of CD39 and CD73 can help shape cellular responses to extracellular ATP. In a previous study, we demonstrated that coupled CD39 and CD73 activity within synapse-like junctions is strongly controlled by the enzymes' co-localization, their surface charge densities, and the electrostatic potential of the surrounding cell membranes. In this study, we demonstrate that crowders within synaptic junctions, which can include globular proteins like cytokines and membrane-bound proteins, impact coupled CD39 and CD73 ectonucleotidase activity and, in turn, the availability of intrasynapse ATP. Specifically, we developed a spatially explicit, reaction-diffusion model for the coupled conversion of ATP → AMP and AMP → adenosine in a model synaptic junction with crowders that is solved via the finite element method. Our modeling results suggest that the association rate for ATP to CD39 is strongly influenced by the density of intrasynaptic protein crowders, as increasing crowder density generally suppressed ATP association kinetics. Much of this suppression can be rationalized based on a loss of configurational entropy. The surface charges of crowders can further influence the association rate, with the surprising result that favorable crowder-nucleotide electrostatic interactions can yield CD39 association rates that are faster than crowder-free configurations. However, attractive crowder-nucleotide interactions decrease the rate and efficiency of adenosine production, which in turn increases the availability of ATP and AMP within the synapse relative to crowder-free configurations. These findings highlight how CD39 and CD73 ectonucleotidase activity, electrostatics, and crowding within synapses influence the availability of nucleotides for intercellular communication.

Dynamics in natural and designed elastins and their relation to elastic fiber structure and recoil

Elastin fibers assemble in the extracellular matrix from the precursor protein tropoelastin and provide the flexibility and spontaneous recoil required for arterial function. Unlike many proteins, a structure-function mechanism for elastin has been elusive. We have performed detailed NMR relaxation studies of the dynamics of the minielastins 24x′ and 20x′ using solution NMR, and of purified bovine elastin fibers in the presence and absence of mechanical stress using solid state NMR. The low sequence complexity of the minielastins enables us to determine average dynamical timescales and degrees of local ordering in the cross-link and hydrophobic modules separately using NMR relaxation by taking advantage of their residue-specific resolution. We find an extremely high degree of disorder, with order parameters for the entirety of the hydrophobic domains near zero, resembling that of simple chemical polymers and less than the order parameters that have been observed in other intrinsically disordered proteins. We find that average backbone order parameters in natural, purified elastin fibers are comparable to those found in 24x′ and 20x′ in solution. The difference in dynamics, compared with the minielastins, is that backbone correlation times are significantly slowed in purified elastin. Moreover, when elastin is mechanically stretched, the high chain disorder in purified elastin is retained, showing that any change in local ordering is below that detectable in our experiment. Combined with our previous finding of a 10-fold increase in the ordering of water when fully hydrated elastin fibers are stretched by 50%, these results support the hypothesis that stretch induced solvent ordering, i.e., the hydrophobic effect, is a key player in the elastic recoil of elastin as opposed to configurational entropy loss.

Theoretical and Mechanistic Validation of Global Kinetic Parameters of the Inactivation of GABA Aminotransferase by OV329 and CPP-115

((S)-3-Amino-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (OV329) is a recently discovered inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), which has 10 times better inactivation efficiency than its predecessor, CPP-115, despite the only structural difference being an endocyclic double bond in OV329. Both compounds are mechanism-based enzyme inactivators (MBEIs), which inactivate GABA-AT by a similar mechanism. Here, a combination of a variety of computational chemistry tools and experimental methods, including quantum mechanical (QM) calculations, molecular dynamic simulations, progress curve analysis, and deuterium kinetic isotope effect (KIE) experiments, are utilized to comprehensively study the mechanism of inactivation of GABA-AT by CPP-115 and OV329 and account for their experimentally obtained global kinetic parameters kinact and KI. Our first key finding is that the rate-limiting step of the inactivation mechanism is the deprotonation step, and according to QM calculations and the KIE experiments, kinact accurately represents the enhancement of the rate-limiting step for the given mechanism. Second, the present study shows that the widely used simple QM models do not accurately represent the geometric criteria that are present in the enzyme for the deprotonation step. In contrast, QM cluster models successfully represent both the ground state destabilization and the transition state stabilization, as revealed by natural bond orbital analysis. Furthermore, the globally derived KI values for both of the inactivators represent the inhibitor constants for the initial binding complexes (Kd) and indicate the inactivator competition with the substrate according to progress curve analysis and the observed binding isotope effect. The configurational entropy loss accounts for the difference in KI values between the inactivators. The approach we describe in this work can be employed to determine the validity of globally derived parameters in the process of MBEI optimization for given inactivation mechanisms.

Analyzing the driving forces of insulin stability in the basic amino acid solutions: A perspective from hydration dynamics.

Amino acids having basic side chains, as additives, are known to increase the stability of native-folded state of proteins, but their relative efficiency and the molecular mechanism are still controversial and obscure as well. In the present work, extensive atomistic molecular dynamics simulations were performed to investigate the hydration properties of aqueous solutions of concentrated arginine, histidine, and lysine and their comparative efficiency on regulating the conformational stability of the insulin monomer. We identified that in the aqueous solutions of the free amino acids, the nonuniform relaxation of amino acid-water hydrogen bonds was due to the entrapment of water molecules within the amino acid clusters formed in solutions. Insulin, when tested with these solutions, was found to show rigid conformations, relative to that in pure water. We observed that while the salt bridges formed by the lysine as an additive contributed more toward the direct interactions with insulin, the cation-π was more prominent for the insulin-arginine interactions. Importantly, it was observed that the preferentially more excluded arginine, compared to histidine and lysine from the insulin surface, enriches the hydration layer of the protein. Our study reveals that the loss of configurational entropy of insulin in arginine solution, as compared to that in pure water, is more as compared to the entropy loss in the other two amino acid solutions, which, moreover, was found to be due to the presence of motionally bound less entropic hydration water of insulin in arginine solution than in histidine or lysine solution.

Multibasin Quasi-Harmonic Approach for the Calculation of the Configurational Entropy of Small Molecules in Solution.

Entropy is a key thermodynamic property governing most biomolecular processes, including binding. Nonetheless, quantification of the configurational entropy of a single molecule in solution remains a grand challenge. Here, we present an original approach for the calculation of absolute molecular entropies based on the analysis of converged molecular dynamics (MD) simulations. Our method, named quasi-harmonic multibasin (QHMB), relies on a multibasin decomposition of the simulated trajectory by root-mean-square deviation clustering and subsequent quasi-harmonic analysis (QHA) of extracted sub-trajectories. Last, the entropy of the landscape is evaluated using the Gibbs formula. Because of the nature of QHA, this method is directly applicable to explicit-solvent simulations to access configurational entropies in solution. When compared with calorimetric data from NIST, QHMB is shown to predict absolute entropies in the gas phase for 23 small molecules with a root-mean-squared error of 0.36 kcal/mol from the experiments. In addition, the introduction of a QHMB correction in MM/GBSA calculations to account for the ligand configurational entropy loss on binding is shown to improve the correlation between calculated and experimental binding affinities with R2 increasing from 0.67 to 0.78. Because this entropy correction penalizes large and flexible ligands more strongly, it might be useful to reduce the false-positive rate in virtual screening. The availability of an automatic procedure to compute QHMB entropies makes it a new available tool in the field of drug discovery.

Effects of macromolecular crowding on the folding of a polymer chain: A Wang–Landau simulation study

A flexible polymer chain in the presence of inert macromolecular crowders will experience a loss of configurational entropy due to the crowder excluded volume. This entropy reduction will be most pronounced in good solvent conditions where the chain assumes an expanded coil conformation. For polymers that undergo a folding transition from a coil to a compact ordered state, as is the case for many globular proteins, macromolecular crowding is expected to stabilize the folded state and thereby shift the transition location. Here, we study such entropic stabilization effects for a tangent square-well sphere chain (monomer diameter σ) in the presence of hard-sphere (HS) crowders (diameter D ≥ σ). We use the Wang-Landau simulation algorithm to construct the density of states for this chain in a crowded environment and are thus able to directly compute the reduction in configurational entropy due to crowding. We study both a chain that undergoes all-or-none folding directly from the coil state and a chain that folds via a collapsed-globule intermediate state. In each case, we find an increase in entropic stabilization for the compact states with an increase in crowder density and, for fixed crowder density, with a decrease in crowder size (concentrated, small crowders have the largest effect). The crowder significantly reduces the average size for the unfolded states while having a minimal effect on the size of the folded states. In the athermal limit, our results directly provide the confinement free energy due to crowding for a HS chain in a HS solvent.

Observing dynamic and static Rashba effects in a thin layer of 3D hybrid perovskite nanocrystals using transient absorption spectroscopy

The dynamic and static Rashba effects in hybrid methylammonium (MA) lead halide perovskites have recently been theoretically predicted. However, only the static effect was experimentally confirmed so far. Here, we report on the dynamic (sub-picosecond/picosecond timescale) and static (nanosecond/microsecond timescale) Rashba effects observed in a fully encapsulated layer with various thicknesses (ranging from ∼40 nm to ∼100 nm) of ∼20-nm-sized 3D MAPbBr3 nanocrystals (NCs) using transient absorption (TA) spectroscopy. The effect appears as a splitting of the corresponding peaks in TA spectra. We argue that the physical reason for the Rashba effect to be observed is fundamentally determined by configurational entropy loss in NCs possessing a strong spin asymmetry. Specifically, owing to an enhanced flexibility of the NC lattice, a built-in electric field initially induced by an ultrashort (100 fs) pumping pulse through the photo-Dember effect and subsequently developed due to dynamic charge separation throughout NCs is able to initiate the order–disorder transition associated with the MA cation reorientations, the process that efficiently breaks structural inversion symmetry and hence induces the Rashba spin–orbit interaction. The dynamic Rashba effect is found to be strongly dependent on photoexcited carrier density (pumping power), whereas it weakens sharply upon increasing the NC layer thickness up to ∼80 nm due to the NC stacking effect. The integrated intensities of the corresponding spin-split subbands demonstrate a photon-helicity-dependent asymmetry, thus proving the Rashba-type spin-splitting. The magnitudes of the Rashba and Fröhlich polaron effects and the methods of controlling the dynamic Rashba effect are discussed.

Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association

We report the free-energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here, we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free-energy profile also captured the crucial role of allosteric IN inhibitors in promoting multimerization and explained why several C-terminal domain mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation, the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, interprotein water molecules are expelled to the bulk, resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side-chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. Although the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.

Hydrogen induced vacancy clustering and void formation mechanisms at grain boundaries in palladium

Hydrogen has a significant impact on the formation of vacancies, clusters and voids in palladium and other metals. The formation of vacancy-hydrogen complexes in bulk Pd and at Σ3 and Σ5 grain boundaries was investigated using first-principles calculations and thermodynamic models. Equilibrium vacancy and cluster concentrations were evaluated as a function of temperature and hydrogen partial pressure based on the Gibbs energy of formation including vibrational and configurational entropies. Vacancies were found to be significantly stabilized by association with interstitial hydrogen, leading to enhanced concentrations by several orders of magnitude. Vacancy clusters were further stabilized at grain boundaries, with equilibrium concentrations reaching site saturation for clusters comprising up to three vacancies. Nanovoids were investigated based on Wulff constructions from calculated surface energies of the (0 0 1) and (1 1 1) terminations as a function of temperature and coverage of hydrogen adsorbates. The most stable termination changed from (1 1 1) in vacuum to (0 0 1) in H2, and the surface energies were lowered due to hydrogen adsorbates. Consequently, voids were also stabilized in the presence of hydrogen. Coalescing of vacancies into nanovoids was found to be thermodynamically unfavorable due to the loss of configurational entropy. It was therefore concluded that enhanced concentrations of vacancies and clusters does not directly cause the formation of voids. The formation of voids in Pd-based membranes was discussed in terms of microstructural characteristics, and strain due to chemical expansion and plastic deformation.

Structural phase transitions and photoluminescence mechanism in a layer of 3D hybrid perovskite nanocrystals

Although structural phase transitions in single-crystal hybrid methyl-ammonium (MA) lead halide perovskites (MAPbX3, X = Cl, Br, I) as a function of temperature are common phenomena, they have never been observed in the corresponding nanocrystals. Here, we demonstrate that two-photon-excited photoluminescence (PL) spectroscopy is capable of monitoring structural phase transitions in MAPbX3 nanocrystals because nonlinear susceptibilities govern the incident light absorption rates. We provide experimental evidence that the orthorhombic-to-tetragonal structural phase transition in a single layer of 20-nm-sized 3D MAPbBr3 nanocrystals is spread out within the T ∼ 70 K–140 K temperature range. This structural phase instability is believed to arise because, unlike in single-crystal MAPbX3, free rotations of MA ions in the corresponding nanocrystals are no longer restricted by a long-range MA dipole order. The resulting configurational entropy loss can be even enhanced by the interfacial electric field arising due to charge separation at the MAPbBr3/ZnO heterointerface, extending the structural phase instability range from T ∼ 70 K–230 K. We conclude that weak sensitivity of conventional one-photon-excited PL spectroscopy to structural phase transitions in 3D MAPbX3 nanocrystals results from structural phase instability and hence from negligible distortions of PbX6 octahedra. In contrast, the intensity of two-photon-excited PL and electric-field-induced one-photon-excited PL show higher sensitivity since nonlinear susceptibilities are involved. We also show that room-temperature PL may originate from the radiative recombination of the optical-phonon vibrationally excited polaronic excitons with energies might exceed the ground-state Fröhlich polaron and Rashba energies due to optical-phonon bottleneck.

Hydrogen Induced Vacancy Clustering and Void Formation Mechanisms at Grain Boundaries in Palladium

Hydrogen has a significant impact on the formation of vacancies, clusters and voids in palladium and other metals. The formation of vacancy-hydrogen complexes in bulk Pd and at Σ3 and Σ5 grain boundaries was investigated using first-principles calculations and thermodynamic models. Equilibrium vacancy and cluster concentrations were evaluated as a function of temperature and hydrogen partial pressure based on the Gibbs energy of formation including vibrational and configurational entropies. Vacancies were found to be significantly stabilized by association with interstitial hydrogen, leading to enhanced concentrations by several orders of magnitude. Vacancy clusters were further stabilized at grain boundaries, with equilibrium concentrations reaching site saturation for clusters comprising up to three vacancies. Nanovoids were investigated based on Wulff constructions from calculated surface energies of the (0 0 1) and (1 1 1) terminations as a function of temperature and coverage of hydrogen adsorbates. The most stable termination changed from (1 1 1) in vacuum to (0 0 1) in H2, and the surface energies were lowered due to hydrogen adsorbates. Consequently, voids were also stabilized in the presence of hydrogen. Coalescing of vacancies into nanovoids was found to be thermodynamically unfavorable due to the loss of configurational entropy. It was therefore concluded that enhanced concentrations of vacancies and clusters does not directly cause the formation of voids. The formation of voids in Pd-based membranes was discussed in terms of microstructural characteristics, and strain due to chemical expansion and plastic deformation.

Do String-like Cooperative Motions Predict Relaxation Times in Glass-Forming Liquids?

The Adam-Gibbs theory of glass formation posits that the growth in the activation barrier of fragile liquids on cooling emerges from a loss of configurational entropy and concomitant growth in "cooperatively rearranging regions" (CRRs). A body of literature over 2 decades has suggested that "string-like" cooperatively rearranging clusters observed in molecular simulations may be these CRRs-a scenario that would have profound implications for the understanding of the glass transition. The central element of this postulate is the report of an apparent zero-parameter relationship between the mass of string-like CRRs and the relaxation time. Here, we show, based on molecular dynamics simulations of multiple glass-forming liquids, that this finding is the result of an implicit adjustable parameter-a "replacement distance". This parameter is equivalent to an adjustable exponent within a generalized Adam-Gibbs relation, such that it tunes the entire functional form of the relation. Moreover, we are unable to find any objective criterion, based on the radial distribution function or the cluster fractal dimension, for selecting this replacement distance across multiple systems. We conclude that the present data do not establish that string-like cooperative rearrangements, as presently defined, are predictive of segmental relaxation via an Adam-Gibbs-like physical model.

Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation

Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are tetrameric non-specific cation channels in the plasma membrane that are activated by either cAMP or cGMP binding to specific binding domains incorporated in each subunit. Typical apparent affinities of these channels for these cyclic nucleotides range from several hundred nanomolar to tens of micromolar. Here we synthesized and characterized novel cAMP and cGMP derivatives by substituting either hydrophobic alkyl chains or similar-sized more hydrophilic heteroalkyl chains to the 8-position of the purine ring with the aim to obtain full agonists of higher potency. The compounds were tested in homotetrameric CNGA2, heterotetrameric CNGA2:CNGA4:CNGB1b and homotetrameric HCN2 channels. We show that nearly all compounds are full agonists and that longer alkyl chains systematically increase the apparent affinity, at the best more than 30 times. The effects are stronger in CNG than HCN2 channels which, however, are constitutively more sensitive to cAMP. Kinetic analyses reveal that the off-rate is significantly slowed by the hydrophobic alkyl chains. Molecular dynamics simulations and free energy calculations suggest that an intricate enthalpy - entropy compensation underlies the higher apparent affinity of the derivatives with the longer alkyl chains, which is shown to result from a reduced loss of configurational entropy upon binding.

Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.

Calorimetric studies of protein-ligand binding sometimes yield thermodynamic data that are difficult to understand. Today, molecular simulations can be used to seek insight into such calorimetric puzzles, and, when simulations and experiments diverge, the results can usefully motivate further improvements in computational methods. Here, we apply near-millisecond duration simulations to estimate the relative binding enthalpies of four peptidic ligands with the Grb2 SH2 domain. The ligands fall into matched pairs, where one member of each pair has an added bond that preorganizes the ligand for binding and thus may be expected to favor binding entropically, due to a smaller loss in configurational entropy. Calorimetric studies have shown that the constrained ligands do in fact bind the SH2 domain more tightly than the flexible ones, but, paradoxically, the improvement in affinity for the constrained ligands is enthalpic, rather than entropic. The present enthalpy calculations yield the opposite trend, as they suggest that the flexible ligands bind more exothermically. Additionally, the small relative binding enthalpies are found to be balances of large differences in the energies of structural components such as ligand and the binding site residues. As a consequence, the deviations from experiment in the relative binding enthalpies represent small differences between these large numbers and hence may be particularly susceptible to error, due, for example, to approximations in the force field. We also computed first-order estimates of changes in configurational entropy on binding. These too are, arguably, paradoxical, as they tend to favor binding of the flexible ligands. The paradox is explained in part by the fact that the more rigid constrained ligands reduce the entropy of binding site residues more than their flexible analogs do, at least in the simulations. This result offers a rather general counterargument to the expectation that preorganized ligands should be associated with more favorable binding entropies, other things being equal.

Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry.

Osmolytes affect hydrophobic collapse and protein folding equilibria. The underlying mechanisms are, however, not well understood. We report large-scale conformational sampling of two hydrophobic polymers with secondary and tertiary amide side chains using extensive molecular dynamics simulations. The calculated free energy of unfolding increases with urea for the secondary amide, yet decreases for the tertiary amide, in agreement with experiment. The underlying mechanism is rooted in opposing entropic driving forces: while urea screens the hydrophobic macromolecular interface and drives unfolding of the tertiary amide, urea's concomitant loss in configurational entropy drives collapse of the secondary amide. Only at sufficiently high urea concentrations bivalent urea hydrogen bonding interactions with the secondary amide lead to further stabilisation of its collapsed state. The observations provide a new angle on the interplay between side chain chemistry, urea hydrogen bonding, and the role of urea in attenuating or strengthening the hydrophobic effect.

Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study.

Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state". In agreement with past experimental observations of Luo and Kiick, upon anchoring ELP oligomers to a point to mimic ELP oligomers conjugated to another macromolecule, there is an apparent slight shift in the transition temperature to lower values compared to free (unconjugated) ELP oligomers. However, these atomistic simulations are limited to small systems of short ELPs, and as such do not capture the multiple chain aggregation/phase separation observed in experiments of ELPs. Therefore, we utilize phenomenological coarse-grained (CG) MD simulations to probe how conjugating a block of generic-LCST polymer to another rigid unresponsive macromolecular block impacts the transition temperatures at concentrations and length scales larger than atomistic simulations. We find that when multiple LCST polymer chains are conjugated to a rigid unresponsive polymer block, the increased local crowding of the LCST polymers shifts the transition marked by onset of chain aggregation to smaller effective polymer-polymer attraction energies compared to the free LCST polymer chains. The driving force needed for aggregation is reduced in the conjugates compared to free LCST polymer due to reduction in the loss of polymer configurational entropy upon aggregation.

An Atomistic Statistically Effective Energy Function for Computational Protein Design.

Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical potentials.

Multi-shell model of ion-induced nucleic acid condensation

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into "external" and "internal" ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregationfree energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the "external" shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregationfree energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNAcondensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the "internal" shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NAcondensation lends support to proposed NAcondensation picture based on the multivalent "ion binding shells."