Allosteric changes in the conformational landscape of Src kinase upon substrate binding.

Precise regulation of protein kinase activity is crucial in cell functions, and its loss is implicated in various diseases. The kinase activity is regulated by interconverting active and inactive states in the conformational landscape. However, how protein kinases switch conformations in response to different signals such as the binding at distinct sites remains incompletely understood.

Coexistence of two coacervate phases of polyglycine in water suggested by polymer reference interaction site model theory.

Mixing Gibbs energy and phase equilibria of aqueous solutions of polyglycine were studied theoretically by means of polymer reference interaction site model integral equation theory combined with the Gibbs-Duhem method. In addition to the ordinary liquid-liquid phase separation between dilute and concentrated solutions, the theoretical calculation predicted the coexistence of two coacervate phases, namely, the lower- and higher-density coacervates. The relative thermodynamic stabilities of these two phases change with the polymerization degree of polyglycine.

Effects of intramolecular chain conformation on the hydration and miscibility of polyethylene glycol in water studied by means of polymer reference interaction site model theory.

To examine the conventional idea that the gauche conformation of the OCCO dihedral angle promotes the dissolution of polyethylene glycol (PEG) in water through strong hydration, the thermodynamic properties of liquid mixtures of PEG and water were studied by means of polymer reference interaction site model (PRISM) theory. The intramolecular correlation functions required as input for PRISM theory were calculated by the generator matrix method, accompanied by changes in the distribution of dihedral angles. In the infinite dilution limit, the increased probability of gauche conformation of the OCCO dihedral angles stabilizes the hydration of PEG through enhanced hydrogen bonding between the ether oxygen of PEG and water.

Comparing the influence of explicit and implicit solvation models on site-specific thermodynamic stability of proteins.

Understanding the molecular basis for protein stability requires a thermodynamic analysis of protein folding. Thermodynamic analysis is often performed by sampling many atomistic conformations using molecular simulations that employ either explicit or implicit water models. However, it remains unclear to what extent thermodynamic results from different solvation models are reliable at the molecular level.

Phase equilibrium of three-component liquid systems composed of water, alcohol, and sodium chloride studied by the reference interaction-site model integral equation theory.

A theoretical method for calculating the thermodynamic properties and phase equilibria of a binary liquid mixture using the reference interaction-site model (RISM) integral equation theory, which we had proposed recently, was extended to ternary liquid systems containing salt. A novel dielectric correction of the RISM theory for a mixture of solvents was also proposed. The theory was applied to mixtures composed of water, alcohol, and NaCl, where the alcohol was either methanol or ethanol.

Evolutionary conservation of amino acids contributing to the protein folding transition state.

The question of whether amino acids critical to protein folding kinetics are evolutionarily conserved has been investigated intensively in the past, but no consensus has yet been reached. Recently, we have demonstrated that the transition state, dictating folding kinetics, is characterized as the state of maximum dynamic cooperativity, i.e.

Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies.

Understanding how protein-protein binding affinity is determined from molecular interactions at the interface is essential in developing protein therapeutics such as antibodies, but this has not yet been fully achieved. Among the major difficulties are the facts that it is generally difficult to decompose thermodynamic quantities into contributions from individual molecular interactions and that the solvent effect-dehydration penalty-must also be taken into consideration for every contact formation at the binding interface. Here, we present an atomic-level thermodynamics analysis that overcomes these difficulties and illustrate its utility through application to SARS-CoV-2 neutralizing antibodies.

Study of phase equilibria and thermodynamic properties of liquid mixtures using the integral equation theory: Application to water and alcohol mixtures.

A theoretical method for calculating the thermodynamic properties and phase equilibria of liquid-liquid mixtures using the integral equation theory is proposed. The solvation chemical potentials of the two components are evaluated by the integral equation theory and the isothermal-isobaric variation of the total density with composition is determined to satisfy the Gibbs-Duhem relation. Given the density of a pure component, the method can calculate the densities of the mixture at any composition.

Time-dependent communication between multiple amino acids during protein folding.

Cooperativity is considered to be a key organizing principle behind biomolecular assembly, recognition and folding. However, it has remained very challenging to quantitatively characterize how cooperative processes occur on a concerted, multiple-interaction basis. Here, we address how and when the folding process is cooperative on a molecular scale.

Mutation effects on FAS1 domain 4 based on structure and solubility.

Mutations in the fasciclin 1 domain 4 (FAS1-4) of transforming growth factor β-induced protein (TGFBIp) are associated with insoluble extracellular deposits and corneal dystrophies (CDs). The decrease in solubility upon mutation has been implicated in CD; however, the exact molecular mechanisms are not well understood. Here, we performed molecular dynamics simulations followed by solvation thermodynamic analyses of the FAS1-4 domain and its three mutants-R555W, R555Q, and A546T-linked to granular corneal dystrophy type 1, Thiel-Behnke corneal dystrophy and lattice corneal dystrophy, respectively.

Site-Specific Backbone and Side-Chain Contributions to Thermodynamic Stabilizing Forces of the WW Domain.

The native structure of a protein is stabilized by a number of interactions such as main-chain hydrogen bonds and side-chain hydrophobic contacts. However, it has been challenging to determine how these interactions contribute to protein stability at single amino acid resolution. Here, we quantified site-specific thermodynamic stability at the molecular level to extend our understanding of the stabilizing forces in protein folding.

Local environment effects on charged mutations for developing aggregation-resistant monoclonal antibodies.

Protein aggregation is a major concern in biotherapeutic applications of monoclonal antibodies. Introducing charged mutations is among the promising strategies to improve aggregation resistance. However, the impact of such mutations on solubilizing activity depends largely on the inserting location, whose mechanism is still not well understood.

Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins.

Folding funnel is the essential concept of the free energy landscape for ordered proteins. How does this concept apply to intrinsically disordered proteins (IDPs)? Here, we address this fundamental question through the explicit characterization of the free energy landscapes of the representative α-helical (HP-35) and β-sheet (WW domain) proteins and of an IDP (pKID) that folds upon binding to its partner (KIX). We demonstrate that HP-35 and WW domain indeed exhibit the steep folding funnel: the landscape slope for these proteins is ca.

Explicit Characterization of the Free Energy Landscape of pKID-KIX Coupled Folding and Binding.

The most fundamental aspect of the free energy landscape of proteins is that it is globally funneled such that protein folding is energetically biased. Then, what are the distinctive characteristics of the landscape of intrinsically disordered proteins, apparently lacking such energetic bias, that nevertheless fold upon binding? Here, we address this fundamental issue through the explicit characterization of the free energy landscape of the paradigmatic pKID-KIX system (pKID, phosphorylated kinase-inducible domain; KIX, kinase interacting domain). This is done based on unguided, fully atomistic, explicit-water molecular dynamics simulations with an aggregated simulation time of >30 μs and on the computation of the free energy that defines the landscape.

Publisher Correction: Examining a Thermodynamic Order Parameter of Protein Folding.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Examining a Thermodynamic Order Parameter of Protein Folding.

Dimensionality reduction with a suitable choice of order parameters or reaction coordinates is commonly used for analyzing high-dimensional time-series data generated by atomistic biomolecular simulations. So far, geometric order parameters, such as the root mean square deviation, fraction of native amino acid contacts, and collective coordinates that best characterize rare or large conformational transitions, have been prevailing in protein folding studies. Here, we show that the solvent-averaged effective energy, which is a thermodynamic quantity but unambiguously defined for individual protein conformations, serves as a good order parameter of protein folding.

Dynamics of Hydration Water Plays a Key Role in Determining the Binding Thermodynamics of Protein Complexes.

Interfacial waters are considered to play a crucial role in protein-protein interactions, but in what sense and why are they important? Here, using molecular dynamics simulations and statistical thermodynamic analyses, we demonstrate distinctive dynamic characteristics of the interfacial water and investigate their implications for the binding thermodynamics. We identify the presence of extraordinarily slow (~1,000 times slower than in bulk water) hydrogen-bond rearrangements in interfacial water. We rationalize the slow rearrangements by introducing the "trapping" free energies, characterizing how strongly individual hydration waters are captured by the biomolecular surface, whose magnitude is then traced back to the number of water-protein hydrogen bonds and the strong electrostatic field produced at the binding interface.

Computer Simulations of Intrinsically Disordered Proteins.

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields.

Anomalous Dynamics of Water Confined in Protein-Protein and Protein-DNA Interfaces.

Confined water often exhibits anomalous properties not observable in the bulk phase. Although water in hydrophobic confinement has been the focus of intense investigation, the behavior of water confined between hydrophilic surfaces, which are more frequently found in biological systems, has not been fully explored. Here, we investigate using molecular dynamics simulations dynamical properties of the water confined in hydrophilic protein-protein and protein-DNA interfaces.

New Computational Approach for External Entropy in Protein-Protein Binding.

Molecular recognition through the noncovalent association of biomolecules is of central importance in biology and pharmacology. Developing reliable computational methods for estimating binding thermodynamic parameters is therefore of great practical value. However, considerable uncertainty remains regarding the external entropy that is associated with the reduction in the external (positional and orientational) degrees of freedom upon complex formation.

Thermodynamic-ensemble independence of solvation free energy.

Solvation free energy is the fundamental thermodynamic quantity in solution chemistry. Recently, it has been suggested that the partial molar volume correction is necessary to convert the solvation free energy determined in different thermodynamic ensembles. Here, we demonstrate ensemble-independence of the solvation free energy on general thermodynamic grounds.

Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

Quantifying how the rugged nature of the underlying free-energy landscape determines the entropic cost a protein must incur upon folding and ligand binding is a challenging problem. Here, we present a novel computational approach that dissects the protein configurational entropy on the basis of the classification of protein dynamics on the landscape into two separate components: short-term vibrational dynamics related to individual free-energy wells and long-term conformational dynamics associated with transitions between wells. We apply this method to separate the configurational entropy of the protein villin headpiece subdomain into its conformational and vibrational components.

Structural and Thermodynamic Characteristics of Amyloidogenic Intermediates of β-2-Microglobulin.

β-2-microglobulin (β2m) self-aggregates to form amyloid fibril in renal patients taking long-term dialysis treatment. Despite the extensive structural and mutation studies carried out so far, the molecular details on the factors that dictate amyloidogenic potential of β2m remain elusive. Here we report molecular dynamics simulations followed by the solvation thermodynamic analyses on the wild-type β2m and D76N, D59P, and W60C mutants at the native (N) and so-called aggregation-prone intermediate (IT) states, which are distinguished by the native cis- and non-native trans-Pro32 backbone conformations.

Distinct role of hydration water in protein misfolding and aggregation revealed by fluctuating thermodynamics analysis.

Protein aggregation in aqueous cellular environments is linked to diverse human diseases. Protein aggregation proceeds through a multistep process initiated by conformational transitions, called protein misfolding, of monomer species toward aggregation-prone structures. Various forms of aggregate species are generated through the association of misfolded monomers including soluble oligomers and amyloid fibrils.

Site-directed analysis on protein hydrophobicity.

Hydrophobicity of a protein is considered to be one of the major intrinsic factors dictating the protein aggregation propensity. Understanding how protein hydrophobicity is determined is, therefore, of central importance in preventing protein aggregation diseases and in the biotechnological production of human therapeutics. Traditionally, protein hydrophobicity is estimated based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein.