Thermodynamics of protein folding: a microscopic view.

No abstract is available for this paper.

• Publication year

  2002

• Venue

  Biophysical Chemistry

• Publication date

  2002-12-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1016/S0301-4622(02)00293-4PMID 12646378
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Heat capacity in proteins.

  2005cited by this paper
• Weak temperature dependence of the free energy surface and folding pathways of structured peptides

  2002cited by this paper
• Free energy simulations come of age: protein-ligand recognition.

  2002cited by this paper
• Solvent size vs cohesive energy as the origin of hydrophobicity.

  2001cited by this paper
• Solvent Reorganization Energy and Entropy in Hydrophobic Hydration

  2000cited by this paper
• Thermodynamics in biology

  2000cited by this paper
• Hydrophobicity at Small and Large Length Scales

  1999cited by this paper
• Detecting protein function and protein-protein interactions from genome sequences.

  1999cited by this paper
• Effective energy function for proteins in solution

  1999cited by this paper
• Is cooperative oxygen binding by hemoglobin really understood?

  1999cited by this paper
• Discrimination of the native from misfolded protein models with an energy function including implicit solvation.

  1999cited by this paper
• Heat capacity and compactness of denatured proteins.

  1999cited by this paper
• Design by Directed Evolution

  1998cited by this paper
• Metastable states and folding free energy barriers

  1998cited by this paper
• All-atom empirical potential for molecular modeling and dynamics studies of proteins.

  1998cited by this paper
• Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

  1998cited by this paper
• Theory of simple liquids

  1998cited by this paper
• Structure and mechanism in protein science

  1998cited by this paper
• A metastable state in folding simulations of a protein model

  1998cited by this paper
• Simulations of the structural and dynamical properties of denatured proteins: the "molten coil" state of bovine pancreatic trypsin inhibitor.

  1998cited by this paper
• Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory

  1998cited by this paper
• Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids

  1998cited by this paper
• Additivity Principles in Biochemistry*

  1997cited by this paper
• "New view" of protein folding reconciled with the old through multiple unfolding simulations.

  1997cited by this paper
• Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

  1997cited by this paper
• Circular dichroism of denatured barstar suggests residual structure,.

  1997cited by this paper
• Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway.

  1997cited by this paper
• Cumulant expansion of the free energy: Application to free energy derivatives and component analysis

  1996cited by this paper
• On the decomposition of free energies.

  1996cited by this paper
• An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution.

  1996cited by this paper
• A Comprehensive Analytical Treatment of Continuum Electrostatics

  1996cited by this paper
• The denatured state (the other half of the folding equation) and its role in protein stability

  1996cited by this paper
• Hydrogen bonding stabilizes globular proteins.

  1996cited by this paper
• Orientational correlations and entropy in liquid water

  1996cited by this paper
• Energetics of protein structure.

  1995cited by this paper
• Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR.

  1995cited by this paper
• Free energy balance in protein folding.

  1995cited by this paper
• Acid and thermal denaturation of barnase investigated by molecular dynamics simulations.

  1995cited by this paper
• Hsien Wu and the First Theory of Protein Denaturation (1931)

  1995cited by this paper
• The meaning of component analysis: decomposition of the free energy in terms of specific interactions.

  1995cited by this paper
• Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics.

  1995cited by this paper
• The heat capacity of proteins

  1995cited by this paper
• Classical electrostatics in biology and chemistry.

  1995cited by this paper
• Decomposition of interaction free energies in proteins and other complex systems.

  1995cited by this paper
• Studies on denaturation of proteins. XIII. A theory of denaturation. 1931.

  1995cited by this paper
• Molten globule and protein folding.

  1995cited by this paper
• Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies.

  1994cited by this paper
• Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute

  1994cited by this paper
• Simulation Studies of the Hydration Entropy of Simple, Hydrophobic Solutes

  1994cited by this paper
• Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant.

  1994cited by this paper
• Modeling compact denatured states of proteins.

  1994cited by this paper
• Kinetics versus thermodynamics in protein folding.

  1994cited by this paper
• Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques

  1994cited by this paper
• Aspects of protein energetics and dynamics.

  1993cited by this paper
• An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes

  1993cited by this paper
• Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration.

  1993cited by this paper
• FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA

  1993cited by this paper
• Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size

  1993cited by this paper
• An effective solvation term based on atomic occupancies for use in protein simulations

  1993cited by this paper
• Entropy of hydrophobic hydration: a new statistical mechanical formulation

  1992cited by this paper
• Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations.

  1992cited by this paper
• Modeling the effects of mutations on the denatured states of proteins

  1992cited by this paper
• Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water.

  1992cited by this paper
• Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect.

  1992cited by this paper
• Atomic solvation parameters applied to molecular dynamics of proteins in solution

  1992cited by this paper
• The role of packing interactions in stabilizing folded proteins.

  1992cited by this paper
• Thermodynamics of structural stability and cooperative folding behavior in proteins.

  1992cited by this paper
• The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability.

  1992cited by this paper
• Contribution of hydrogen bonding to the conformational stability of ribonuclease T1.

  1992cited by this paper
• Protein hydration in aqueous solution.

  1991cited by this paper
• Solid model compounds and the thermodynamics of protein unfolding.

  1991cited by this paper
• Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase.

  1991cited by this paper
• The energy landscapes and motions of proteins.

  1991cited by this paper
• Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition.

  1991cited by this paper
• Energetics of repacking a protein interior.

  1991cited by this paper
• Denatured states of proteins.

  1991cited by this paper
• Electrostatic interactions in macromolecules: theory and applications.

  1990cited by this paper
• Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease.

  1990cited by this paper
• Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: hydration effect.

  1990cited by this paper
• A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

  1990cited by this paper
• Molecular Simulations of Protein Structure, Dynamics and Thermodynamics

  1990cited by this paper
• Semianalytical treatment of solvation for molecular mechanics and dynamics

  1990cited by this paper
• C. L. Brooks III, M. Karplus, B. M. Pettitt. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Volume LXXI, in: Advances in Chemical Physics, John Wiley & Sons, New York 1988. 259 Seiten, Preis: US $ 65.25

  1990cited by this paper
• Excluded volume approximation to protein-solvent interaction. The solvent contact model.

  1990cited by this paper
• MOLECULAR SIMULATION: Applications to Chemical and Biomolecular Systems

  1989cited by this paper
• Energetics of complementary side-chain packing in a protein hydrophobic core.

  1989cited by this paper
• Hydrophobic effect in protein folding and other noncovalent processes involving proteins.

  1989cited by this paper
• Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.

  1989cited by this paper
• Heat capacity and conformation of proteins in the denatured state.

  1989cited by this paper
• Hypernetted chain closure reference interaction site method theory of structure and thermodynamics for alkanes in water

  1988cited by this paper
• Relationships between apparent binding energies measured in site-directed mutagenesis experiments and energetics of binding and catalysis.

  1988cited by this paper
• Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics

  1988cited by this paper
• Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3

  1988cited by this paper
• A thermodynamic analysis of solvation

  1988cited by this paper
• Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

  1987cited by this paper
• Configurational entropy of native proteins.

  1987cited by this paper
• The structure and function of the hemagglutinin membrane glycoprotein of influenza virus.

  1987cited by this paper
• Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.

  1987cited by this paper
• Interior and surface of monomeric proteins.

  1987cited by this paper
• The hydrogen bond in molecular recognition

  1987cited by this paper

• ThermoRL:Structure-Aware Reinforcement Learning for Protein Mutation Design to Enhance Thermostability

  2025cites this paper
• On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super‐Gaussian Poisson–Boltzmann model

  2024cites this paper
• Challenges and limitations in computational prediction of protein misfolding in neurodegenerative diseases

  2024cites this paper
• Applications of a Single Molecule Theory of Protein Dynamics

  2024cites this paper
• Energy, water, and protein folding: A molecular dynamics‐based quantitative inventory of molecular interactions and forces that make proteins stable

  2024influential citation
• Free Energy Density of a Fluid and Its Role in Solvation and Binding.

  2024cites this paper
• Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution

  2024cites this paper
• The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering

  2023cites this paper
• Comparing the influence of explicit and implicit solvation models on site‐specific thermodynamic stability of proteins

  2023cites this paper
• Molecular Interactions and Forces that Make Proteins Stable: A Quantitative Inventory from Atomistic Molecular Dynamics Simulations

  2023cites this paper
• Simulating Time-Resolved Dynamics of Biomolecular Systems

  2022cites this paper
• Nature-Derived Compounds as Potential Bioactive Leads against CDK9-Induced Cancer: Computational and Network Pharmacology Approaches

  2022cites this paper
• Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment

  2022cites this paper
• Towards Compilation of Balanced Protein Stability Datasets: Flattening the ΔΔG Curve through Systematic Under-sampling

  2021cites this paper
• An arginine residue in the outer segment of hASIC1a TM1 affects both proton affinity and channel desensitization

  2021cites this paper
• The relation between intrinsic protein conformational changes and ligand binding

  2020cites this paper
• Conserved internal hydration motifs in protein kinases

  2020cites this paper
• Thermodynamics of Biological Phenomena

  2020cites this paper
• The relation between intrinsic protein conformational changes and ligand binding

  2020cites this paper
• Systematic Investigation of the Data Set Dependency of Protein Stability Predictors

  2020cites this paper
• Thermodynamics of protein folding: methodology, data analysis and interpretation of data

  2019cites this paper
• Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins

  2019cites this paper
• A protein interaction free energy model based on amino acid residue contributions: Assessment of point mutation stability of T4 lysozyme.

  2019cites this paper
• Explicit Characterization of the Free Energy Landscape of pKID–KIX Coupled Folding and Binding

  2019cites this paper
• Examining a Thermodynamic Order Parameter of Protein Folding

  2018cites this paper
• Publisher Correction: Examining a Thermodynamic Order Parameter of Protein Folding

  2018cites this paper
• Molecular insights into the improved clinical performance of PEGylated interferon therapeutics: a molecular dynamics perspective

  2018cites this paper
• Finding the needle in the haystack: towards solving the protein-folding problem computationally

  2018cites this paper
• A Survey of the Structural Parameters Used for Computational Prediction of Protein Folding Process

  2018cites this paper
• Computer Simulations of Intrinsically Disordered Proteins.

  2017cites this paper
• NMR Spectroscopy for the Characterization of GPCR Energy Landscapes

  2017cites this paper
• Explicit Solvent Hydration Benchmark for Proteins with Application to the PBSA Method.

  2017cites this paper
• Thermodynamics, ecology and evolutionary biology: A bridge over troubled water or common ground?

  2017cites this paper
• Modified Poisson equations for calculating solvation free energy.

  2017cites this paper
• Proteomic indicators of oxidation and hydration state in colorectal cancer

  2016cites this paper
• Functional Modulation of a G Protein-Coupled Receptor Conformational Landscape in a Lipid Bilayer.

  2016cites this paper
• Protein stability: a crystallographer’s perspective

  2016cites this paper
• Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

  2016cites this paper
• Modified Poisson equation for the electric field and electric field gradient

  2016cites this paper
• Incorporating excluded solvent volume and physical dipoles for computing solvation free energy

  2015cites this paper
• Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

  2015cites this paper
• Distinct role of hydration water in protein misfolding and aggregation revealed by fluctuating thermodynamics analysis.

  2015cites this paper
• Amino Acid Distribution Rules Predict Protein Fold: Protein Grammar for Beta-Strand Sandwich-Like Structures

  2015cites this paper
• Structural versus energetic approaches for protein conformational entropy

  2015cites this paper
• Life's a Gas: A Thermodynamic Theory of Biological Evolution

  2015cites this paper
• Thermodynamic Principle Revisited: Theory of Protein Folding

  2015influential citation
• Local Stability Analysis of Hydrogen Bonding and Other Non-Covalent Interactions

  2014cites this paper
• Drug-Like Protein–Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

  2014cites this paper
• Protein folding thermodynamics: a new computational approach.

  2014cites this paper
• Incorporating the excluded solvent volume and surface charges for computing solvation free energy

  2014cites this paper
• Probing the free energy landscape of the fast-folding gpW protein by relaxation dispersion NMR.

  2014cites this paper
• Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method

  2014cites this paper
• Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

  2014cites this paper
• Drug design benefits from molecular dynamics: some examples.

  2013cites this paper
• Binding of a perfluorinated surfactant to β-lactoglobulin in aqueous solutions

  2013cites this paper
• Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap

  2013cites this paper
• Conformational entropy of intrinsically disordered protein.

  2013cites this paper
• Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

  2013cites this paper
• Ben-Naim’s “Pitfall”: Don Quixote’s Windmill

  2013influential citation
• Thermodynamics of mixtures containing amines: XIII. Application of the ERAS model to cyclic amine + alkane mixtures

  2013cites this paper
• Does water drive protein folding

  2013cites this paper
• NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

  2013cites this paper
• Studies of molecular modeling on drug design of Listeria monocytogenes internalin B β-sheet

  2012influential citation
• Designing and Probing Open Quantum Systems: Quantum Annealing, Excitonic Energy Transfer, and Nonlinear Fluorescence Spectroscopy

  2012cites this paper
• Visualizing internal stabilization in weakly bound systems using atomic energies: hydrogen bonding in small water clusters.

  2012cites this paper
• Balanced and Bias-Corrected Computation of Conformational Entropy Differences for Molecular Trajectories.

  2012cites this paper
• Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol

  2012cites this paper
• Ligand and Receptor Conformational Energies

  2012cites this paper
• Gibbs Free Energy Formula for Protein Folding

  2012cites this paper
• Chapter 0 Gibbs Free Energy Formula for Protein Folding

  2012influential citation
• Protein Folding: The Gibbs Free Energy

  2012cites this paper
• Unraveling universal thermodynamic and structural behavior of HP model protein adsorption

  2012cites this paper
• Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

  2011cites this paper
• Equilibrium unfolding studies of monellin: the double-chain variant appears to be more stable than the single-chain variant.

  2011cites this paper
• Mathematical criteria to observe mesoscopic emergence of protein biochemical properties

  2011cites this paper
• Methods development and force field evaluation for molecular simulations of iinteractions between structured peptides and functionalized material surfaces

  2011cites this paper
• Prediction of three-dimensional transmembrane helical protein structures

  2010cites this paper
• Geometry, thermodynamics, and protein.

  2010cites this paper
• Interplay between multiple length and time scales in complex chemical systems

  2010cites this paper
• Protein Folding: A Perspective From Statistical Physics

  2010cites this paper
• Ways and means of coping with uncertainties of the relationship of the genetic blue print to protein structure and function in the cell

  2010cites this paper
• Are long-chain alkanes hydrophilic?

  2010cites this paper
• Finding order within disorder: elucidating the structure of proteins associated with neurodegenerative disease.

  2009cites this paper
• SEMINAR PROTEIN SELF-ASSEMBLY

  2009cites this paper
• Computational studies of tau protein : implications for the pathogenesis and treatment of neurodegenerative diseases

  2009cites this paper
• Entropy and Thermodynamics in Biomolecular Simulation

  2009cites this paper
• Construction of model Hamiltonians for adiabatic quantum computation and its application to finding low-energy conformations of lattice protein models

  2008cites this paper
• CXC and CC Chemokines Form Mixed Heterodimers

  2008cites this paper
• The role of kinetics of and amide bonding in protein stability.

  2008cites this paper
• An integral equation theory for inhomogeneous molecular fluids: the reference interaction site model approach.

  2008cites this paper
• The "Hot-Solvent/Cold-Solute" Problem Revisited.

  2008cites this paper
• Volumetric properties of the glycyl group of proteins in aqueous solution at high pressures.

  2008cites this paper
• The importance of excluded solvent volume effects in computing hydration free energies.

  2008cites this paper
• Environmental Influence on α-Helical Peptides

  2007cites this paper
• chapter 2 Obtaining Molecular Thermochemistry from Calculations

  2007cites this paper
• Stability of a protein tethered to a surface.

  2007cites this paper
• Introduction to protein folding for physicists

  2007influential citation
• Water at biomolecular binding interfaces.

  2007cites this paper
• Dynamics of alpha helix formation in the CSAW model

  2007cites this paper
• Local-structural diversity and protein folding: application to all-beta off-lattice protein models.

  2006cites this paper