ArticleProtein science : a publication of the Protein Society2002
Interatomic potentials and solvation parameters from protein engineering data for buried residues.
Article in Protein science : a publication of the Protein Society, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- COCOMO2: A coarse-grained model for interacting folded and disordered proteins.bioRxiv : the preprint server for biology · 2024Article
- Life at the border: adaptation of proteins to anisotropic membrane environment.Protein science : a publication of the Protein Society · 2014Review
- Forces stabilizing proteins.FEBS letters · 2014Review
- Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach.Journal of chemical theory and computation · 2013Article
- Structural adaptations of proteins to different biological membranes.Biochimica et biophysica acta · 2013Article
- Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes.Journal of chemical information and modeling · 2011Article
- The contribution of surface residues to membrane binding and ligand transfer by the α-tocopherol transfer protein (α-TTP).Journal of molecular biology · 2011Article
- Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.BMC bioinformatics · 2008Article
- Effects of serine-to-cysteine mutations on beta-lactamase folding.Biophysical journal · 2007Article
- Quantification of helix-helix binding affinities in micelles and lipid bilayers.Protein science : a publication of the Protein Society · 2004Article
- Protein structure, stability and solubility in water and other solvents.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2004Review
- H-bonding in protein hydration revisited.Protein science : a publication of the Protein Society · 2004Article
- iMOT: an interactive package for the selection of spatially interacting motifs.Nucleic acids research · 2004Article
- On the conformation of the COOH-terminal domain of the large mechanosensitive channel MscL.The Journal of general physiology · 2003Article
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Abstract
Van der Waals (vdW) interaction energies between different atom types, energies of hydrogen bonds (H-bonds), and atomic solvation parameters (ASPs) have been derived from the published thermodynamic stabilities of 106 mutants with available crystal structures by use of an originally designed model for the calculation of free-energy differences. The set of mutants included substitutions of uncharged, inflexible, water-inaccessible residues in alpha-helices and beta-sheets of T4, human, and hen lysozymes and HI ribonuclease. The determined energies of vdW interactions and H-bonds were smaller than in molecular mechanics and followed the "like dissolves like" rule, as expected in condensed media but not in vacuum. The depths of modified Lennard-Jones potentials were -0.34, -0.12, and -0.06 kcal/mole for similar atom types (polar-polar, aromatic-aromatic, and aliphatic-aliphatic interactions, respectively) and -0.10, -0.08, -0.06, -0.02, and nearly 0 kcal/mole for different types (sulfur-polar, sulfur-aromatic, sulfur-aliphatic, aliphatic-aromatic, and carbon-polar, respectively), whereas the depths of H-bond potentials were -1.5 to -1.8 kcal/mole. The obtained solvation parameters, that is, transfer energies from water to the protein interior, were 19, 7, -1, -21, and -66 cal/moleA(2) for aliphatic carbon, aromatic carbon, sulfur, nitrogen, and oxygen, respectively, which is close to the cyclohexane scale for aliphatic and aromatic groups but intermediate between octanol and cyclohexane for others. An analysis of additional replacements at the water-protein interface indicates that vdW interactions between protein atoms are reduced when they occur across water.
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