← Back to Search
Local Water Bridges And Protein Conformational Stability
M. Petukhov, D. Cregut, C. M. Soares, L. Serrano
Published 1999 · Chemistry, Medicine
Save to my Library
Download PDFAnalyze on Scholarcy
Recent studies have pointed out the important role of local water structures in protein conformational stability. Here, we present an accurate and computationally effective way to estimate the free energy contribution of the simplest water structure motif–the water bridge. Based on the combination of empirical parameters for accessible protein surface area and the explicit consideration of all possible water bridges with the protein, we introduce an improved protein solvation model. We find that accounting for water bridge formation in our model is essential to understand the conformational behavior of polypeptides in water. The model formulation, in fact, does not depend on the polypeptide nature of the solute and is therefore applicable to other flexible biomolecules (i.e., DNAs, RNAs, polysaccharides, etc.).
This paper references
Electrostatic effects in macromolecules: fundamental concepts and practical modeling.
A. Warshel (1998)
Surface area included in energy refinement of proteins. A comparative study on atomic solvation parameters.
B. von Freyberg (1993)
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.
T. Ooi (1987)
Hydration of amino acid side chains: dependence on secondary structure.
A. S. Morris (1992)
Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation.
L. Serrano (1995)
Protein hydration in aqueous solution.
G. Otting (1991)
Electrostatic interactions in macromolecules: theory and applications.
K. Sharp (1990)
1H‐nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH
A. Bundi (1979)
Role of hydration and water structure in biological and colloidal interactions
J. Israelachvili (1996)
The name is bond — H bond
T. W. Martin (1999)
Calculations of electrostatic interactions in biological systems and in solutions.
A. Warshel (1984)
A Simple Functional Representation of Angular-Dependent Hydrogen-Bonded Systems. 1. Amide, Carboxylic Acid, and Amide-Carboxylic Acid Pairs
K. T. No (1995)
A statistical mechanical description of biomolecular hydration.
G. Hummer (1996)
Toward a Description of the Conformations of Denatured States of Proteins. Comparison of a Random Coil Model with NMR Measurements
K. Fiebig (1996)
Water:A Comprehensive Treatise
F. Franks (1972)
Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNH.alpha.) coupling constants in 15N-enriched proteins
Geerten W. Vuister (1993)
A new analysis of proton chemical shifts in proteins
K. Osapay (1991)
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell (1995)
Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding
A. H. Juffer (1995)
Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator.
A. Bonvin (1998)
ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS
W. F. Gunsteren (1977)
Hydrogen-bond geometry in organic crystals
R. Taylor (1984)
New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles.
R. Abagyan (1989)
Surface topography dependence of biomolecular hydrophobic hydration
Yuen-Kit Cheng (1998)
Hydrogen bond energy of the water dimer
Martin W. Feyereisen (1996)
Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins.
N. Thanki (1990)
Solvation energy in protein folding and binding
D. Eisenberg (1986)
Analysis of protein main-chain solvation as a function of secondary structure.
N. Thanki (1991)
The effects of guanidine hydrochloride on the ’random coil‘ conformations and NMR chemical shifts of the peptide series GGXGG
K. Plaxco (1997)
Solvent structure at a hydrophobic protein surface
H. Kovacs (1997)
The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
F. Eisenhaber (1995)
Empirical solvation models in the context of conformational energy searches: Application to bovine pancreatic trypsin inhibitor
R. L. Williams (1992)
Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
G. Némethy (1983)
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
F. Momany (1975)
This paper is referenced by
A new amphipathy scale I. Determination of the scale from molecular dynamics data.
F. M. Mazzé (2005)
Contribution of cation-π interaction and its effect on the structural stability of laccase enzymes - a computational study.
K. Ramanathan (2010)
Computationally accessible method for estimating free energy changes resulting from site‐specific mutations of biomolecules: Systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins
J. Burnett (2001)
Dynamic properties of SOD1 mutants can predict survival time of patients carrying familial amyotrophic lateral sclerosis
N. Alemasov (2017)
Very empirical treatment of solvation and entropy: a force field derived from Log Po/w
G. Kellogg (2001)
Heat capacity of hydrogen-bonded networks: an alternative view of protein folding thermodynamics.
A. Cooper (2000)
Water structure and interactions with protein surfaces.
T. Raschke (2006)
Deciphering the factors responsible for the stability of a GFP variant resistant to alkaline pH using molecular dynamics simulations
Sriram Sokalingam (2013)
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations.
C. Kiel (2005)
Development of experimental methods to assess adsorption free energy for peptide-surface interactions
Yang Wei (2010)
A novel main chain motif in proteins bridged by cationic groups: the niche.
G. Torrance (2009)
The FoldX web server: an online force field
J. Schymkowitz (2005)
The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes.
C. Kiel (2006)
A detailed thermodynamic analysis of ras/effector complex interfaces.
C. Kiel (2004)
Dynamics of a protein and water molecules surrounding the protein: Hydrogen‐bonding between vibrating water molecules and a fluctuating protein
S. Yoshioki (2002)
Engineering and functional properties of biodegradable pellets developed from various agro-industrial wastes using extrusion technology
K. Jan (2015)
Complement activation turnover on surfaces of nanoparticles.
S. Moghimi (2017)
Light chain amyloidosis: Where are the light chains from and how they play their pathogenic role?
Chunlan Zhang (2017)
The relationship between sequence and structure in elementary folding units.
L. Serrano (2000)
Insight into the Structure, Dynamics and the Unfolding Property of Amylosucrases: Implications of Rational Engineering on Thermostability
M. Liu (2012)
Modeling the interaction of interferon α-1b to bovine serum albumin as a drug delivery system.
Q. Luo (2014)
Review: immunoglobulin light chain amyloidosis--the archetype of structural and pathogenic variability.
V. Bellotti (2000)
3D model of RNA polymerase and bidirectional transcription.
P. Bhattacharya (2007)
Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6.
Ozlem Kempkens (2006)
Protein-water interactions in a dynamic world.
C. Mattos (2002)
POWAINDv1.0: A Program for Protein-Water Interactions Determination
Sahini Banerjee (2018)
Computational Methods in Biomolecules:Study of Hydrophilic Interactions in Protein Folding & Constant-pH Molecular Simulation of pH Sensitive Lipid MORC16
W. Zhang (2018)
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking
C. Su (2014)
Computational Methods in the Optimization of Biologic Modalities
S. Dixit (2015)
Computational design and studies of neuro-active peptides and the effects of calcium on nicotinic acetylcholine receptors in relation to neurodegenerative disorders
A. Suresh (2016)
ω-Transaminases as Promising Biocatalysts for the Chiral Synthesis of β-Amino Acids
O. Buß (2018)
The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
D. Beck (2008)See more