Topological analysis of hydrogen-bonds and weak interactions in protein helices
نویسندگان
چکیده
منابع مشابه
Strength of hydrogen bonds in helices
> < ABSTRACT: The intramolecular helix backbone C O H— N hydrogen Ž . bonding energies in poly L-alanine a helices have been estimated both in vacuum and in an aqueous environment using the parameter sets of five of the most commonly used force fields for modeling biomolecules, namely AMBER, CHARMM, ECEPP, GROMOS, and OPLS. The relative capabilities of these force fields in describing the H-bon...
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Protein environments substantially influence the balance of molecular interactions that generate structural stability. Transmembrane helices exist in the relatively uniform low dielectric interstices of the lipid bilayer, largely devoid of water and with a very hydrophobic distribution of amino acid residues. Here, through an analysis of bacteriorhodopsin crystal structures and the transmembran...
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Hydrophobic free energy has been widely accepted as a major force driving protein folding [1, 2], although a dispute over its proper definition earlier made this issue controversial. When a hydrocarbon solute is transferred from water to a nonaqueous solvent, or a nonpolar side chain of a protein is buried in its hydrophobic core through folding, the transfer free energy is referred to as hydro...
متن کاملHigh-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics
Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and...
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ژورنال
عنوان ژورنال: Acta Crystallographica Section A Foundations of Crystallography
سال: 2012
ISSN: 0108-7673
DOI: 10.1107/s0108767312098923