Hydrogen-bond disruption probability in proteins by a modified self-consistent harmonic approach.
Modified self-consistent harmonic approach was employed to calculate the probability for the disruption of each individual hydrogen bonds (H bonds) in x-ray crystal structure of several proteins. The computed probability for 82% of intraprotein and water-protein H bonds studied were found to be roughly consistent with estimated free energies from protein engineering and hydrogen exchange experiments. Hydrogen bonds have been proposed as part of a stereochemical code for protein folding. Proteins fold into unique three-dimensional structures; therefore those bonds involved in the folding code are expected to be stable. We have applied this method to tens of hydrogen bonds in a protein assumed to be involved in the folding code of a protein. 58% of these H bonds were found to have a lower disruption probability (-1.8 kcal/mol). Our results showed that modified self-consistent harmonic approach might be explored as a method supplement to existing methods in analysis of hydrogen bonds in proteins.
Cao
Z W
ZW
Department of Computational Science, National University of Singapore, 3 Science Drive 2, Singapore 117543.
Chen
Y Z
YZ
D000465:Algorithms; D003460:Crystallization; D018360:Crystallography, X-Ray; D004734:Energy Metabolism; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008968:Molecular Conformation; D009113:Muramidase / Q000737:chemistry; D011487:Protein Conformation; D015202:Protein Engineering; D017510:Protein Folding; D012259:Ribonuclease, Pancreatic / Q000737:chemistry* / Q000235:genetics; D014867:Water / Q000737:chemistry
D014867:Water; D012259:Ribonuclease, Pancreatic; D009113:Muramidase