Premium
Stability and Dynamics of Domain‐Swapped Bovine‐Seminal Ribonuclease
Author(s) -
Chakrabarti Kalyan S.,
Sanjeev B. S.,
Vishveshwara Saraswathi
Publication year - 2004
Publication title -
chemistry and biodiversity
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.427
H-Index - 70
eISSN - 1612-1880
pISSN - 1612-1872
DOI - 10.1002/cbdv.200490062
Subject(s) - chemistry , dimer , side chain , rnase p , ribonuclease , molecular dynamics , monomer , intermolecular force , hydrogen bond , crystallography , molecule , protein dynamics , ribonuclease iii , protein structure , biophysics , rna , computational chemistry , biochemistry , polymer , gene , organic chemistry , rna interference , biology
The proteins of the ribonuclease‐A (RNase‐A) family are monomeric, with the exception of bovine‐seminal ribonuclease (BS‐RNase). BS‐RNase is formed by swapping the N‐terminal helices across the two monomeric units. A molecular‐dynamics (MD) study has been performed on the protein for a simulation time of 5.5 ns to understand the factors responsible for the stability of the dimer. Essential dynamics analysis and motional correlation of the protein atoms yielded the picture of a stabilising, yet flexible, interface. We have investigated the role of intermolecular H‐bonding, protein/water interaction, and protein/water networks in stabilising the dimer. The networks of interchain H‐bonds involving side‐chain/side‐chain or side‐chain/main‐chain (ScHB) interactions between the two chains have also been studied. The ability of protein atoms in retaining particular H 2 O molecules was investigated as a function of the accessible surface area ( ASA ), depth , and hydration parameters, as well as their participation in protein/water networks.