Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability release_loqjlnpksfcqlgg4s2foerdg7m

by Zhiguo Chen, Yi Fu, Wenbo Xu, Ming Li

Published in Mathematical Problems in Engineering by Hindawi Limited.

2013   Volume 2013, p1-12

Abstract

<jats:italic>Bacillus amyloliquefaciens</jats:italic>ribonuclease Barnase (RNase Ba) is a 12 kD (kilodalton) small extracellular ribonuclease. It has broad application prospects in agriculture, clinical medicine, pharmaceutical, and so forth. In this work, the thermal stability of Barnase has been studied using molecular dynamics simulation at different temperatures. The present study focuses on the contribution of noncovalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profiles of root mean square deviation and root mean square fluctuation identify thermostable and thermosensitive regions of Barnase. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bonds and salt bridge interactions indicate distinct differences in different temperature simulations. In the simulations, Four three-member salt bridge networks (Asp8-Arg110-Asp12, Arg83-Asp75-Arg87, Lys66-Asp93-Arg69, and Asp54-Lys27-Glu73) have been identified as critical salt bridges for thermostability which are maintained stably at higher temperature enhancing stability of three hydrophobic cores. The study may help enlighten our knowledge of protein structural properties, noncovalent interactions which can stabilize secondary peptide structures or promote folding, and also help understand their actions better. Such an understanding is required for designing efficient enzymes with characteristics for particular applications at desired working temperatures.
In application/xml+jats format

Archived Files and Locations

application/pdf  5.5 MB
file_il4b5mdkircd3cli2jvcubdq2q
downloads.hindawi.com (publisher)
web.archive.org (webarchive)
Read Archived PDF
Preserved and Accessible
Type  article-journal
Stage   published
Year   2013
Language   en ?
Container Metadata
Open Access Publication
In DOAJ
In ISSN ROAD
In Keepers Registry
ISSN-L:  1024-123X
Work Entity
access all versions, variants, and formats of this works (eg, pre-prints)
Catalog Record
Revision: d5dbe871-7304-4705-b956-ccfe831a8523
API URL: JSON