Structure and effect of sarcosine on water and urea by using molecular dynamics simulations: Implications in protein stabilization
DSpace at IIT Bombay
View Archive InfoField | Value | |
Title |
Structure and effect of sarcosine on water and urea by using molecular dynamics simulations: Implications in protein stabilization
|
|
Creator |
KUMAR, N
KISHORE, N |
|
Subject |
Sarcosine
Urea Molecular dynamics simulation Radial distribution function Hydrogen bond dynamics Diffusion constant TRIMETHYLAMINE-N-OXIDE AQUEOUS UREA PREFERENTIAL SOLVATION DIMETHYL-SULFOXIDE DENATURED STATE FORCE-FIELD STABILITY THERMODYNAMICS COUNTERACTION OSMOLYTES |
|
Description |
Sarcosine is one of the most important protecting osmolytes which is also known to counteract the denaturing effect of urea. We used molecular dynamics simulation methods to investigate the mechanism of protein stabilization and counteraction of urea by sarcosine. We found that sarcosine enhanced the tetrahedral structure of water and strengthened its hydrogen bonding network. We also found that sarcosine did not form clusters unlike glycine. Our results show strong interaction between sarcosine and urea molecules. Addition of sarcosine enhanced the urea-water structure and urea-water lifetime indicated an increase in the solvation of urea. These findings suggest that sarcosine indirectly stabilizes protein by enhancing water-water structure thus decreasing the hydrophobic effect and counteracts the effect of urea by increasing the solvation of urea and directly interacting with it leaving urea less available to interact with protein. (C) 2012 Elsevier B.V. All rights reserved.
|
|
Publisher |
ELSEVIER SCIENCE BV
|
|
Date |
2014-10-16T05:44:07Z
2014-10-16T05:44:07Z 2013 |
|
Type |
Article
|
|
Identifier |
BIOPHYSICAL CHEMISTRY, 1719-15
http://dx.doi.org/10.1016/j.bpc.2012.11.004 http://dspace.library.iitb.ac.in/jspui/handle/100/15368 |
|
Language |
en
|
|