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Structure and effect of sarcosine on water and urea by using molecular dynamics simulations: Implications in protein stabilization

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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