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For the Sequence YKGQ, the Turn and Extended Conformational Forms Are Separated by Small Barriers and the Turn Propensity Persists Even at High Temperatures: Implications for Protein Folding

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Title For the Sequence YKGQ, the Turn and Extended Conformational Forms Are Separated by Small Barriers and the Turn Propensity Persists Even at High Temperatures: Implications for Protein Folding
 
Creator KAUR, H
SASIDHAR, YU
 
Subject MOLECULAR-DYNAMICS SIMULATIONS
POLYPROLINE II HELIX
GLYCINE METHYL-ESTER
AMINO-ACID-RESIDUES
PARTICLE MESH EWALD
STAPHYLOCOCCAL NUCLEASE
BETA-HAIRPIN
MICROSCOPIC REVERSIBILITY
THERMOPHILIC PROTEINS
HYDROGEN-EXCHANGE
 
Description The folding of the sequence (21)DTVKLMYKGQPMTFR(35) from staphylococcal nuclease into a beta-hairpin, nucleated by the turn region YKGQP, is known to be an early folding event. With YKGQ being the shortest sequence for a beta-turn model and in view of its importance to the folding of staphylococcal nuclease, we investigated the thermodynamics of turn formation at a range of temperatures from 280 to 380 K, with a regular interval of 10 K. Eleven independent molecular dynamics simulations (under NPT conditions) were performed using the GROMACS package of programs and the OPLS-AA/L all-atom force field, each for a time period of 1 mu s. Turn formation is supported by enthalpy at lower temperatures, while entropy supports it at higher temperatures. There are modest free energy barriers between turn and extended conformational ensembles. The turn propensity persists even at elevated temperatures. The role of proline in driving the turn formation has been re-examined, and it is inferred that the absence of proline does not affect turn propensity.
 
Publisher AMER CHEMICAL SOC
 
Date 2014-10-16T06:48:40Z
2014-10-16T06:48:40Z
2012
 
Type Article
 
Identifier JOURNAL OF PHYSICAL CHEMISTRY B, 116(12)3850-3860
http://dx.doi.org/10.1021/jp210227s
http://dspace.library.iitb.ac.in/jspui/handle/100/15474
 
Language en