All-atom ab initio native structure prediction of a mixed fold (1FME): a comparison of structural and folding characteristics of various beta beta alpha miniproteins

The Journal of Chemical Physics
Eunae KimYoungshang Pak

Abstract

We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold beta beta alpha miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other beta beta alpha miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue beta beta alpha miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1-->Glu1 and Ile7-->Tyr7) of 1FSD were investigated in...Continue Reading

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Citations

Sep 17, 2013·Journal of Chemical Theory and Computation·Adam K SieradzanUlrich H E Hansmann
Mar 16, 2012·The Journal of Physical Chemistry. B·In-Ho LeeJooyoung Lee
Aug 13, 2013·Journal of Chemical Theory and Computation·Pandian SokkarYoung Min Rhee

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Methods Mentioned

BETA
NMR
PCA
circular dichroism

Software Mentioned

RATTLE
GBSA
REMD
- REMD
TINKER
STRIDE
param99MOD5

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