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Kwak, Sang Kyu
Kyu’s MolSim Lab @ UNIST
Research Interests
  • Molecular modeling and simulation, statistical thermodynamics, molecular physics

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Three-dimensional structure of human β-defensin 28 via homology modelling and molecular dynamics

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Title
Three-dimensional structure of human β-defensin 28 via homology modelling and molecular dynamics
Author
Chen, Wen WenTay, Derrick Kok SingLeong, Susanna Su JanKwak, Sang Kyu
Keywords
homology modelling; human β-defensin protein; molecular dynamics
Issue Date
2012-02
Publisher
TAYLOR & FRANCIS LTD
Citation
MOLECULAR SIMULATION, v.38, no.2, pp.90 - 101
Abstract
The 3D structure of the human β-defensin 28 (HBD-28) has been investigated via homology modelling and molecular dynamics (MD) approach. With known high-resolution structures of HBD-2 and -3, single- and multiple-template sequence alignments are applied to find highly probable candidates for HBD-28, which are in turn refined through MD simulations in pure water and 50% trifluoroethanol/water mixture. The models obtained from homology modelling were assessed by protein structure validation software suite, which includes Procheck, MolProbity, Verify-3D and various structure validation tools. We found that modelling quality is proportionally related to the sequence alignment accuracy. In comparison with circular dichroism experimental data as well as stabilities of β-sheets and α-helix, HBD-28 with a reliable 3D structure was found.
URI
https://scholarworks.unist.ac.kr/handle/201301/6804
DOI
10.1080/08927022.2011.604854
ISSN
0892-7022
Appears in Collections:
ECHE_Journal Papers
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