1. Three-dimensional structure of human β-defensin 28 via homology modelling and molecular dynamics.
- Author
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Chen, Wen Wen, Sing Tay, Derrick Kok, Leong, Susanna Su Jan, and Kwak, Sang Kyu
- Subjects
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MOLECULAR structure , *DEFENSINS , *MOLECULAR dynamics , *MOLECULAR models , *FLUOROETHANOL , *PROTEINS , *SIMULATION methods & models , *CIRCULAR dichroism - 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. [ABSTRACT FROM PUBLISHER]
- Published
- 2012
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