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

• Main Authors: Kwak, Sang Kyu, Chen, Wenwen, Tay, Derrick Kok Sing, Leong, Susanna Su Jan
• Other Authors: School of Chemical and Biomedical Engineering
• Format: Article
• Language: English
• Published: 2013
• Online Access: https://hdl.handle.net/10356/101877; http://hdl.handle.net/10220/11140
• Institution: Nanyang Technological University

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.