Paper Citing NAMD - Abstract
Toubar, Rabab A.; Zhmurov, Artem; Barsegov, Valeri; Marx, Kenneth A.
Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:174-194, FEB 1 2013
Human defensins play important roles in a broad range of biological functions, such as microbial defense and immunity. Yet, little is known about their molecular properties, i.e. secondary structure stability, structural variability, important side chain interactions, surface charge distribution, and resistance to thermal fluctuations, and how these properties are related to their functions. To assess these factors, we studied the native human beta-defensin-1 monomer and dimer as well as several single-site mutants using molecular dynamics simulations. The results showed that disulfide bonds are important determinants in maintaining the defensins structural integrity, as no structural transitions were observed at 300?K and only minor structural unfolding was detected upon heating to 500?K. The a-helix was less thermally stable than the core beta-sheet structure held together by hydrogen bonds and hydrophobic interactions. The monomer a-helix stability was directly correlated, whereas the end-to-end distance was inversely correlated to the experimentally measured beta-defensin-1 chemotactic activity, in the order: mutant 2 (Gln24Glu)?>?mutant 3 (Lys31Ala)?=?wild type?>?mutant 1 (Asn4Ala). The structural stability of the beta-defensin-1 dimer species exhibited an inverse correlation to their chemotactic activity. In dimers formed by mutants 2 and 3, we observed sliding of one monomer upon the surface of the other in the absence of unbinding. This dynamic sliding feature may enhance the molecular oligomerization of beta-defensin-1 peptides contributing to their antibacterial activity. It could also help these peptides orient correctly in the CC chemokine receptor 6 binding site, thereby initiating their chemotactic activity. In agreement with this notion, the remarkable sliding behavior was observed only for the mutants with the highest chemotactic activity.
