caa a22 4500 605512736 CHVBK 20210128100657.0 cr unu---uuuuu 210128e20150401xx s 000 0 eng 10.1007/s00894-015-2645-x doi (NATIONALLICENCE)springer-10.1007/s00894-015-2645-x Molecular dynamics simulation and conformational analysis of some catalytically active peptides [Elektronische Daten] [Bahareh Honarparvar, Adam Skelton] The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, molecular dynamics simulations in explicit water of two catalytically active peptides (peptide 1: Fmoc-Phe1-Phe2-His-CONH2; peptide 2: Fmoc-Phe1-Phe2-Arg-CONH2) were performed at temperatures of 300, 400, and 500K. Conformational analysis of these peptides using Ramachandran plots identified the secondary structures of the amino acid residues involved (Phe1, Phe2, His, Arg) and confirmed their conformational flexibility in solution. Furthermore, Ramachandran maps revealed the intrinsic preference of the constituent residues of these compounds for a helical conformation. Long-range interaction distances and radius of gyration (R g) values obtained during 20 ns MD simulations confirmed their tendency to form folded conformations. Results showed a decrease in side-chain (Phe1, Phe2, His ring, and Arg) contacts as the temperature was raised from 300 to 400K and then to 500K. Finally, the radial distribution functions (RDF) of the water molecules around the nitrogen atoms in the catalytically active His and Arg residues of peptide 1 and peptide 2 revealed that the strongest water-peptide interaction occurred with the arginine nitrogen atoms in peptide 2. Our results highlight differences in the secondary structures of the two peptides that can be explained by the different arrangement of water molecules around the nitrogen atoms of Arg in peptide 2 as compared to the arrangement of water molecules around the nitrogen atoms of His in peptide 1. The results of this work thus provide detailed insight into peptide conformations which can be exploited in the future design of peptide analogs. Springer-Verlag Berlin Heidelberg, 2015 Catalytic peptides nationallicence Molecular dynamics (MD) nationallicence Ramachandran plots nationallicence Radius of gyration ( R g) nationallicence Radial distribution function (RDF) nationallicence Honarparvar Bahareh School of Pharmacy and Pharmacology, University of KwaZulu-Natal, 4001, Durban, South Africa aut Skelton Adam School of Pharmacy and Pharmacology, University of KwaZulu-Natal, 4001, Durban, South Africa aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/4(2015-04-01), 1-12 1610-2940 21:4<1 2015 21 894 https://doi.org/10.1007/s00894-015-2645-x text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2645-x text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Honarparvar Bahareh School of Pharmacy and Pharmacology, University of KwaZulu-Natal, 4001, Durban, South Africa aut NATIONALLICENCE 700 1- Skelton Adam School of Pharmacy and Pharmacology, University of KwaZulu-Natal, 4001, Durban, South Africa aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/4(2015-04-01), 1-12 1610-2940 21:4<1 2015 21 894