computer modeling in molecular biology.pdf

3 Molecular Dynamics Simulations of Peptides 39Table 3-1. Some recent examples of molecular dynamics studies on small peptides.Examples of system studied Remarks ReferenceaBoc-Cys-Val-Pro-Pro-Phe-Phe-Cys-OMecyclo enkephalin analoguesMD in water Zannoti et al., 1993Chew et al., 1993cyclic hexapeptide NK-2analoguesneuropeptide Y analogueTyr-Pro-Gly-Asp-Valdeltorphin-I1antifreeze peptide 38 residueHPLC-6antamanideLHRH antagonistsanti-adhesive RGD peptidesdefensin antimicrobialsHNP-1 and NP-2c(G1y-Pro-D-Phe-Gly-Val)oxytocinBoc-Ala-Aib-Ala-OMeAc-Pro-D-Ala-Ala-NMe withCa2 +lanthionine-bridged enkephalinanaloguesdermophin analogueszinc-finger peptidecyclic analogue of substance P0-glycosylated cyclic peptidesmastoparan-Xribunuclease-S peptidec(G1y-Pro-Phe-Val-Phe-Phe)cyclic peptide templatesbombesin and GRP analoguestuftsin and analoguesneurokinin antagonistGRF analoguesBoc-Gly-Val-Gly-Gly-Leu-OMeMD in polar and apolarenvironsNOE-restrained MDMD used to confirmstructuresMD in solutionNOE-restrained MDMD on iceMD in chloroformNOE-restrained MD invacuo and solventrestrained and free MDNOE-restrained MDMD in vacuo comparedwith NMRrestrained MDMD with time-averagedconstraintsMD coupled with randomsearchMD compared with NOEdataMD at 600 K with 4starting pointsMD in vacuo and waterNOE-restrained MD inDMSONOE-restrained MD invacuo and solventsNOE-restrained MDMD and free energiesMD in vacuo and DMSOMD at 900 KNOE-restrained MDhigh temperature quenchedMDNOE-restrained MDNOE-restrained MDMD in vacuoWollborn et al., 1993BeckSickinger et al., 1993Karpen et al., 1993,Tobias et al., 1991Ohno et al., 1993Jorgensen et al., 1993Bruschweiler et al., 1992Rizo et al.. 1992Gurrath et al., 1992Pardi et al., 1992Liu and Giersch, 1992Bhaskaran et al., 1992Brunne and Leibfritz, 1992Michel et al., 1992Polinsky et al., 1992Wilkes and Schiller, 1992Palmer and Case, 1992Saulitius et al., 1992Kessler et al., 1991, 1992Sukumar and Higashijima,1992Simonson and Brunger, 1992Kessler et al., 1992Floegel and Mutter, 1992Malikayil et al., 1992O’Connor et al., 1992Malikayil and Harbeson,1992Fry et al., 1992Lelj et al., 1992