The ability of a,a-di-n-alkyl glycines with linear and cyclic alkyl side chains to stabilize helical conformations has been compared using a model heptapeptide sequence. The conformations of five synthetic heptapeptides (Boc–Val–Ala–Leu–Xxx–Val–Ala–Leu–OMe, Xxx 5 Ac8c, Ac7c, Aib, Dpg ,and Deg, where Ac8c 5 1-aminocyclooctane-1-carboxylic acid, Ac7c 5 1-aminocycloheptane1-carboxylic acid, Aib 5 ...

The title compond, C(19)H(24)O(5)·H(2)O, has two gibberellin A4 mol-ecules and two water mol-ecules in the asymmetric unit. The A and B rings have chair conformations, whereas the C and D rings have envelope conformations; the two rings which contain the lactone and carbonyl bridge adopt chair and envelope conformations. The crystal structure is established by O-H⋯O hydrogen bonds and supported...

The development of an energy or scoring function for protein structure prediction is greatly enhanced by testing the function on a set of computer-generated conformations (decoys) to determine whether it can readily distinguish native-like conformations from nonnative ones. We have created "Decoys 'R' Us," a database containing many such sets of conformations, to provide a resource that allows ...

Ab initio HF/6-3 lG(d. p) and density functional theory B3LYP/6-31G (d, p) calculations were carried out to investigate the conformations of pyrrolidinium ion. Two conformations, corresponding to twisted (C2) and envelope (Cs) forms were optimized. Vibrational analysis showed that the twisted form is at a local minimum point and the envelope form at a saddle point. The energy difference between...

Multiple crystal structures of the homo-trimeric protein disulphide isomerase PmScsC reveal that peptide which links trimerization stalk and catalytic domain can adopt helical, β-strand loop conformations. This region has been called a ‘shape-shifter’ peptide. Characterisation this using NMR experiments MD simulations shown it is essentially disordered in solution. Analysis identifies role inte...

Selecting near-native conformations from the immense number of conformations generated by docking programs remains a major challenge in molecular docking. We introduce DockRank, a novel approach to scoring docked conformations based on the degree to which the interface residues of the docked conformation match a set of predicted interface residues. DockRank uses interface residues predicted by ...

Suppression of Tumorigenicity 2 (ST2), a member of the interleukin-1 receptor (IL-1R) family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC) analysis on the ...

NMDA receptors are tetrameric ligand-gated ion channels. In the continuous presence of saturating agonists, NMDA receptors undergo stationary gating, in which the channel stochastically switches between an open state that permits ion conductance and a closed state that prevents permeation. The ligand-binding domains (LBDs) of the four subunits are expected to have closed clefts in the channel-o...

The major human immunodeficiency virus type 1 (HIV-1) coreceptors are the chemokine receptors CCR5 and CXCR4. The patterns of expression of the major coreceptors and their use by HIV-1 strains largely explain viral tropism at the level of entry. However, while virus infection is dependent upon the presence of CD4 and an appropriate coreceptor, it can be influenced by a number of factors, includ...