The structure and energetics of zinc chlorides (ZnCl n 2-n , n ) 0-4) in aqueous solution are studied by ab initio molecular orbital methods. The first solvation shell is included explicitly, the remainder of the solvent being modeled by the polarizable continuum method. The species Zn(H 2 O) 6 2+ , ZnCl 2 (H 2 O) 2 , ZnCl 3 (H 2 O) -, and ZnCl 4 2-are predicted to occur in an aqueous environment. The predictions are consistent with the limited structural and energetic data available. A comparison with the predictions of the continuum model alone shows the necessity of including the first solvation shell explicitly to model solvation energies, although the continuum model is successful in predicting structural changes of ZnCl + and ZnCl 2 upon hydration.
Molecular dynamics computer simulations have been performed on Mouse (Mo) and Syrian Hamster (SHa) prion proteins. These proteins differ, primarily, in that the SHa form incorporates additional residues at the C-terminus and also includes a segment of the unstructured N-terminal region that is required for infectivity. The 1-ns simulations have been analyzed by using a combination of dynamical cross-correlation maps, residue-residue contact plots, digital filtering, and residue-based root-mean-square deviations. The results show that the extra residues present in the SHa form at the C- and N-termini produce changes in the stability of key regions of the protein. The loop region between strand S2 and helix B that contains part of the proposed discontinuous binding site for the chaperone, protein X, is found to be more stable in SHa than in the Mo protein; these results are consistent with the NMR data of James et al. (James et al. Proc Natl Acad Sci USA 1997;94:10086-10091). In addition, a degree of flexibility within the region between and including strand S1 and helix A is also shown in SHa, which is not present in the Mo form; the cross-correlation maps suggest that this is a consequence of the additional unstructured N-terminal region. Furthermore, the extra residues in the N-terminal region of SHa are found to form a beta-bridge with the beta-sheet, within which critical point mutations associated with prion diseases lie. The implications of these results for the conformational interconversion pathway of the prion protein are discussed.
The structure of the central repetitive domain of the high molecular weight glutenin subunits, a group of elastomeric proteins from the seeds of wheat, were modeled using structure prediction and molecular dynamics. Models were generated with spiral structures, based on repetitive β‐reverse turns, within and spanning the repeat motifs of the central domains. The models were consistent with available data from biophysical studies on the intact proteins and spectroscopic (infra‐red and nuclear magnetic resonance) studies of synthetic peptides.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.