Computational studies on the backbone-dependent side-chain orientation induced by the (S,S)-CXC motif (Journal article)

Stavrakoudis, A./ Tsikaris, V.

Disulfide cyclization is a well-known procedure to impose conformational restriction to peptides undergoing backbone flexibility. Rigid conformations are induced only for small rings with a specific combination of amino acids. In this work. we present: a computational search of the backbone and backbone-dependent side-chain orientation of two series of linear and cyclic peptide analogs. The -C[XY]C- scaffold (where X,Y is arginine, aspartic acid or alanine residue) in Its open and (S,S) cyclic form was used for the design of the studied analogs Thidy-six compounds, resulting from the extension with one residue at either the N- or the C-termius were studied with classical MD. The local backbone conformation and the relative orientation of the X and Y side chains induced by either cyclization and/or the presence of file charged residues are discussed. From the present. study it is concluded that cyclization has a great impact on the synplanar orientation of the X and Y side chains in the (S,S)Ac-XCYC-NH(2) series of compounds while charge-charge Interaction has only a weak synergic effect. On the contrary, the antiplanar orientation is favored in the case of (S,S)Ac-CXCY-NH(2). Copyright (c) 2008 European Peptide Society and John Wiley & Sons, Ltd.
Institution and School/Department of submitter: Πανεπιστήμιο Ιωαννίνων. Σχολή Θετικών Επιστημών. Τμήμα Χημείας
Keywords: computational alanine scanning,backbone-dependent orientation,charge-charge interaction,computer simulation,cyclic peptides,disulfide cyclization,molecular dynamics,side-chain conformation,opioid receptor pharmacophore,tetrapeptide tyr-c<d-cys-phe-d-pen>oh jom-13,molecular-dynamics simulations,cyclic-peptides,active-site,cxxc motif,model,tool,replacements,prediction
ISSN: 1075-2617
Link: <Go to ISI>://000262016400005
Appears in Collections:Άρθρα σε επιστημονικά περιοδικά ( Ανοικτά)

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