Computational screening of branched cyclic peptide motifs as potential enzyme mimetics
Φόρτωση...
Ημερομηνία
Συγγραφείς
Stavrakoudis, A.
Makropoulou, S.
Tsikaris, V.
Sakarellos-Daitsiotis, M.
Sakarellos, C.
Demetropoulos, I. N.
Τίτλος Εφημερίδας
Περιοδικό ISSN
Τίτλος τόμου
Εκδότης
Wiley
Περίληψη
Τύπος
Είδος δημοσίευσης σε συνέδριο
Είδος περιοδικού
peer reviewed
Είδος εκπαιδευτικού υλικού
Όνομα συνεδρίου
Όνομα περιοδικού
Journal of Peptide Science
Όνομα βιβλίου
Σειρά βιβλίου
Έκδοση βιβλίου
Συμπληρωματικός/δευτερεύων τίτλος
Περιγραφή
In a previous work we described the design, synthesis and catalytic activity of a branched cyclic peptide as a serine protease mimic. To maximize its catalytic activity we present now a systematic search of a large number of homologous peptides for potential enzyme activity as revealed by the topological arrangement of the catalytic triad residues. This process is accomplished by applying a combined molecular mechanics and molecular dynamics conformational search of about 200 molecules. Starting from a previously synthesized compound that showed some hydrolytic activity several analogues were modelled by amino acid substitutions in the main molecular framework using the Insight II molecular modelling environment with some script automation. Also presented is an algorithm that: (a) generates all possible combinations of residue substitutions, (b) scans the conformational space for each molecule via high temperature molecular dynamics, (c) picks the set of molecules the trajectories of which retained, to a considerable degree, the catalytic triad molecular arrangement, (d) subjects the selected molecules to layer solvation and energy minimization and chooses the molecules, the conformations of which could preserve the catalytic triad arrangement. Finally, a modelling with periodic boundary conditions, was performed to further support the reported algorithm. We found that at least one of the analogues could be a potential serine protease mimic, as revealed by the root-mean-square comparison between the catalytic triad in two molecular dynamics trajectories of the peptide and the corresponding residues in the crystal structure of trypsin. The most promising model candidate was synthesized and tested for its catalytic activity. Copyright: (C) 2003 European Peptide Society and John Wiley Sons, Ltd.
Περιγραφή
Λέξεις-κλειδιά
branched cyclic peptide, computational screening, cyclization on solid support, molecular dynamics, serine protease models, design, chemistry, trypsin
Θεματική κατηγορία
Παραπομπή
Σύνδεσμος
<Go to ISI>://000181997900001
http://onlinelibrary.wiley.com/store/10.1002/psc.441/asset/441_ftp.pdf?v=1&t=h0e0sl7w&s=baf5d69673c92264579ced5dd85444ec58ffd288
http://onlinelibrary.wiley.com/store/10.1002/psc.441/asset/441_ftp.pdf?v=1&t=h0e0sl7w&s=baf5d69673c92264579ced5dd85444ec58ffd288
Γλώσσα
en
Εκδίδον τμήμα/τομέας
Όνομα επιβλέποντος
Εξεταστική επιτροπή
Γενική Περιγραφή / Σχόλια
Ίδρυμα και Σχολή/Τμήμα του υποβάλλοντος
Πανεπιστήμιο Ιωαννίνων. Σχολή Θετικών Επιστημών. Τμήμα Χημείας