Homology modeling and molecular dynamics simulations of MUC1-9/H-2K(b) complex suggest novel binding interactions
Φόρτωση...
Ημερομηνία
Συγγραφείς
Σταυρακούδης, Αθανάσιος
Tsoulos, I. G.
Uray, K.
Hudecz, F.
Apostolopoulos, V.
Τίτλος Εφημερίδας
Περιοδικό ISSN
Τίτλος τόμου
Εκδότης
Περίληψη
Τύπος
Είδος δημοσίευσης σε συνέδριο
Είδος περιοδικού
peer reviewed
Είδος εκπαιδευτικού υλικού
Όνομα συνεδρίου
Όνομα περιοδικού
Journal of Molecular Modeling
Όνομα βιβλίου
Σειρά βιβλίου
Έκδοση βιβλίου
Συμπληρωματικός/δευτερεύων τίτλος
Περιγραφή
Human MUC1 is over-expressed in human adenocarcinomas and has been used as a target for immunotherapy studies. The 9-mer MUC1-9 peptide has been identified as one of the peptides which binds to murine MHC class I H-2K(b). The structure of MUC1-9 in complex with H-2K(b) has been modeled and simulated with classical molecular dynamics, based on the x-ray structure of the SEV9 peptide/H-2K(b) complex. Two independent trajectories with the solvated complex (10 ns in length) were produced. Approximately 12 hydrogen bonds were identified during both trajectories to contribute to peptide/MHC complex, as well as 1-2 water mediated hydrogen bonds. Stability of the complex was also confirmed by buried surface area analysis, although the corresponding values were about 20% lower than those of the original x-ray structure. Interestingly, a bulged conformation of the peptide's central region, partially characterized as a beta-turn, was found exposed form the binding groove. In addition, P1 and P9 residues remained bound in the A and F binding pockets, even though there was a suggestion that P9 was more flexible. The complex lacked numerous water mediated hydrogen bonds that were present in the reference peptide x-ray structure. Moreover, local displacements of residues Asp4, Thr5 and Pro9 resulted in loss of some key interactions with the MHC molecule. This might explain the reduced affinity of the MUC1-9 peptide, relatively to SEV9, for the MHC class I H-2K(b).
Περιγραφή
Λέξεις-κλειδιά
Amino Acid Sequence, Amino Acids/chemistry, Animals, Binding Sites, H-2 Antigens/*chemistry/metabolism, Humans, Mice, *Molecular Dynamics Simulation, Mucin-1/chemistry/metabolism, Multiprotein Complexes/chemistry, Peptides/chemistry/metabolism, Protein Binding, Protein Conformation
Θεματική κατηγορία
Παραπομπή
Σύνδεσμος
http://www.ncbi.nlm.nih.gov/pubmed/21080018
Γλώσσα
en
Εκδίδον τμήμα/τομέας
Όνομα επιβλέποντος
Εξεταστική επιτροπή
Γενική Περιγραφή / Σχόλια
Ίδρυμα και Σχολή/Τμήμα του υποβάλλοντος
Πανεπιστήμιο Ιωαννίνων. Σχολή Οικονομικών και Κοινωνικών Επιστημών. Τμήμα Οικονομικών Επιστημών