Protein Science Sheba protein
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by DE-SIMONE, G.
Right arrow Articles by PAVONE, V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by DE-SIMONE, G.
Right arrow Articles by PAVONE, V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Protein Science, Vol 7, Issue 2 243-253, Copyright © 1998 by Cold Spring Harbor Laboratory Press

ARTICLE

Hirunorms are true hirudin mimetics. The crystal structure of human {alpha}-thrombin-hirunorm V complex

G. DE-SIMONE, A. LOMBARDI, S. GALDIERO, F. NASTRI, R. D. MORTE, N. STAIANO, C. PEDONE, M. BOLOGNESI and V. PAVONE
Centro Interuniversitario di Ricerca su Peptidi Bioattivi, & Centro di Studio di Biocristallografia--CNR, University of Napoli ``Federico II,'' via Mezzocannone 4, 80134 Napoli, Italy

A novel class of synthetic, multisite-directed thrombin inhibitors, known as hirunorms, has been described recently. These compounds were designed to mimic the binding mode of hirudin, and they have been proven to be very strong and selective thrombin inhibitors. Here we report the crystal structure of the complex formed by human {alpha}-thrombin and hirunorm V, a 26-residue polypeptide containing non-natural amino acids, determined at 2.1 A resolution and refined to an R-factor of 0.176. The structure reveals that the inhibitor binding mode is distinctive of a true hirudin mimetic, and it highlights the molecular basis of the high inhibitory potency (K(i) is in the picomolar range) and the strong selectivity of hirunorm V. Hirunorm V interacts through the N-terminal tetrapeptide with the thrombin active site in a nonsubstrate mode; at the same time, this inhibitor specifically binds through the C-terminal segment to the fibrinogen recognition exosite. The backbone of the N-terminal tetrapeptide Chg(1)"-Val(2)"-2-Nal(3)"-Thr(4)" (Chg, cyclohexyl-glycine; 2-Nal, {beta}-(2-naphthyl)-alanine) forms a short {beta}-strand parallel to thrombin main-chain residues Ser(214)-Gly(219). The Chg(1)" side chain fills the S2 subsite, Val(2)" is located at the entrance of S1, whereas 2-Nal(3)" side chain occupies the aryl-binding site. Such backbone orientation is very close to that observed for the N-terminal residues of hirudin, and it is similar to that of the synthetic retro-binding peptide BMS-183507, but it is opposite to the proposed binding mode of fibrinogen and of small synthetic substrates. Hirunorm V C-terminal segment binds to the fibrinogen recognition exosite, similarly to what observed for hirudin C-terminal tail and related compounds. The linker polypeptide segment connecting hirunorm V N- and C-terminal regions is not observable in the electron density maps. The crystallographic analysis proves the correctness of the design and it provides a compelling proof on the interaction mechanism for this novel class of high potency multisite-directed synthetic thrombin inhibitors.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?




HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1998 by The Protein Society.