Paper Citing NAMD - Abstract
de Brevern, A.G.; Wong, H.; Tournamille, C.; Colin, Y.; Van Kim, C.L.; Etchebest, C.
A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC)
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1724:288-306, AUG 5 2005
The Duffy antigen/receptor for chemokine (DARC) is an erythrocyte receptor for malaria parasites (Plasmodium vivax and Plasmodium knowlesi) and for chemokines. In contrast to other chemokine receptors, DARC is a promiscuous receptor that binds chemokines of both CC and CXC classes. The four extracellular domains (ECDs) of DARC are essential for its interaction with chemokines, whilst the first (ECD1) is sufficient for the interaction with malaria erythrocyte-binding protein. In this study, we elaborate and analyze structural models of the DARC. The construction of the 3D models is based on a comparative modeling process and on the use of many procedures to predict transmembrane segments and to detect far homologous proteins with known structures. Threading, ab initio, secondary structure and Protein Blocks approaches are used to build a very large number of models. The conformational exploration of the ECDs is performed with simulated annealing. The second and fourth ECDs are strongly constrained. On the contrary, the ECD1 is highly flexible, but seems composed of three consecutive regions: a small beta-sheet, a linker region and a structured loop. The chosen structural models encompass most of the biochemical features and reflect the known experimental data. They may be used to analyze functional interaction properties. (c) 2005 Elsevier B.V. All rights reserved.
