Paper Citing NAMD - Abstract
Floquet, Nicolas; Dedieu, Stephane; Martiny, Laurent; Dallchez, Manuel; Perahia, David
Human thrombospondin's (TSP-1) C-terminal domain opens to interact with the CD-47 receptor: A molecular modeling study
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 478:103-109, OCT 1 2008
Thrombospondin-1 (TSP-1) interaction with the membranous receptor CD-47 involves the peptide RFYVVMWK( (4N-1) located in its C-terminal domain. However, the available X-ray Structure of TSP-1 describes this peptide as completely buried into a hydrophobic pocket, preventing any interaction. Where classical standard methods failed, an appropriate approach combining normal mode analysis and an adapted protocol of energy minimization identified the large amplitude motions responsible of the partial solvent exposure of 4N-1. In agreement, the obtained model of the open TSP-1 was further used for protein-protein clocking experiments against a homology model generated for CD-47. Considering the multiple applications of the CD-47 receptor as a target, Our results open new pharmacological perspectives for the design of TSP-1:CD-47 inhibitors and CD-47 antagonists. We also Suggest a common opening mechanism for proteins sharing the same fold as TSP-1. This work also Suggests the Usefulness Of Our approach in other topics in which predictions of protein-protein interactions are of importance. (c) 2008 Elsevier Inc. All rights reserved.
