tailieunhanh - Báo cáo khoa học: Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach

Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic con-ditions retinol-binding protein undergoes a transition to the molten globule state, and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state. | iFEBS Journal Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach Emanuele Paci1 Lesley H. Greene2 Rachel M. Jones2 and Lorna J. Smith2 1 Institute of Molecular Biophysics Schoolof Physics and Astronomy University of Leeds UK 2 Department of Chemistry and Oxford Centre for Molecular Sciences Chemistry Research Laboratory University of Oxford UK Keywords lipocalin molecular dynamics molten globule protein folding retinol-binding protein Correspondence L. J. Smith Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK Fax 44 1865 285002 Tel 44 1865 275961 E-mail E. Paci Institute of Molecular Biophysics School of Physics and Astronomy University of Leeds Leeds LS2 9JT UK Tel 44 113 3433806 E-mail Received 25 May 2005 revised 12 July 2005 accepted 3 August 2005 Retinol-binding protein transports retinol and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic conditions retinol-binding protein undergoes a transition to the molten globule state and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state. Simulation conformers with a radius of gyration at least A greater than that of the native state contain on average 37 b-sheet secondary structure. In these conformers the central regions of the two orthogonal b-sheets that make up the b-barrel in the native protein are highly persistent. However there are sizable fluctuations for residues in the outer regions of the b-sheets and large variations in side chain packing even in the protein core. Significant conformational changes are seen in the simulation conformers for residues 85-104 b-strands E and F and the E-F loop . These changes give an opening of the retinol-binding site.

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