tailieunhanh - báo cáo khoa hoc : Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation – possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold

Prediction and understanding of the folding and stability of the 3D struc-ture of proteins is still a challenge. The different atomic interactions, such as non polar contacts and hydrogen bonding, are known but their exact relative weights and roles when contributing to protein folding and stability are not identified. | IFEBS Journal Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation - possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold Andreas P. Eichenberger1 Lorna J. Smith2 and Wilfred F. van Gunsteren1 1 Laboratory of PhysicalChemistry Swiss Federallnstitute of Technology ETH Zurich Switzerland 2 Department of Chemistry Inorganic Chemistry Laboratory University of Oxford UK Keywords bio molecular simulation compact fold experimentalobservables hydrogen bonding secondary structure Correspondence W. F. van Gunsteren Laboratory of Physical Chemistry Swiss Federallnstitute of Technology ETH Wolfgang-Pauli-Strasse 10 8093 Zurich Switzerland Fax 41 44 632 10 39 Tel 41 44 632 55 02 E-mail wfvgn@ Received 12 July 2011 revised 1 November 2011 accepted 8 November 2011 doi Prediction and understanding of the folding and stability of the 3D structure of proteins is still a challenge. The different atomic interactions such as non polar contacts and hydrogen bonding are known but their exact relative weights and roles when contributing to protein folding and stability are not identified. Initiated by a previous molecular dynamics simulation of fully ester-linked hen egg white lysozyme HEWL which showed a more compact fold of the ester-linked molecule compared to the native one three variants of this protein are analyzed in the present study. These are 129-residue native HEWL partly ester-linked HEWL in which only 34 peptide linkages that are not involved in the helical or b-strand parts of native HEWL were replaced by ester linkages and fully 126 residues ester-linked HEWL. Native and partly ester-linked HEWL showed comparable behaviour whereas fully ester-linked HEWL could not maintain the native secondary structure of HEWL in the simulation and adopted a more compact fold. The conformational changes were analyzed by .