tailieunhanh - Influence of disulfide bridge on the structural stability of human neuroglobin: A molecular dynamics simulation using latest data entry

In this paper, we investigated the role of the disulfide bridge in the structural stability of wild-type human neuroglobin. The classical simulation of the neuroglobin without the disulfide bridge was performed for a long simulation run of 240 ns using a new parameter set of Gromos96 force field and the latest data entry as the initial topologies. We used the analyzed data of original neuroglobin with the remained disulfide bridge to compare to the ones from this simulation. | Communications in Physics, Vol. 26, No. 2 (2016), pp. 151-157 DOI: INFLUENCE OF DISULFIDE BRIDGE ON THE STRUCTURAL STABILITY OF HUMAN NEUROGLOBIN: A MOLECULAR DYNAMICS SIMULATION USING LATEST DATA ENTRY BUI THI LE QUYEN Thai Binh University of Medicine and Pharmacy, 373 Ly Bon, Thai Binh, Vietnam. NGUYEN THI LAM HOAI AND NGO VAN THANH† Institute of Physics, Vietnam Academy of Science and Technology, 10 Daotan, Badinh, Hanoi, Vietnam. † E-mail: nvthanh@ Received 17 August 2016 Accepted for publication 15 September 2016 Abstract. In this paper, we investigated the role of the disulfide bridge in the structural stability of wild-type human neuroglobin. The classical simulation of the neuroglobin without the disulfide bridge was performed for a long simulation run of 240 ns using a new parameter set of Gromos96 force field and the latest data entry as the initial topologies. We used the analyzed data of original neuroglobin with the remained disulfide bridge to compare to the ones from this simulation. Our results showed that, the structure of neuroglobin was still very stable although the disulfide bridge was absent. There was only a few residues in B and C helices having a higher mobility. The most interesting result we obtained was that the increasing distance between the distal histidine and heme group could allow oxygen to bind more easily. Keywords: molecular dynamics simulation; neuroglobin; crystal structure of protein. Classification numbers: , , . I. INTRODUCTION In the past decade, a new member of globin family, neuroglobin (Ngb) has been discovered in the brain of vertebrates [1]. Ngb is not only expressed in the nervous system of vertebrates [1–4], but in retina, and other nerve tissues as well [5]. Ngb is composed of a single polypeptide of 151 amino acids and a heme prosthetic group which is able to bind to various gaseous ligands (O2 , NO or CO) at the central heme iron .

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