title: Molecular dynamics simulations indicate that tyrosineB10 limits motions of distal histidine to regulate CO binding in soybean leghemoglobin.
abstract: Myoglobin (Mb) uses strong electrostatic interaction in its distal heme pocket to regulate ligand binding. The mechanism of regulation of ligand binding in soybean leghemoglobin a (Lba) has been enigmatic and more so due to the absence of gaseous ligand bound atomic resolution three-dimensional structure of the plant globin. While the 20-fold higher oxygen affinity of Lba compared with Mb is required for its dual physiological function, the mechanism by which this high affinity is achieved is only emerging. Extensive mutational analysis combined with kinetic and CO-FT-IR spectroscopic investigation led to the hypothesis that Lba depended on weakened electrostatic interaction between distal HisE7 and bound ligand achieved by invoking B10Tyr, which itself hydrogen bonds with HisE7 thus restricting it in a single conformation detrimental to Mb-like strong electrostatic interaction. Such theory has been re-assessed here using CO-Lba in silico model and molecular dynamics simulation. The investigation supports the presence of at least two major conformations of HisE7 in Lba brought about by imidazole ring flip, one of which makes hydrogen bonds effectively with B10Tyr affecting the former's ability to stabilize bound ligand, while the other does not. However, HisE7 in Lba has limited conformational freedom unlike high frequency of imidazole ring flips observed in Mb and in TyrB10Leu mutant of Lba. Thus, it appears that TyrB10 limits the conformational freedom of distal His in Lba, tuning down ligand dissociation rate constant by reducing the strength of hydrogen bonding to bound ligand, which the freedom of distal His of Mb allows.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
authors.forename: Smriti
authors.initials: S
authors.lastname: Sharma
authors.affiliation: Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India.
authors.forename: Suman
authors.initials: S
authors.lastname: Kundu
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
authors.forename: Pradipta
authors.initials: P
authors.lastname: Bandyopadhyay
mesh_terms: D002248:Carbon Monoxide / Q000737:chemistry / Q000378:metabolism*; D006639:Histidine / Q000737:chemistry* / Q000378:metabolism; D007874:Leghemoglobin / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D013025:Glycine max / Q000737:chemistry*; D014443:Tyrosine / Q000737:chemistry* / Q000378:metabolism
chemical_list: D007874:Leghemoglobin; D014443:Tyrosine; D006639:Histidine; D002248:Carbon Monoxide; D010100:Oxygen
keywords: CO bound leghemoglobin model; HisE7 conformational freedom; TyrB10; imidazole ring flip; molecular dynamics simulation of leghemoglobin