title: Molecular modeling of Gly80 and Ser80 variants of human group IID phospholipase A2 and their receptor complexes: potential basis for weight loss in chronic obstructive pulmonary disease.
abstract: Weight loss is a well known systemic manifestation of chronic obstructive pulmonary disease (COPD). A Gly80Ser mutation on human group IID secretory phospholipase A2 (sPLA2) enhances expression of the cytokines that are responsible for weight loss. In this study, we seek to establish a structural correlation of wild type sPLA2 and the Gly80Ser mutation with function. sPLA2 with glycine and serine at the 80th positions and the M-type receptor were modelled. The enzymes were docked to the receptor and molecular dynamics was carried out to 70 ns. Structural analysis revealed the enzymes to comprise three helices (H1-H3), two short helices (SH1 and SH2), and five loops including a calcium binding loop (L1-L5), and to be stabilized by seven disulfide bonds. The overall backbone folds of the two models are very similar, with main chain RMSD of less than 1 Å. The active site within the substrate binding channel shows a catalytic triad of water-His67-Asp112, showing a hydrogen bonded network. Major structural differences between wild type and mutant enzymes were observed locally at the site of the mutation and in their global conformations. These differences include: (1) loop-L3 between H2 and H3, which bears residue Gly80 in the wild type, is in a closed conformation with respect to the channel opening, while in the mutant enzyme it adopts a relatively open conformation; (2) the mutant enzyme is less compact and has higher solvent accessible surface area; and (3) interfacial binding contact surface area is greater, and the quality of interactions with the receptor is better in the mutant enzyme as compared to the wild type. Therefore, the structural differences delineated in this study are potential biophysical factors that could determine the increased potency of the mutant enzyme with macrophage receptor for cytokine secreting function, resulting in exacerbation of cachexia in COPD.
authors: Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
authors: Mohd Imran
authors: MI
authors: Khan
authors: Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
authors: Ashish Kumar
authors: AK
authors: Gupta
authors: Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
authors: Domada Ratna
authors: DR
authors: Kumar
authors: Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
authors: Manoj
authors: M
authors: Kumar
authors: Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
authors: Abdul Samarth
authors: AS
authors: Ethayathulla
authors: Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India. g.hariprasad@rediffmail.com.
authors: Gururao
authors: G
authors: Hariprasad
mesh_terms: D001665:Binding Sites; D054501:Group II Phospholipases A2 / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D029424:Pulmonary Disease, Chronic Obstructive / Q000150:complications* / Q000201:enzymology* / Q000235:genetics; D054507:Receptors, Phospholipase A2 / Q000737:chemistry*; D015431:Weight Loss / Q000235:genetics*
chemical_list: D054507:Receptors, Phospholipase A2; D054501:Group II Phospholipases A2
keywords: Chronic obstructive pulmonary disease; Conformational state; Glycine; Mutation; Phospholipase A2; Receptor interaction; Serine; Weight loss