Molecular Dynamics Simulations of Hemoglobin I Active Site Mutations

Hemoglobin I (HbI) from the clam Lucina pectinata is a monomeric protein composed of 142 amino acids. Its primarily biological function is to transport hydrogen sulfide from its environment to a symbiotic bacteria. The active site of this hemoglobin has a peculiar arrangement of Phenylalanine residues [Phe29(B10), Phe43(CD1), and Phe68(E11)] and has a distal Gln64(E7). Another hemoglobin generally taken as a monomeric hemoglobin model is Myoglobin. This hemoglobin differs from Lucina Pectinata's HbI in residues His(64)E7, Leu(29)B10 and Val(68)E11. Each of these and other double site-directed mutations in the active site area were performed in HbI using PdbSwiss Viewer, followed by a molecular dynamics simulations on an aqueous solution, implemented for 2 ns with periodic boundary conditions, of each system using GROMACS simulation package version 3.2.1. Employing computer aided molecular simulations of these mutants enables the comparision between experimental data and subsequent analysis of its behavior and structural functionality. Residue fluctuation data showed that the most affected amino acid sequence for the majority of the mutations were the regions comprising residues from 42 to 58. These sequences found in the native HbI were structurally affected by the mutations by adopting different secondary structure conformations. These new secondary structure conformations lie far from the mutated active site of the hemoglobin. The conformational dynamics of protein molecules is encoded in their structure and it is a critical element of their function, thus through this study we will provide molecular-level insights into how point mutations affect protein structures.