Molecular Dynamics Models of Two Proposed Protein Structures of Salmon Protamine

Abstract

Listen

Translate article

Protamine is an arginine rich 32 residue DNA binding protein. It is hypothesized that protamine allows DNA to be densely packed in the later stages of spermogenesis, although no experimental structures of DNA-bound protamine have been solved. We present models of two possible bound structures for salmon protamine to DNA. The first structure has an extended conformation within the major groove (s1) and a second structure modelled with an alpha-helix between the 19th and 23rd residues (s2). These protamine structures were modeled into a 40mer of double stranded B-form DNA and simulated by molecular dynamics with explicit water using the Amber99SB force field. The structure of protamine bound DNA did not significantly differ from a control simulation of DNA. The positively charged protamine displaced sodium counter ions from the DNA backbone decreasing the density of sodium around the nucleotide. The arginines additionally displaced the water molecules within 20 A from the phosphates on the DNA backbone. Calculated binding energies for the s1 and s2 protamine:DNA complexes were −680.6 kJ/mol and −692.7 kJ/mol, respectively. The protamine displacing the water and counter ions could allow DNA packing with greater density, while retaining a near-B-form DNA structure.