A Molecular Dynamics Study of Reovirus Attachment Protein σ1 Reveals Conformational Changes in σ1 Structure

摘要

Molecular dynamics simulations were performed using the recently determined crystal structure of the reovirus attachment protein, σ1. These studies were conducted to improve an understanding of two unique features of σ1 structure: the protonation state of Asp³⁴⁵, which is buried in the σ1 trimer interface, and the flexibility of the protein at a defined region below the receptor-binding head domain. Three copies of aspartic acids Asp³⁴⁵ and Asp³⁴⁶ cluster in a solvent-inaccessible and hydrophobic region at the σ1 trimer interface. These residues are hypothesized to mediate conformational changes in σ1 during viral attachment or cell entry. Our results indicate that protonation of Asp³⁴⁵ is essential to the integrity of the trimeric structure seen by x-ray crystallography, whereas deprotonation induces structural changes that destabilize the trimer interface. This finding was confirmed by electrostatic calculations using the finite difference Poisson-Boltzmann method. Earlier studies show that σ1 can exist in retracted and extended conformations on the viral surface. Since protonated Asp³⁴⁵ is necessary to form a stable, extended trimer, our results suggest that protonation of Asp³⁴⁵ may allow for a structural transition from a partially detrimerized molecule to the fully formed trimer seen in the crystal structure. Additional studies were conducted to quantify the previously observed flexibility of σ1 at a defined region below the receptor-binding head domain. Increased mobility was observed for three polar residues (Ser²⁹¹, Thr²⁹², and Ser²⁹³) located within an insertion between the second and third β-spiral repeats of the crystallized portion of the σ1 tail. These amino acids interact with water molecules of the solvent bulk and are responsible for oscillating movement of the head of ∼50° during 5 ns of simulations. This flexibility may facilitate viral attachment and also function in cell entry and disassembly. These findings provide new insights about the conformational dynamics of σ1 that likely underlie the initiation of the reovirus infectious cycle.