Molecular movie of nucleotide binding to a motor protein

• Published in: Biochimica et biophysica acta. General subjects Vol. 1864; no. 10; p. 129654
• Main Authors: Bondar, Ana-Nicoleta, Mishima, Hirokazu, Okamoto, Yuko
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2020
• Subjects: active sites; adenosine diphosphate; Adenosine Triphosphatases - metabolism; adenosine triphosphate; Adenosine Triphosphate - metabolism; ADP release; bacteria; Binding Sites; Cations, Divalent - metabolism; Escherichia coli - chemistry; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; H-bond networks; Hydrogen Bonding; hydrolysis; Magnesium; Magnesium - metabolism; Molecular Dynamics Simulation; molecular motor proteins; plasma membrane; Protein Binding; Protein Conformation; Protein Domains; Protein motor; SecA; SecA Proteins - chemistry; SecA Proteins - metabolism; ADP release; H-bond networks; Magnesium; Protein motor; SecA
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2020.129654

The SecA DEAD (Asp-Glu-Ala-Asp) motor protein uses binding and hydrolysis of adenosine triphosphate (ATP) to push secretory proteins across the plasma membrane of bacteria. The reaction coordinate of nucleotide exchange is unclear at the atomic level of detail. We performed multiple atomistic computations of the DEAD motor domain of SecA with different occupancies of the nucleotide and magnesium ion sites, for a total of ~1.7 μs simulation time. To characterize dynamics at the active site we analyzed hydrogen-bond networks. ATP and ADP can bind spontaneously at the interface between the nucleotide binding domains, albeit at an intermediate binding site distinct from the native site. Binding of the nucleotide is facilitated by the presence of a magnesium ion close to the glutamic group of the conserved DEAD motif. In the absence of the magnesium ion, protein interactions of the ADP molecule are perturbed. A protein hydrogen-bond network whose dynamics couples to the occupancy of the magnesium ion site helps guide the nucleotide along the nucleotide exchange path. In SecA, release of magnesium might be required to destabilize the ADP binding site prior to release of the nucleotide. We identified dynamic hydrogen-bond networks that help control nucleotide exchange in SecA, and stabilize ADP at an intermediate site that could explain slow release. The reaction coordinate of the protein motor involves complex rearrangements of a hydrogen-bond network at the active site, with perturbation of the magnesium ion site likely occurring prior to the release of ADP. [Display omitted] •An extensive network of H-bonds at the active site of SecA includes ADP•When the Mg2+ site is occupied, ADP and ATP can bind spontaneously to an intermediate binding site•In the bulk, ADP and ATP bind sodium, whose unbinding precludes native binding pose•The ADP H-bond network is perturbed when the Mg2+ site is empty