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. 2004 Jun;86(6):3423-31.
doi: 10.1529/biophysj.103.030825.

A molecular dynamics study of reovirus attachment protein sigma1 reveals conformational changes in sigma1 structure

Andrea Cavalli  1 , Andrea E Prota, Thilo Stehle, Terence S Dermody, Maurizio Recanatini, Gerd Folkers, Leonardo Scapozza
Affiliations

A molecular dynamics study of reovirus attachment protein sigma1 reveals conformational changes in sigma1 structure

Andrea Cavalli et al. Biophys J. 2004 Jun.

Abstract

Molecular dynamics simulations were performed using the recently determined crystal structure of the reovirus attachment protein, sigma1. These studies were conducted to improve an understanding of two unique features of sigma1 structure: the protonation state of Asp(345), which is buried in the sigma1 trimer interface, and the flexibility of the protein at a defined region below the receptor-binding head domain. Three copies of aspartic acids Asp(345) and Asp(346) cluster in a solvent-inaccessible and hydrophobic region at the sigma1 trimer interface. These residues are hypothesized to mediate conformational changes in sigma1 during viral attachment or cell entry. Our results indicate that protonation of Asp(345) 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 sigma1 can exist in retracted and extended conformations on the viral surface. Since protonated Asp(345) is necessary to form a stable, extended trimer, our results suggest that protonation of Asp(345) 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 sigma1 at a defined region below the receptor-binding head domain. Increased mobility was observed for three polar residues (Ser(291), Thr(292), and Ser(293)) located within an insertion between the second and third beta-spiral repeats of the crystallized portion of the sigma1 tail. These amino acids interact with water molecules of the solvent bulk and are responsible for oscillating movement of the head of approximately 50 degrees 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 sigma1 that likely underlie the initiation of the reovirus infectious cycle.

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Figures

FIGURE 1
FIGURE 1
Ribbon tracing of the crystallized C-terminal fragment of reovirus attachment protein σ1. Monomers A, B, and C of σ1 are shown in orange, cyan, and purple, respectively. Each monomer consists of a compact head domain and a fibrous tail. The different protein regions are annotated.
FIGURE 2
FIGURE 2
RMSD values of σ1 backbone atoms. (A) RMSD values from the minimized crystallographic structure of backbone atoms (black) of σ1 simulated with protonated Asp345. The RMSD of the backbone atoms of σ1 head (dark shaded), tail (light shaded), and “head + tail” (shaded) are also shown, revealing that rigid-body segmental motions of the head with respect to the tail may be responsible for the overall dynamic behavior. (B) RMSD values from the minimized crystallographic structure of backbone atoms (black) of σ1 simulated with deprotonated Asp345. The RMSD of the backbone atoms of both the σ1 head (dark shaded) and tail (light shaded) are also shown.
FIGURE 3
FIGURE 3
The protonation state of Asp345. (A) RMSD values from the minimized crystallographic structure of all nonhydrogen atoms of Tyr313, Arg314, Asp345, Asp346, and Tyr347 during the simulation with protonated (ASH345, black) and deprotonated (ASP345, shaded) Asp345. The dynamic behavior of these residues is strongly dependent on the protonation state of Asp345. (B) Asp345 and Asp346 residues as they appear interlinked in the trimer from a minimized snapshot at 5 ns of the MD simulation performed with ASH345 (protonated Asp345, left) and ASP345 (deprotonated Asp345, right). The hydrogen bond pattern (in red) that was observed in the crystal structure is only preserved during the simulation of σ1 with protonated Asp345 (ASH345, left).
FIGURE 4
FIGURE 4
Separation of the σ1 head. (A) Average interchain distances (AB, AC, BC) during 5 ns of MD simulations between Cα carbons of Tyr313, Arg314, Asp345, Asp346, and Tyr347 belonging to two different chains. The average distances calculated during 5 ns of MD simulations with protonated and deprotonated Asp345 are shown in black and shaded, respectively. The average distances calculated during the MD simulations using σ1 containing ASH345 (black) are similar to those observed in the crystal structure. (B) The σ1 head after 5 ns of MD simulations. The Connolly surface of the residues at the base of the head is shown (radius 1.4 Å). The σ1 heads appear to separate during the simulation with fully ionized Asp345-containing σ1. The Asp-rich region might trigger separation of the σ1 heads.
FIGURE 5
FIGURE 5
RMSD values of all σ1 amino acids. (A) Average RMSD values of the backbone atoms of each amino acid from the minimized crystallographic structure within the simulation interval 1–2 ns. (B) Average RMSD values of the backbone atoms of each amino acid from the minimized crystallographic structure within the simulation interval 2–3 ns. (C) Average RMSD values of the backbone atoms of each amino acid from the minimized crystallographic structure within the simulation interval 3.5–4.5 ns.
FIGURE 6
FIGURE 6
The basis of σ1 flexibility. (A) The σ1 crystal structure (red) and snapshots at 2.5 ns (green) and 4 ns (blue) from the ASH345-based MD simulation. (B) Superimposition of two snapshots representative of the overall protein dynamics onto the crystallographic structure of σ1. The three-dimensional alignment was accomplished by fitting the backbone atoms of amino acids (255–288) of the σ1 tail. (C) Schematic representation of the three superimposed structures. Angle values were defined by first estimating the centers of mass (centroids) of the protein head, tail, and head-tail junction. The axes of both head and tail were defined as the segments connecting the head centroid to the head-tail centroid, and from the tail centroid to the head-tail centroid, respectively. The oscillating movement was estimated as the angle between the head axis of two different snapshots (maximum value of ∼50° was calculated between a snapshot at 2.5 ns and a snapshot at 4 ns). The bending down movement of the head was defined as the angle between the head and tail axes (maximum calculated value ∼150°).
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References

    1. Barton, E. S., J. C. Forrest, J. L. Connolly, J. D. Chappell, Y. Liu, F. J. Schnell, A. Nusrat, C. A. Parkos, and T. S. Dermody. 2001. Junction adhesion molecule is a receptor for reovirus. Cell. 104:441–451. - PubMed
    1. Berendsen, H. J. C., J. P. M. Postma, W. F. Van Gunsteren, A. Di Nola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684–3690.
    1. Bullough, P. A., F. M. Hughson, J. J. Skehel, and D. C. Wiley. 1994a. Structure of influenza haemagglutinin at the pH of membrane fusion. Nature. 371:37–43. - PubMed
    1. Bullough, P. A., F. M. Hughson, A. C. Treharne, R. W. Ruigrok, J. J. Skehel, and D. C. Wiley. 1994b. Crystals of a fragment of influenza haemagglutinin in the low pH induced conformation. J. Mol. Biol. 236:1262–1265. - PubMed
    1. Case, D. A., D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III, W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz, R. V. Stanton, J. J. Vincent, M. Crowley, D. M. Ferguson, R. J. Radmer, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollman. 1999. AMBER 6. University of California, San Francisco, CA.

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