Oligomerization of a retroviral matrix protein is facilitated by backbone flexibility on nanosecond time scale

Abstract

The oligomerization capacity of the retroviral matrix protein is an important feature that affects assembly of immature virions and their interaction with cellular membrane. A combination of NMR relaxation measurements and advanced analysis of molecular dynamics simulation trajectory provided an unprecedentedly detailed insight into internal mobility of matrix proteins of the Mason-Pfizer monkey virus. Strong evidence have been obtained that the oligomerization capacity of the wild-type matrix protein is closely related to the enhanced dynamics of several parts of its backbone on a nanosecond time scale. Increased flexibility has been observed for two regions: the loop between α-helices α2 and α3 and the C-terminal half of α-helix α3 which accommodate amino acid residues that form the oligomerization interface. On the other hand, matrix mutant R55F that has changed structure and does not exhibit any specific oligomerization in solution was found considerably more rigid. Our results document that conformational selection mechanism together with induced fit and favorable structural preorganization play an important role in the control of the oligomerization process.

Figure 1

Experimental backbone amide ¹⁵N relaxation rates R₁, R_2, steady state {¹H}-¹⁵N NOE values and R₂/R₁ ratios together with primary amino acid sequence of WT and R55F MAs.

Figure 2

Generalized order parameters for WT and R55F MAs obtained from the experiments and MD simulations. The experimental S²_LS values are shown by asterisks and for the residues subjected to the extended LS model, asterisk corresponds to S²_mf and circle to S²_f. The calculated S²(w) are plotted by bars and colored according to the window length w as indicated.

Figure 3

Correlation coefficients |r| >0.5 shown in the form of two-dimensional maps for WT and R55F MAs. The value of each correlation is color-coded according to the scale and helical regions are highlighted by thick lines.

Figure 4

Distributions of backbone torsion angles Φ and Ψ for five selected residues of helix α3 with characteristic behavior as obtained from MD simulations of monomer, dimer and trimer of WT MA. W56 is rigid in monomer and remains unchanged upon oligomerization, V59 shows a different conformation in dimer and the residues D65-Y67 narrow the distributions upon oligomerization. The occurrences are normalized with respect to the total number of snapshots in each trajectory.

Figure 5

Characteristics of S²(w) behavior and number of maxima in the histograms of dihedral angles Φ and Ψ shown for residues of WT and R55F MAs. Colors have the following meaning: green - converged S²(w); red - step-wise decrease of S²(w); yellow - a single maximum; orange - several maxima of dihedral angles.

Figure 6

Representative structures of WT MA dimer (A) and trimer (B) during MD simulation trajectory. Helices are colored as follows: α1 orange, α2 green, α3 red, α4 blue. α2α3 loop is shown in cyan. The presence of structural irregularities of helix α3 helps to optimize hydrophobic interactions within oligomerization patch.

Figure 7

Accessibility of aromatic amino acids F63, Y66, Y67 and F70 from the oligomerization interface are shown in two views for WT (A, B) and R55F (C, D) MAs. Surfaces of the neighboring helix α2 and α3α4 loop are shown in green and magenta mesh, respectively.