Representation choice shapes the interpretation of protein conformational dynamics

Abstract

Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single representation. Here, we show that representation choice is not neutral: it fundamentally shapes the conformational organization, similarity relationships, and apparent transitions inferred from identical simulation data. To complement existing representations, we introduce Orientation features, a geometrically grounded, rotation-aware encoding of protein backbone. We compare it against common descriptions across three dynamical regimes: fast-folding proteins, large-scale domain motions, and protein-protein association. Across these systems, we find that different representations emphasize complementary aspects of conformational space, and that no single representation provides a complete picture of the underlying dynamics. To facilitate systematic comparison, we developed ManiProt, a library for efficient computation and analysis of multiple protein representations. Our results motivate a comparative, representation-aware framework for the interpretation of molecular dynamics simulations.

Figures (30)

• Figure 1: Orientation Features Workflow. (1) A Local Coordinate System is constructed for each residue from the amide nitrogen (N), alpha carbon (C$\alpha$), and carbonyl carbon (C) positions, forming an orthonormal basis. (2) Each LCS is aligned to the per-residue intrinsic mean orientation and projected onto the tangent space at the identity element of SO(3), yielding features in the Lie algebra $\mathfrak{so}(3)$.
• Figure 2: Kinetic Characterization of Fast-Folding Proteins. (A) VAMP-2 scores for each molecular representation (y-axis) evaluated at the comparison lag time. Systems are shown along the x-axis. (B, left) TICA landscapes of 1FME for Orientation $\odot$ and torsion angle representations. The x- and y-axes show TIC1 and TIC2, respectively, with implied timescales annotated. Points are colored by Orientation $\odot$ cluster assignment; darker shades indicate unassigned frames. (B, right) Representative centroid structures for each cluster, shown in cartoon representation.
• Figure 3: nsp13 Gram Matrices Analysis. (A) Gram matrices for Orientation and Orientation $\odot$ representations. Axes represent time across merged trajectories; color intensity indicates pairwise inner product values. Black squares highlight closed-like conformations. Top row: full Gram matrices. Bottom row: first two rank-1 projection matrices. (B) Spearman correlation coefficients between Gram matrices and structural similarity measures. Blue bars: correlation with RMSD; red bars: correlation with lDDT. Inner bars show correlations for rank-1 components.
• Figure 4: nsp13 Clusters. (A) Clustering agreement across representations. Upper triangle: Adjusted Rand Score; lower triangle: Adjusted Mutual Information. (B) PC1–PC2 projections for each representation. Points are colored by Orientation $\odot$ cluster assignment. (C) Centroid structures of the five most populated Orientation $\odot$ clusters in panel B, aligned on the stalk and RecA1 domains. The monomeric nsp13 protein is shown in a ribbon representation, with domains color-coded as follows: ZB (orange), Stalk (pink), 1B (yellow), RecA1 (red) and RecA2 (Purple).
• Figure 5: Molecular Representations for Barnase–Barstar Association. Results for (A) Orientation $\odot$, (B) C$\alpha$ coordinates, and (C) torsion angles. In all panels: (.1) PC1 (y-axis) versus IRMSD (x-axis). Interacting frames shown in purple-to-orange gradient (by IRMSD); non-interacting frames in orange. Gray region: interquartile range $[Q_1{-}1.5\,\mathrm{IQR},\, Q_3{+}1.5\,\mathrm{IQR}]$; Pearson Correlation Coefficient (PCC) annotated. In all panels: (.2) PC1 density distributions for interacting/non-interacting states with quartile lines. In all panels: (.3) Reference structure (Barstar: light gray; Barnase: dark gray). Top 10 PC1-contributing residues highlighted in red; hydrogen bonds shown as dashed lines (red: involving contributors; blue: other).