Using Local States To Drive the Sampling of Global Conformations in Proteins

Conformational changes associated with protein function often occur beyond the time scale currently accessible to unbiased molecular dynamics (MD) simulations, so that different approaches have been developed to accelerate their sampling. Here we investigate how the knowledge of backbone conformations preferentially adopted by protein fragments, as contained in precalculated libraries known as structural alphabets (SA), can be used to explore the landscape of protein conformations in MD simulations. We find that (a) enhancing the sampling of native local states in both metadynamics and steered MD simulations allows the recovery of global folded states in small proteins; (b) folded states can still be recovered when the amount of information on the native local states is reduced by using a low-resolution version of the SA, where states are clustered into macrostates; and (c) sequences of SA states derived from collections of structural motifs can be used to sample alternative conformations of preselected protein regions. The present findings have potential impact on several applications, ranging from protein model refinement to protein folding and design

Comparison of dynamic cross-correlation networks.

<p>Difference DCCM matrices (ΔDCCM) calculated between pairs of OM-bound and Apo simulations are mapped onto the initial structures of each OM-bound simulation. Edges connect residue pairs that have a positive (red) and a negative (green) ΔDCCM value, using a threshold of 0.16. Residues in the OM-binding site are represented as yellow spheres, while the CLD domain is coloured in blue.</p

OM-protein interactions.

<p>A. X-ray structure of the OM-binding site in cardiac myosin (PDB ID: 4PA0, chain A). Residues within contact distance from OM are shown as sticks and coloured according to the subdomain they belong to. B. Frequency of OM-residue contacts during OM-bound MD simulations. Each bar represents the fraction of the simulated time for which the corresponding residue was found in contact with OM (minimum distance between any non-hydrogen atom < 4 Å). Residues are labelled for frequencies larger than 0.5.</p

Mapping of C^α RMSF profiles onto the cMotorD structure.

<p>RMSF values from Apo and OM-bound simulations are colour mapped onto the cMotorD structure from blue (0 Å) to red (3.4 Å). The average structure is used for each simulation. The thickness of the tube representation is proportional to the RMSF value. High flexibility regions and the OM binding site are also labelled.</p

Collective motions in Apo and OM-bound simulations.

<p>A. Porcupine representation of PC1 (top panels) and PC2 (bottom) in ApoA1 (left panels) and OMA1 (right) simulations. The orange spikes show the direction and relative amplitude of motion of each residue along the PC. The approximate direction of the CLD hinge axis is also shown for Apo simulations (orange arrows). The two insets show the anti-correlated (Apo) and correlated (OM-bound) motions of the CLD (blue) and SH3 (green) subdomains. B. DynDom dynamic domain decomposition for ApoA1 PC1 (top) and the recovery stroke (bottom). The analysis was performed on the structures with minimum and maximum PC1 value from the MD simulation and on the experimental structures representing the pre-power stroke (PDB ID: 1QVI) and near-rigor (PDB ID: 1SR6) states for the recovery stroke. The fixed (white) and moving (yellow) domains identified by DynDom are shown, together with the hinge axis (orange) and the hinge regions (magenta).</p

Structure of the myosin motor domain and acto-myosin cycle.

<p>A. Cartoon representation of the motor domain structure (PDB ID: 4PA0 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005826#pcbi.1005826.ref008" target="_blank">8</a>]), with the subdomains highlighted in different colours and OM shown as purple spheres. The motor domain is connected to the rest of myosin through the lever arm and the regulatory domain (not shown). B. Simplified representation of the acto-myosin cycle, where myosin switches between actin-bound (bottom) and -unbound (top) states and between up and down conformations of the lever arm.</p

Communication pathways from the OM-binding site in the network of local dynamic correlations.

<p>A. The shortest paths calculated from fragment V698 (magenta) to selected functional regions are reported as purple edges for Apo (top) and OM-bound (bottom) simulations. Fragments are mapped onto the structure by using the first residue in the fragment. The functional regions (F and G helix, β3–5, Switch 2 and SH1 helix) were selected among those with a stronger preferential connection to V698 in OM-bound simulations compared to the Apo ones. The nodes in the paths are represented as spheres coloured according to the subdomain they belong to and with a radius proportional to the number of paths going through them (so that larger spheres correspond to hubs). Edge thickness is proportional to the correlation value. B. Boxplot representation of the path lengths for the shortest paths reported in A for Apo (green) and OM-bound (cyan) simulations.</p

Network of inter-residue contacts in the OM-binding site.

<p>Red edges connect pairs of residues that are found in contact for at least 70% of the simulation. All the residues within 8 Å from OM were included in the analysis. Contacts are reported for replica 1 only (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005826#pcbi.1005826.s014" target="_blank">S4 Fig</a> for all the replicas). For each chain, pairs that were consistently found in contact in both OM-bound simulations and in none of the Apo ones are labelled.</p

Pathways connecting the OM-binding site and the G-helix in the contact change network.

<p>The shortest paths connecting V698 (magenta) and G helix residues (red) in the network of OM-Apo contact changes are represented as yellow edges. The paths are calculated from a consensus contact change matrix calculated over all the simulations. Only contacts with a change in frequency larger than 0.1 were considered. The edge thickness is proportional to the difference between OM and Apo contact frequency. For each pair of endpoints, the top 5 shortest paths are represented. The nodes in the paths are represented as spheres coloured according to the subdomain they belong to and with a radius proportional to the number of paths going through them. The top 10 residues for number of paths are also labelled.</p

Bending of the relay helix during the MD simulations.

<p>The relay helix bending was measured by calculating the angle formed by residues I478, F489 and E500 (C^α atoms only). The central plot shows the probability distribution of the angle values observed during Apo (green hues) and OM-bound (blue hues) simulations. Arrows indicate the approximate value of the angle measured for representative experimental structures of the pre-power stroke state (PDB IDs shown). Apo trajectories showed a higher propensity for bent conformations (lower angles) than OM-bound simulations. The insets show representative Apo bent (green, left) and OM-bound straight (cyan, right) structures. Experimental structures of the relay helix in the near-rigor (NR, white, PDB ID: 1SR6) and pre-power stroke (PPS, magenta, PDB ID: 1QVI) state from scallop myosin are also represented as reference.</p