CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

<div><p>Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at <a href="http://www.caver.cz">http://www.caver.cz</a>.</p> </div

Characteristics of the top ranked tunnels of DhaA identified by CAVER 3.0 in molecular dynamics trajectory using the probe radius of 0.9 Å and the clustering threshold of 3.5.

a<p>number of snapshots in which at least one pathway with bottleneck radius ≥0.9 Å was identified;</p>b<p>number of snapshots in which at least one pathway with bottleneck radius ≥1.4 Å was identified;</p>c<p>characteristics averaged over identified pathways (i.e. pathways with bottleneck radius ≥0.9 Å), real values will be lower, especially for p1a′, p1b, p2a, p2c and p3 tunnels, which were identified only in a small portion of snapshots.</p

Comparison of the DhaA tunnels identified by CAVER 3.0 with the previously proposed pathways.

<p>(A) The top ranked collective pathways identified throughout the molecular dynamics simulation of DhaA by CAVER 3.0 are all depicted in one frame as pathway centerlines. The p2a and p2b tunnels were initially identified as one collective pathway—p2ab—using the clustering threshold of 4.3. Decreasing the clustering threshold to 3.5 led to the separation of the p2a and p2b tunnels as well as the splitting of the p1 collective pathway into three clusters—p1a, p1a′ and p1b. A random subsample of identified tunnels is shown for clarity. (B) Representative DhaA pathways (surface representation) for the release of products and/or exchange of water solvent as identified previously by RAMD and classical MD simulations <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002708#pcbi.1002708-Klvana1" target="_blank">[15]</a>.</p

Time evolution of the bottleneck radii of DhaA tunnels identified by CAVER 3.0.

<p>The color map ranges from very narrow (green) to wide (red) bottlenecks. White color indicates that no pathway with bottleneck radius ≥0.9 Å was identified for the given pathway cluster in the given snapshot.</p

The Indo-European flyway:opportunities and constraints reflected by Common Rosefinches breeding across Europe

Abstract Aim: The configuration of the earth's landmasses influences global weather systems and spatiotemporal resource availability, thereby shaping biogeographical patterns and migratory routes of animals. Here, we aim to identify potential migratory barriers and corridors, as well as general migration strategies within the understudied Indo-European flyway. Location: Europe, Central Asia. Major taxon studied: Common rosefinches. Methods: We used a combination of theoretical optimization modelling and empirical tracking of Common Rosefinches (Carpodacus erythrinus) breeding across a large latitudinal gradient in Europe. First, we identified optimal migration routes driven by wind and resource availability along the Indo-European flyway. Second, we tracked rosefinches from five breeding populations using light-level geolocators. Finally, we compared to what extent empirical tracks overlapped with the modelled optimal routes. Results: In autumn, theoretical wind driven migration routes formed a broad-front corridor connecting Europe and the Indian Subcontinent while the theoretical resource driven routes formed a distinct north-south divide. The latter pattern also reflected the rosefinch tracks with all but the most southerly breeding birds making a northern detour towards non-breeding sites in Pakistan and India. In spring, the resource availability model predicted a similar migratory divide, however, the southern route seemed relatively more favourable and closely matched with the optimal wind driven migration routes. Spring tracking data showed larger overlap with the modelled wind driven migration routes compared to the resource driven routes. Main conclusions: Optimal wind and resource driven migration routes along the Indo-European flyway are seasonally specific and to a large extend do not overlap with one another. Under these conditions, migratory birds adopt seasonally distinct migration strategies following energy minimization strategy in autumn, driven by resource availability, and time minimizing strategy in spring, driven by wind conditions. Our optimal migration models can be applied worldwide and used to validate against empirical data to explain large-scale biogeographic pattern of migratory animals