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

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 http://www.caver.cz.

This is a PLOS Computational Biology Software Article

     

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels

We have developed an algorithm, "MOLE," for the rapid, fully automated location and characterization of molecular channels, tunnels, and pores. This algorithm has been made freely available on the Internet (http://mole.chemi.muni.cz/) and overcomes many of the shortcomings and limitations of the recently developed CAVER software. The core of our MOLE algorithm is a Dijkstra's path search algorithm, which is applied to a Voronoi mesh. Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium channels, DNA quadruplexes, ribozymes, and the large ribosomal subunit have demonstrated that the MOLE algorithm performs well. MOLE is thus a powerful tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories in which analysis of a large number of snapshots is required.     

Exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations

Acylpeptide hydrolases (APH) catalyze the removal of an N-acylated amino acid from blocked peptides. APH is significantly more sensitive than acetylcholinesterase, a target of Alzheimer’s disease, to inhibition by organophosphorus (OP) compounds. Thus, OP compounds can be used as a tool to probe the physiological functions of APH. Here, we report the results of a computational study of molecular dynamics simulations of APH bound to the OP compounds and an exploration of the chlorpyrifos escape pathway using steered molecular dynamics (SMD) simulations. In addition, we apply SMD simulations to identify potential escape routes of chlorpyrifos from hydrolase hydrophobic cavities in the APH-inhibitor complex. Two previously proposed APH pathways were reliably identified by CAVER 3.0, with the estimated relative importance of P1 > P2 for its size. We identify the major pathway, P2, using SMD simulations, and Arg526, Glu88, Gly86, and Asn65 are identified as important residues for the ligand leaving via P2. These results may help in the design of APH-targeting drugs with improved efficacy, as well as in understanding APH selectivity of the inhibitor binding in the prolyl oligopeptidase family.     

BAPS 2: enhanced possibilities for the analysis of genetic population structure

Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset. AVAILABILITY: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.     

Alopex-B: a new, simpler, but yet faster version of the alopex training algorithm

Experimenting with some changes and simplifications to the Alopex algorithm, we obtained a new faster version (Alopex-B), that also shows lower failure rates on training attempts. Like Alopex, our version is network-architecture independent, does not require error or transfer functions to be differentiable, has a high potential for parallelism, and is stochastic (which helps avoid local minima), but unlike Alopex it follows no annealing scheme, and uses less parameters which makes it simpler to implement and to use.     

Dispatching,routing, and scheduling of two automated guided vehicles in a flexible manufacturing system

This article presents a new approach for planning the dispatching, conflict-free routing, and scheduling of automated guided vehicles in a flexible manufacturing system. The problem is solved optimally in an integrated manner, contrary to the traditional approach in which the problem is decomposed in three steps that are solved sequentially. The algorithm is based on dynamic programming and is solved on a rolling time horizon. Three dominance criteria are used to limit the size of the state space. The method finds the transportation plan minimizing the makespan (the completion time for all the tasks). Various results are discussed. A heuristic version of the algorithm is also proposed for an extension of the method to many vehicles.     

Improved AMYR program: an algorithm for the theoretical simulation of molecular associations,including geometrical and topological characterization of the dimers

Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility of carrying out energy minimizations through variable metric methods, as well as the optional calculation of geometrical and topological indices. Program AMYR has been adapted also for high-performance computing and vectorization. An interactive version of the program carries out real-time molecular graphics showing simultaneously the energy profile of the calculations.     

Stability of Ca2+-, Cd2+-, Cu2+-[illite-humic] complexes and pH influence

Decomposition of fresh plant residues in soil is expected to produce humic fractions varying in molecular size. It was hypothesized that metal adsorption by soil, to some degree, will depend on humic acid content and molecular size. The latter is expected to vary in number and type of functional groups. In this study, illite-humic complexes were used to evaluate Ca²⁺, Cd²⁺, and Cu²⁺ adsorption and how this adsorption was affected by humic acids, differing in molecular size, under various pH values. Potentiometric titration using ion-selective electrodes with a stop-and-go procedure was employed to evaluate metal-[illite-humic] complex formation. The results showed that illite-humic complexes exhibited at least two types of metal-ion adsorption sites (low and high affinity) and molecular size of humic fractions had a large potential influence on total metal adsorption but a relatively smaller influence on metal-complex stability. Relative strength of metal-ion-[illite-humic] complexes followed the order of Cu²⁺>Cd²⁺>Ca²⁺ and were affected by pH, especially for low metal-ion affinity sites. Magnitude of metal-[illite-humic] stability constants, depending on molecular size of humic fraction and pH, varied on a log-scale from 3.52 to 4.21 for Ca²⁺, 4.38 to 5.18 for Cd²⁺and from 5.23 to 5.83 for Cu²⁺. There was an approximate 5-fold difference in these stability constants between the three different sizes of humic fractions. The larger the humic fraction, the lower the metal-[illite-humic] stability constant. This revised version was published online in June 2006 with corrections to the Cover Date. This revised version was published online in June 2006 with corrections to the Cover Date. This revised version was published online in June 2006 with corrections to the Cover Date.     

Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10

The catalytic site of haloalkane dehalogenase DhlA is buried more than 10 A from the protein surface. While potential access channels to this site have been reported, the precise mechanism of substrate import and product export is still unconfirmed. We used computational methods to examine surface pockets and their putative roles in ligand access to and from the catalytic site. Computational solvent mapping moves small organic molecule as probes over the protein surface in order to identify energetically favorable sites, that is, regions that tend to bind a variety of molecules. The mapping of three DhlA structures identifies seven such regions, some of which have been previously suggested to be involved in the binding and the import/export of substrates or products. These sites are the active site, the putative entrance of the channel leading to the active site, two pockets that bind Br- ions, a pocket in the slot region, and two additional sites between the main domain and the cap of DhlA. We also performed mapping and free energy analysis of the DhlA structures using the substrate, 1,2-dichloroethane, and halide ions as probes. The findings were compared to crystallographic data and to results obtained by CAVER, a program developed for finding routes from protein clefts and cavities to the surface. Solvent mapping precisely reproduced all three Br- binding sites identified by protein crystallography and the openings to four channels found by CAVER. The analyses suggest that (i) the active site has the highest affinity for the substrate molecule, (ii) the substrate initially binds at the entrance of the main tunnel, (iii) the site Br2, close to the entrance, is likely to serve as an intermediate binding site in product export, (iv) the site Br3, induced in the structure at high concentrations of Br-, could be part of an auxiliary route for product release, and (v) three of the identified sites are likely to be entrances of water-access channels leading to the active site. For comparison, we also mapped haloalkane dehalogenases DhaA and LinB, both of which contain significantly larger and more solvent accessible binding sites than DhlA. The mapping of DhaA and LinB places the majority of probes in the active site, but most of the other six regions consistently identified in DhlA were not observed, suggesting that the more open active site eliminates the need for intermediate binding sites for the collision complex seen in DhlA.     

The diet transform of lattice patterns,equivalence relations,and similarity measures

The diet algorithm is introduced for the reduction of square-cell lattice patterns to simpler graphs that contain fewer C ₄ cells. By repeated applications of the algorithm, the lattice pattern is converted into a graph representing the skeletal structure of the pattern. Based on the algorithm, equivalence relations and dissimilarity measures are introduced for lattice patterns, providing tools for shape analysis of planar patterns, such as projections of molecular contour surfaces used in molecular design. This algorithm is applied to a series of examples, illustrating the features of the method.     

PROPHET, a national computing resource for life science research.

PROPHET is a national computing resource tailored to meet the data management and analysis needs of life scientists working in a wide variety of disciplines, ranging from pharmacology to molecular biology. The PROPHET system offers a fully integrated graphics-oriented environment designed to aid research scientists in the manipulation and analysis of scientific spreadsheets of data, graphs, molecular structures, biological simulation models, and protein and nucleic acid sequences, and it includes access to a range of molecular structure and sequence databases. This paper briefly describes the PROPHET system, some of its current capabilities, and plans for a new fully distributed version of the system now under development.     

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood

We present an evolutionary placement algorithm (EPA) and a Web server for the rapid assignment of sequence fragments (short reads) to edges of a given phylogenetic tree under the maximum-likelihood model. The accuracy of the algorithm is evaluated on several real-world data sets and compared with placement by pair-wise sequence comparison, using edit distances and BLAST. We introduce a slow and accurate as well as a fast and less accurate placement algorithm. For the slow algorithm, we develop additional heuristic techniques that yield almost the same run times as the fast version with only a small loss of accuracy. When those additional heuristics are employed, the run time of the more accurate algorithm is comparable with that of a simple BLAST search for data sets with a high number of short query sequences. Moreover, the accuracy of the EPA is significantly higher, in particular when the sample of taxa in the reference topology is sparse or inadequate. Our algorithm, which has been integrated into RAxML, therefore provides an equally fast but more accurate alternative to BLAST for tree-based inference of the evolutionary origin and composition of short sequence reads. We are also actively developing a Web server that offers a freely available service for computing read placements on trees using the EPA.     

Gibbs-Ensemble Molecular Dynamics: Liquid-Gas Equilibria for Lennard-Jones Spheres and n-Hexane

Abstract

We present a novel method to simulate phase equilibria in atomic and molecular systems. The method is a Molecular Dynamics version of the Gibbs-Ensemble Monte Carlo technique, which has been developed some years ago for the direct simulation of phase equilibria in fluid systems. The idea is to have two separate simulation boxes, which can exchange particles (or molecules) in a thermodynamically consistent fashion. Here we pres the derivation of the generalized equations of motion and discuss the relation of the resulting trajectory averages to the relevant ensemble. We test this Gibbs-Ensemble Molecular Dynamics algorithm by applying it to an atomic and a molecular system, i.e. to the liquid-gas coexistence in a Lennard-Jones fluid and in n-hexane. In both cases our results are in good accord with previous mean field and Gibbs-Ensemble Monte Carlo results as well as with the experimental data in the case of hexane. We also show that our Gibbs-Ensemble Molecular Dynamics algorithm like other Molecular Dynamics techniques can be used to study the dynamics of the system. Self-diffusion coefficients calculated with this method are in agreement with the result of conventional constant temperature Molecular Dynamics.     

A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry

A novel hybrid methodology for the automated identification of peptides via de novo integer linear optimization, local database search, and tandem mass spectrometry is presented in this article. A modified version of the de novo identification algorithm PILOT, is utilized to construct accurate de novo peptide sequences. A modified version of the local database search tool FASTA is used to query these de novo predictions against the nonredundant protein database to resolve any low-confidence amino acids in the candidate sequences. The computational burden associated with performing several alignments is alleviated with the use of distributive computing. Extensive computational studies are presented for this new hybrid methodology, as well as comparisons with MASCOT for a set of 38 quadrupole time-of-flight (QTOF) and 380 OrbiTrap tandem mass spectra. The results for our proposed hybrid method for the OrbiTrap spectra are also compared with a modified version of PepNovo, which was trained for use on high-precision tandem mass spectra, and the tag-based method InsPecT. The de novo sequences of PILOT and PepNovo are also searched against the nonredundant protein database using CIDentify to compare with the alignments achieved by our modifications of FASTA. The comparative studies demonstrate the excellent peptide identification accuracy gained from combining the strengths of our de novo method, which is based on integer linear optimization, and database driven search methods.     

GASP: software for geometric simulations of flexibility in polyhedral and molecular framework structures

Template-based geometric simulation is a specialised method for modelling flexible framework structures made up of rigid units using a simplified, localised physical model. The strengths of the method are its ability to handle large all-atom structural models rapidly and at minimal computational expense, and to provide insights into the links between local bonding and steric geometry and global flexibility. We review the implementation of geometric simulation in the ‘GASP’ software, and its application to the study of materials including zeolites, perovskites and metal–organic frameworks. The latest version (5) of GASP has significant improvements and extensions, in particular an improved algorithm for relaxation of atomic positions, and the capacity to handle both polyhedral and molecular structural units. GASP is freely available to researchers.     

GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy

Identification of protein phosphorylation sites with their cognate protein kinases (PKs) is a key step to delineate molecular dynamics and plasticity underlying a variety of cellular processes. Although nearly 10 kinase-specific prediction programs have been developed, numerous PKs have been casually classified into subgroups without a standard rule. For large scale predictions, the false positive rate has also never been addressed. In this work, we adopted a well established rule to classify PKs into a hierarchical structure with four levels, including group, family, subfamily, and single PK. In addition, we developed a simple approach to estimate the theoretically maximal false positive rates. The on-line service and local packages of the GPS (Group-based Prediction System) 2.0 were implemented in Java with the modified version of the Group-based Phosphorylation Scoring algorithm. As the first stand alone software for predicting phosphorylation, GPS 2.0 can predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy. A large scale prediction of more than 13,000 mammalian phosphorylation sites by GPS 2.0 was exhibited with great performance and remarkable accuracy. Using Aurora-B as an example, we also conducted a proteome-wide search and provided systematic prediction of Aurora-B-specific substrates including protein-protein interaction information. Thus, the GPS 2.0 is a useful tool for predicting protein phosphorylation sites and their cognate kinases and is freely available on line.     

Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era. This revised version was published online in July 2006 with corrections to the Cover Date.     

MAP-XSII: an improved program for the automatic assignment of methyl resonances in large proteins

NMR studies of large proteins have gathered much interest in recent years, especially after methyl-transverse relaxation optimized spectroscopy was successfully applied to systems as large as ~1 MDa in molecular weight. However, to fully take advantage of these spectra, there is a need for convenient and robust methods for making resonance assignments rapidly. Here, we present an improved version of our program MAP-XS (methyl assignment prediction from X-ray structure) for the automatic assignment of methyl peaks, based on nuclear Overhauser effects (NOE) correlations and chemical shifts together with available structures. No manual analysis of the NOE data is needed in this new version, which helps to further accelerate the assignment process. A refined algorithm as well as more efficient sampling produces results from single runs of MAP-XSII using unanalyzed NOE data are comparable to those achieved by the old version using manually curated data with every NOE peak correctly attributed to the two related methyl peaks; in addition, checking the results from multiple parallel runs against each other provides an effective mechanism for getting rid of the wrong assignments while keeping the correct ones, which significantly improves the reliability of final assignments. The new program is tested against three different proteins and delivers ~95 % correct assignments; positive results are also achieved for tests using different cut-off distances for NOEs, structures of lower resolutions, and ambiguous residue types.