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Sobieraj M, Kalinowski MW, Lesyng B. Granger causality based on vector time series and quaternion algebra with possible applications to molecular dynamics data analysis. Phys Rev E 2023; 108:055311. [PMID: 38115496 DOI: 10.1103/physreve.108.055311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/04/2023] [Indexed: 12/21/2023]
Abstract
Causal analysis plays a significant role in physics, chemistry, and biology. Dynamics of complex (bio)molecular and nanosystems, from the microscopic to the macroscopic scale, are characterized by time-dependent vectors such as positions, forces, momenta, angular momenta, or torques. Identification and analysis of causal relationships between these time-dependent signals is an important problem in the multidimensional time-series analysis and is of great practical importance in describing the properties of such dynamical systems, and to understanding their functionality. For linear stochastic systems characterized by multidimensional scalar signals, Granger proposed a simple procedure to detect causal relationships, called Granger causality. In this study we extended this formalism to vector signals representing physical vector quantities. For this purpose, we used quaternion algebra, where vector signals are treated as time-dependent quaternions. The developed analytical model is based on the autoregressive formalism. This formalism (Q-MVAR) and its numerical implementation were validated using two simple dynamic models: a rigid body model represented by a benzenelike molecular fragment, interacting with a short-range harmonic potential with a wall, as well as a system of three model atomic balls moving inside a soft spherical surface and interacting with long range electrostatic forces. Although the motivation to these studies was the analysis of classical motions in complex (bio)molecular systems, described with a mechanical model and based on molecular dynamics (MD) simulations, in particular coarse-grained ones, it should be noted that the developed extended formalism can be applied to any system composed of many rigid elements that interact with arbitrary potentials and are characterized by complex internal motions. A description of the detailed procedure for calculating causality measures is provided in the Appendices of the Supplemental Material. This formalism and the prototype of its numerical implementation can be further developed and applied in many different fields of physical, natural, and engineering sciences.
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Affiliation(s)
- Marcin Sobieraj
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | | | - Bogdan Lesyng
- Division of Biophysics and Center for Machine Learning, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
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ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths. J Comput Aided Mol Des 2019; 33:705-727. [PMID: 31435895 DOI: 10.1007/s10822-019-00216-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
The possible functions of a protein are strongly related to its structural rearrangements in the presence of other molecules or environmental changes. Hence, the evaluation of transition paths of proteins, which encodes conformational changes between stable states, is important since it may reveal the underlying mechanisms of the biochemical processes related to these motions. During the last few decades, different geometry-based methods have been proposed to predict such transition paths. However, in the cases where the solution requires complex motions, these methods, which typically constrain only locally the molecular structures, could produce physically irrelevant solutions involving self-intersection. Recently, we have proposed ART-RRT, an efficient method for finding ligand-unbinding pathways. It relies on the exploration of energy valleys in low-dimensional spaces, taking advantage of some mechanisms inspired from computer graphics to ensure the consistency of molecular structures. This article extends ART-RRT to the problem of finding probable conformational transition between two stable states for proteins. It relies on a bidirectional exploration rooted on the two end states and introduces an original strategy to attempt connections between the explored regions. The resulting method is able to produce at low computational cost biologically realistic paths free from self-intersection. These paths can serve as valuable input to other advanced methods for the study of proteins. A better understanding of conformational changes of proteins is important since it may reveal the underlying mechanisms of the biochemical processes related to such motions. Recently, the ART-RRT method has been introduced for finding ligand-unbinding pathways. This article presents an adaptation of the method for finding probable conformational transition between two stable states of a protein. The method is not only computationally cost-effective but also able to produce biologically realistic paths which are free from self-intersection.
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Ho KC, Hamelberg D. Combinatorial Coarse-Graining of Molecular Dynamics Simulations for Detecting Relationships between Local Configurations and Overall Conformations. J Chem Theory Comput 2018; 14:6026-6034. [DOI: 10.1021/acs.jctc.8b00333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ka Chun Ho
- Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
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Maji S, Shahoei R, Schulten K, Frank J. Quantitative Characterization of Domain Motions in Molecular Machines. J Phys Chem B 2017; 121:3747-3756. [PMID: 28199113 PMCID: PMC5479934 DOI: 10.1021/acs.jpcb.6b10732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories. Our objective is to characterize the motion of each domain as a coordinate transformation using moments of inertia tensor, a method we developed earlier. What has been missing until now are ancillary tools that make this task practical, general, and biologically informative. We have provided a comprehensive solution to this task with a set of tools implemented on the VMD platform. These tools address the need for reproducible segmentation of domains, and provide a generalized description of their motions using principal axes of inertia. Although this methodology has been specifically developed for studying ribosome motion, it is applicable to any molecular machine.
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Affiliation(s)
- Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University
| | - Rezvan Shahoei
- Department of Physics, University of Illinois at Urbana-Champaign
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University
- Howard Hughes Medical Institute, Columbia University
- Department of Biological Sciences, Columbia University
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Calligari P, Gerolin M, Abergel D, Polimeno A. Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions. J Chem Theory Comput 2016; 13:309-319. [DOI: 10.1021/acs.jctc.6b00702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paolo Calligari
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
| | - Marco Gerolin
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
| | - Daniel Abergel
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
| | - Antonino Polimeno
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
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Callaway DJ, Bu Z. Visualizing the nanoscale: protein internal dynamics and neutron spin echo spectroscopy. Curr Opin Struct Biol 2016; 42:1-5. [PMID: 27756047 DOI: 10.1016/j.sbi.2016.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/01/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Abstract
The most complex molecular machines are proteins found within cells. Protein dynamics, in particular dynamics on nanoscales, presents us with a novel paradigm for cell signaling: the idea that proteins and protein complexes can communicate directly within themselves to effect long-range information transfer, via coupled domains and correlated residue clusters. This idea has been little explored, in large part because of a paucity of experimental techniques that can address the necessary questions. Here we review recent progress in developing a promising new approach, neutron spin echo spectroscopy.
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Affiliation(s)
- David Je Callaway
- Department of Chemistry and Biochemistry, City College of New York, PhD Programs in Chemistry and Biochemistry, CUNY, United States
| | - Zimei Bu
- Department of Chemistry and Biochemistry, City College of New York, PhD Programs in Chemistry and Biochemistry, CUNY, United States.
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Daniluk P, Wilczyński B, Lesyng B. WeBIAS: a web server for publishing bioinformatics applications. BMC Res Notes 2015; 8:628. [PMID: 26526344 PMCID: PMC4629404 DOI: 10.1186/s13104-015-1622-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/26/2015] [Indexed: 01/01/2023] Open
Abstract
Background One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. Results In this note we present WeBIAS—a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias. Conclusions WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.
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Affiliation(s)
- Paweł Daniluk
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Pawińskiego 5, 02-106, Warsaw, Poland. .,Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
| | | | - Bogdan Lesyng
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Pawińskiego 5, 02-106, Warsaw, Poland. .,Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
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