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Vervust W, Zhang DT, Ghysels A, Roet S, van Erp TS, Riccardi E. PyRETIS 3: Conquering rare and slow events without boundaries. J Comput Chem 2024; 45:1224-1234. [PMID: 38345082 DOI: 10.1002/jcc.27319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 04/19/2024]
Abstract
We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) and its variations. Apart from a general rewiring of the internal code towards a more modular structure, several recently developed sampling strategies have been implemented. These include recently developed Monte Carlo moves to increase path decorrelation and convergence rate, and new ensemble definitions to handle the challenges of long-lived metastable states and transitions with unbounded reactant and product states. Additionally, the post-analysis software PyVisa is now embedded in the main code, allowing fast use of machine-learning algorithms for clustering and visualising collective variables in the simulation data.
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Affiliation(s)
- Wouter Vervust
- IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium
| | - Daniel T Zhang
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - An Ghysels
- IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium
| | - Sander Roet
- Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Titus S van Erp
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Enrico Riccardi
- Department of Energy Resources, University of Stavanger, Stavanger, Norway
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Zhang DT, Baldauf L, Roet S, Lervik A, van Erp TS. Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps. Proc Natl Acad Sci U S A 2024; 121:e2318731121. [PMID: 38315841 PMCID: PMC10873605 DOI: 10.1073/pnas.2318731121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Capturing rare yet pivotal events poses a significant challenge for molecular simulations. Path sampling provides a unique approach to tackle this issue without altering the potential energy landscape or dynamics, enabling recovery of both thermodynamic and kinetic information. However, despite its exponential acceleration compared to standard molecular dynamics, generating numerous trajectories can still require a long time. By harnessing our recent algorithmic innovations-particularly subtrajectory moves with high acceptance, coupled with asynchronous replica exchange featuring infinite swaps-we establish a highly parallelizable and rapidly converging path sampling protocol, compatible with diverse high-performance computing architectures. We demonstrate our approach on the liquid-vapor phase transition in superheated water, the unfolding of the chignolin protein, and water dissociation. The latter, performed at the ab initio level, achieves comparable statistical accuracy within days, in contrast to a previous study requiring over a year.
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Affiliation(s)
- Daniel T. Zhang
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
| | - Lukas Baldauf
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
| | - Sander Roet
- Department of Chemistry, Utrecht University, Utrecht3584 CH, Netherlands
| | - Anders Lervik
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
| | - Titus S. van Erp
- Department of Chemistry, Norwegian University of Science and Technology, TrondheimN-7491, Norway
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3
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Chaillet ML, van der Schot G, Gubins I, Roet S, Veltkamp RC, Förster F. Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms. Int J Mol Sci 2023; 24:13375. [PMID: 37686180 PMCID: PMC10487639 DOI: 10.3390/ijms241713375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D models that are often reliable for substantial parts of the macromolecules. However, the extent of rotational searches in particle detection has not been investigated due to computational limitations. Here, we provide a GPU implementation of TM as part of the PyTOM software package, which drastically speeds up the orientational search and allows for sampling beyond the Crowther criterion within a feasible timeframe. We quantify the improvements in sensitivity and false-discovery rate for the examples of ribosome identification and detection. Sampling at the Crowther criterion, which was effectively impossible with CPU implementations due to the extensive computation times, allows for automated extraction with high sensitivity. Consequently, we also show that an extensive angular sample renders 3D TM sensitive to the local alignment of tilt series and damage induced by focused ion beam milling. With this new release of PyTOM, we focused on integration with other software packages that support more refined subtomogram-averaging workflows. The automated classification of ribosomes by TM with appropriate angular sampling on locally corrected tomograms has a sufficiently low false-discovery rate, allowing for it to be directly used for high-resolution averaging and adequate sensitivity to reveal polysome organization.
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Affiliation(s)
- Marten L. Chaillet
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Gijs van der Schot
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Ilja Gubins
- Department of Information and Computing Sciences, Utrecht University, 3584 CC Utrecht, The Netherlands; (I.G.); (R.C.V.)
| | - Sander Roet
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Remco C. Veltkamp
- Department of Information and Computing Sciences, Utrecht University, 3584 CC Utrecht, The Netherlands; (I.G.); (R.C.V.)
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
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Roet S, Hooft F, Bolhuis PG, Swenson DWH, Vreede J. Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas. J Phys Chem B 2022; 126:10034-10044. [PMID: 36427204 PMCID: PMC9743084 DOI: 10.1021/acs.jpcb.2c06235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Flexibility is essential for many proteins to function, but can be difficult to characterize. Experiments lack resolution in space and time, while the time scales involved are prohibitively long for straightforward molecular dynamics simulations. In this work, we present a multiple state transition path sampling simulation study of a protein that has been notoriously difficult to characterize in its active state. The GTPase enzyme KRas is a signal transduction protein in pathways for cell differentiation, growth, and division. When active, KRas tightly binds guanosine triphosphate (GTP) in a rigid state. The protein-GTP complex can also visit more flexible states, in which it is not active. KRas mutations can affect the conversion between these rigid and flexible states, thus prolonging the activation of signal transduction pathways, which may result in tumor formation. In this work, we apply path sampling simulations to investigate the dynamic behavior of KRas-4B (wild type, WT) and the oncogenic mutant Q61L (Q61L). Our results show that KRas visits several conformational states, which are the same for WT and Q61L. The multiple state transition path sampling (MSTPS) method samples transitions between the different states in a single calculation. Tracking which transitions occur shows large differences between WT and Q61L. The MSTPS results further reveal that for Q61L, a route to a more flexible state is inaccessible, thus shifting the equilibrium to more rigid states. The methodology presented here enables a detailed characterization of protein flexibility on time scales not accessible with brute-force molecular dynamics simulations.
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Affiliation(s)
- Sander Roet
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands,Department
of Chemistry, Norwegian University of Science
and Technology (NTNU), NO-7491Trondheim, Norway
| | - Ferry Hooft
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands
| | - Peter G. Bolhuis
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands
| | - David W. H. Swenson
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands,Laboratoire
de Physique and Centre Blaise Pascal, CNRS, Univ Lyon, ENS de Lyon, Univ Claude Bernard, 69007Lyon, France
| | - Jocelyne Vreede
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands,
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Roet S, Zhang DT, van Erp TS. Exchanging Replicas with Unequal Cost, Infinitely and Permanently. J Phys Chem A 2022; 126:8878-8886. [DOI: 10.1021/acs.jpca.2c06004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Sander Roet
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491Trondheim, Norway
| | - Daniel T. Zhang
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491Trondheim, Norway
| | - Titus S. van Erp
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491Trondheim, Norway
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Mons E, Roet S, Kim RQ, Mulder MPC. A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations. Curr Protoc 2022; 2:e419. [PMID: 35671150 DOI: 10.1002/cpz1.419] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covalent inhibition has become more accepted in the past two decades, as illustrated by the clinical approval of several irreversible inhibitors designed to covalently modify their target. Elucidation of the structure-activity relationship and potency of such inhibitors requires a detailed kinetic evaluation. Here, we elucidate the relationship between the experimental read-out and the underlying inhibitor binding kinetics. Interactive kinetic simulation scripts are employed to highlight the effects of in vitro enzyme activity assay conditions and inhibitor binding mode, thereby showcasing which assumptions and corrections are crucial. Four stepwise protocols to assess the biochemical potency of (ir)reversible covalent enzyme inhibitors targeting a nucleophilic active site residue are included, with accompanying data analysis tailored to the covalent binding mode. Together, this will serve as a guide to make an educated decision regarding the most suitable method to assess covalent inhibition potency. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol I: Progress curve analysis of substrate association competition Basic Data Analysis Protocol 1A: Two-step irreversible covalent inhibition Basic Data Analysis Protocol 1B: One-step irreversible covalent inhibition Basic Data Analysis Protocol 1C: Two-step reversible covalent inhibition Basic Data Analysis Protocol 1D: Two-step irreversible covalent inhibition with substrate depletion Basic Protocol II: Incubation time-dependent potency IC50 (t) Basic Data Analysis Protocol 2: Two-step irreversible covalent inhibition Basic Protocol III: Preincubation time-dependent inhibition without dilution Basic Data Analysis Protocol 3: Preincubation time-dependent inhibition without dilution Basic Data Analysis Protocol 3Ai: Two-step irreversible covalent inhibition Alternative Data Analysis Protocol 3Aii: Two-step irreversible covalent inhibition Basic Data Analysis Protocol 3Bi: One-step irreversible covalent inhibition Alternative Data Analysis Protocol 3Bii: One-step irreversible covalent inhibition Basic Data Analysis Protocol 3C: Two-step reversible covalent inhibition Basic Protocol IV: Preincubation time-dependent inhibition with dilution/competition Basic Data Analysis Protocol 4: Preincubation time-dependent inhibition with dilution Basic Data Analysis Protocol 4Ai: Two-step irreversible covalent inhibition Alternative Data Analysis Protocol 4Aii: Two-step irreversible covalent inhibition Basic Data Analysis Protocol 4Bi: One-step irreversible covalent inhibition Alternative Data Analysis Protocol 4Bii: One-step irreversible covalent inhibition.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.,Current: Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Sander Roet
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Robbert Q Kim
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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Abstract
![]()
We propose to analyze
molecular dynamics (MD) output via a supervised machine
learning (ML) algorithm, the decision tree.
The approach aims to identify the predominant geometric features which
correlate with trajectories that transition between two arbitrarily
defined states. The data-driven algorithm aims to identify these features
without the bias of human “chemical intuition”. We demonstrate
the method by analyzing the proton exchange reactions in formic acid
solvated in small water clusters. The simulations were performed with ab initio MD combined with a method to efficiently sample
the rare event, path sampling. Our ML analysis identified relevant
geometric variables involved in the proton transfer reaction and how
they may change as the number of solvating water molecules changes.
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Affiliation(s)
- Sander Roet
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Christopher D Daub
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Enrico Riccardi
- Department of Informatics, UiO, Gaustadalléen 23B, 0373 Oslo, Norway
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Riccardi E, Lervik A, Roet S, Aarøen O, Erp TS. PyRETIS 2: An improbability drive for rare events. J Comput Chem 2019; 41:370-377. [DOI: 10.1002/jcc.26112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Enrico Riccardi
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Anders Lervik
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Sander Roet
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Ola Aarøen
- Department of Biotechnology and Food ScienceNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Titus S. Erp
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
- Center for Molecular Modeling (CMM)Ghent University Technologiepark 903 9052 Zwijnaarde Belgium
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