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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.02.538537. [PMID: 37205542 PMCID: PMC10187166 DOI: 10.1101/2023.05.02.538537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
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2
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Hernández‐Sánchez I, Rindfleisch T, Alpers J, Dulle M, Garvey CJ, Knox‐Brown P, Miettinen MS, Nagy G, Pusterla JM, Rekas A, Shou K, Stadler AM, Walther D, Wolff M, Zuther E, Thalhammer A. Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity. Protein Sci 2024; 33:e4989. [PMID: 38659213 PMCID: PMC11043620 DOI: 10.1002/pro.4989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/09/2024] [Accepted: 03/31/2024] [Indexed: 04/26/2024]
Abstract
Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an α-helical molecular recognition feature (α-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.
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Affiliation(s)
- Itzell Hernández‐Sánchez
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center for Desert Agriculture, Biological and Environmental Science and Engineering DivisionKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Tobias Rindfleisch
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
| | - Jessica Alpers
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Dulle
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | | | - Patrick Knox‐Brown
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Present address:
Department of Discovery Pharmaceutical SciencesMerck & Co., Inc.South San FranciscoCaliforniaUSA
| | - Markus S. Miettinen
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesPotsdamGermany
| | - Gergely Nagy
- Neutron Scattering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Julio M. Pusterla
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | - Agata Rekas
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
| | - Keyun Shou
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Dirk Walther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Wolff
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
| | - Ellen Zuther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center of Artificial Intelligence in Public Health Research (ZKI‐PH)Robert Koch InstituteBerlinGermany
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Nencini R, Regnier MLG, Backlund SM, Mantzari E, Dunn CD, Ollila OHS. Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations. Commun Chem 2024; 7:28. [PMID: 38351219 PMCID: PMC10864328 DOI: 10.1038/s42004-024-01115-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not straightforward. Here we show that the dynamic landscape of peptide-containing molecular assemblies can be determined by a synergistic combination of solution state NMR experiments and molecular dynamics (MD) simulations. Solution state NMR experiments are straightforward to implement without an excessive amount of sample, while direct combination of spin relaxation data to MD simulations enables interpretation of dynamic landscapes of peptides and other aggregated molecules. To demonstrate this, we interpret NMR data from transmembrane, peripheral, and tail anchored peptides embedded in micelles. Our results indicate that peptides and detergent molecules do not rotate together as a rigid body, but peptides rotate in a viscous medium composed of detergent micelle. Spin relaxation times also provide indirect information on peptide conformational ensembles. This work gives new perspectives on peptide dynamics in complex biomolecular assemblies.
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Affiliation(s)
- Ricky Nencini
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Cory D Dunn
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- VTT Technical Research Centre of Finland, Espoo, Finland.
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4
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake. Nat Commun 2024; 15:331. [PMID: 38184686 PMCID: PMC10771500 DOI: 10.1038/s41467-023-44606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France.
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5
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Pollet RM, Foley MH, Kumar SS, Elmore A, Jabara NT, Venkatesh S, Vasconcelos Pereira G, Martens EC, Koropatkin NM. Multiple TonB homologs are important for carbohydrate utilization by Bacteroides thetaiotaomicron. J Bacteriol 2023; 205:e0021823. [PMID: 37874167 PMCID: PMC10662123 DOI: 10.1128/jb.00218-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The human gut microbiota, including Bacteroides, is required for the degradation of otherwise undigestible polysaccharides. The gut microbiota uses polysaccharides as an energy source, and fermentation products such as short-chain fatty acids are beneficial to the human host. This use of polysaccharides is dependent on the proper pairing of a TonB protein with polysaccharide-specific TonB-dependent transporters; however, the formation of these protein complexes is poorly understood. In this study, we examine the role of 11 predicted TonB homologs in polysaccharide uptake. We show that two proteins, TonB4 and TonB6, may be functionally redundant. This may allow for the development of drugs targeting Bacteroides species containing only a TonB4 homolog with limited impact on species encoding the redundant TonB6.
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Affiliation(s)
- Rebecca M. Pollet
- Department of Chemistry, Vassar College, Poughkeepsie, New York, USA
- Biochemistry Program, Vassar College, Poughkeepsie, New York, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Matthew H. Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Supriya Suresh Kumar
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amanda Elmore
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Sameeksha Venkatesh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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6
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552980. [PMID: 37609138 PMCID: PMC10441417 DOI: 10.1101/2023.08.11.552980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015 Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
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7
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Pollet RM, Foley MH, Kumar SS, Elmore A, Jabara NT, Venkatesh S, Pereira GV, Martens EC, Koropatkin NM. Multiple TonB Homologs are Important for Carbohydrate Utilization by Bacteroides thetaiotaomicron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548152. [PMID: 37461508 PMCID: PMC10350073 DOI: 10.1101/2023.07.07.548152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The human gut microbiota is able to degrade otherwise undigestible polysaccharides, largely through the activity of the Bacteroides. Uptake of polysaccharides into Bacteroides is controlled by TonB-dependent transporters (TBDT) whose transport is energized by an inner membrane complex composed of the proteins TonB, ExbB, and ExbD. Bacteroides thetaiotaomicron (B. theta) encodes 11 TonB homologs which are predicted to be able to contact TBDTs to facilitate transport. However, it is not clear which TonBs are important for polysaccharide uptake. Using strains in which each of the 11 predicted tonB genes are deleted, we show that TonB4 (BT2059) is important but not essential for proper growth on starch. In the absence of TonB4, we observed an increase in abundance of TonB6 (BT2762) in the membrane of B. theta, suggesting functional redundancy of these TonB proteins. Growth of the single deletion strains on pectin galactan, chondroitin sulfate, arabinan, and levan suggests a similar functional redundancy of the TonB proteins. A search for highly homologous proteins across other Bacteroides species and recent work in B. fragilis suggests that TonB4 is widely conserved and may play a common role in polysaccharide uptake. However, proteins similar to TonB6 are found only in B. theta and closely related species suggesting that the functional redundancy of TonB4 and TonB6 may be limited across the Bacteroides. This study extends our understanding of the protein network required for polysaccharide utilization in B. theta and highlights differences in TonB complexes across Bacteroides species.
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Affiliation(s)
- Rebecca M Pollet
- Department of Chemistry, Vassar College, Poughkeepsie, NY, 12604, USA
- Biochemistry Program, Vassar College, Poughkeepsie, NY, 12604, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Supriya Suresh Kumar
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Amanda Elmore
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nisrine T Jabara
- Biochemistry Program, Vassar College, Poughkeepsie, NY, 12604, USA
| | - Sameeksha Venkatesh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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8
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Antila HS, Kav B, Miettinen MS, Martinez-Seara H, Jungwirth P, Ollila OHS. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J Phys Chem B 2022. [DOI: 10.1021/acs.jpcb.2c01954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne S. Antila
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum
Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Markus S. Miettinen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Biotechonology, University of Helsinki, Helsinki 00014, Finland
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9
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Tempra C, Ollila OHS, Javanainen M. Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension. J Chem Theory Comput 2022; 18:1862-1869. [PMID: 35133839 PMCID: PMC8908734 DOI: 10.1021/acs.jctc.1c00951] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lipid monolayers provide our lungs and eyes their functionality and serve as proxy systems in biomembrane research. Therefore, lipid monolayers have been studied intensively including using molecular dynamics simulations, which are able to probe their lateral structure and interactions with, e.g., pharmaceuticals or nanoparticles. However, such simulations have struggled in describing the forces at the air-water interface. Particularly, the surface tension of water and long-range van der Waals interactions have been considered critical, but their importance in monolayer simulations has been evaluated only separately. Here, we combine the recent C36/LJ-PME lipid force field that includes long-range van der Waals forces with water models that reproduce experimental surface tensions to elucidate the importance of these contributions in monolayer simulations. Our results suggest that a water model with correct surface tension is necessary to reproduce experimental surface pressure-area isotherms and monolayer phase behavior. The latter includes the liquid expanded and liquid condensed phases, their coexistence, and the opening of pores at the correct area per lipid upon expansion. Despite these improvements of the C36/LJ-PME with certain water models, the standard cutoff-based CHARMM36 lipid model with the 4-point OPC water model still provides the best agreement with experiments. Our results emphasize the importance of using high-quality water models in applications and parameter development in molecular dynamics simulations of biomolecules.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic.,Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
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10
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Zhang C, Zhao DX, Feng Y, Wang J, Yang ZZ. Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution. Phys Chem Chem Phys 2022; 24:4232-4250. [DOI: 10.1039/d1cp05676j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe...
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11
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Clerc I, Sagar A, Barducci A, Sibille N, Bernadó P, Cortés J. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. Comput Struct Biotechnol J 2021; 19:3817-3828. [PMID: 34285781 PMCID: PMC8273358 DOI: 10.1016/j.csbj.2021.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/15/2023] Open
Abstract
Intrinsically Disordered Proteins and Regions (IDPs/IDRs) are key components of a multitude of biological processes. Conformational malleability enables IDPs/IDRs to perform very specialized functions that cannot be accomplished by globular proteins. The functional role for most of these proteins is related to the recognition of other biomolecules to regulate biological processes or as a part of signaling pathways. Depending on the extent of disorder, the number of interacting sites and the type of partner, very different architectures for the resulting assemblies are possible. More recently, molecular condensates with liquid-like properties composed of multiple copies of IDPs and nucleic acids have been proven to regulate key processes in eukaryotic cells. The structural and kinetic details of disordered biomolecular complexes are difficult to unveil experimentally due to their inherent conformational heterogeneity. Computational approaches, alone or in combination with experimental data, have emerged as unavoidable tools to understand the functional mechanisms of this elusive type of assemblies. The level of description used, all-atom or coarse-grained, strongly depends on the size of the molecular systems and on the timescale of the investigated mechanism. In this mini-review, we describe the most relevant architectures found for molecular interactions involving IDPs/IDRs and the computational strategies applied for their investigation.
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Affiliation(s)
- Ilinka Clerc
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Alessandro Barducci
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
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12
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Kozak F, Kurzbach D. How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2097-2105. [PMID: 33995905 PMCID: PMC8085671 DOI: 10.1016/j.csbj.2021.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
We review recent advances in modeling structural ensembles of transcription factors from nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopic data, integrated with molecular dynamics (MD) simulations. We focus on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. This combination enables the deduction of functional and structural protein models even if nuclear Overhauser effects (NOEs) are too scarce for conventional structure determination. We highlight recent insights into the folding-upon-DNA binding transitions of intrinsically disordered transcription factors that could be assessed using such integrative approaches.
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Affiliation(s)
- Fanny Kozak
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
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13
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Antila HS, M. Ferreira T, Ollila OHS, Miettinen MS. Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. J Chem Inf Model 2021; 61:938-949. [PMID: 33496579 PMCID: PMC7903423 DOI: 10.1021/acs.jcim.0c01299] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin-lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of ∼1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope-not only for lipid membranes but for all biomacromolecular systems.
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Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Tiago M. Ferreira
- NMR
Group−Institute for Physics, Martin-Luther
University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | | | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
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