1
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van Zwam MC, Dhar A, Bosman W, van Straaten W, Weijers S, Seta E, Joosten B, van Haren J, Palani S, van den Dries K. IntAct: A nondisruptive internal tagging strategy to study the organization and function of actin isoforms. PLoS Biol 2024; 22:e3002551. [PMID: 38466773 PMCID: PMC10957077 DOI: 10.1371/journal.pbio.3002551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/21/2024] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
Mammals have 6 highly conserved actin isoforms with nonredundant biological functions. The molecular basis of isoform specificity, however, remains elusive due to a lack of tools. Here, we describe the development of IntAct, an internal tagging strategy to study actin isoforms in fixed and living cells. We identified a residue pair in β-actin that permits tag integration and used knock-in cell lines to demonstrate that IntAct β-actin expression and filament incorporation is indistinguishable from wild type. Furthermore, IntAct β-actin remains associated with common actin-binding proteins (ABPs) and can be targeted in living cells. We demonstrate the usability of IntAct for actin isoform investigations by showing that actin isoform-specific distribution is maintained in human cells. Lastly, we observed a variant-dependent incorporation of tagged actin variants into yeast actin patches, cables, and cytokinetic rings demonstrating cross species applicability. Together, our data indicate that IntAct is a versatile tool to study actin isoform localization, dynamics, and molecular interactions.
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Affiliation(s)
- Maxime C. van Zwam
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anubhav Dhar
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Willem Bosman
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wendy van Straaten
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Suzanne Weijers
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Emiel Seta
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ben Joosten
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Saravanan Palani
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Koen van den Dries
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
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2
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Stoppelman JP, Ng TT, Nerenberg PS, Wang LP. Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids. J Phys Chem B 2021; 125:11927-11942. [PMID: 34668708 DOI: 10.1021/acs.jpcb.1c07547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phosphorylation of select amino acid residues is one of the most common biological mechanisms for regulating protein structures and functions. While computational modeling can be used to explore the detailed structural changes associated with phosphorylation, most molecular mechanics force fields developed for the simulation of phosphoproteins have been noted to be inconsistent with experimental data. In this work, we parameterize force fields for the phosphorylated forms of the amino acids serine, threonine, and tyrosine using the ForceBalance software package with the goal of improving agreement with experiments for these residues. Our optimized force field, denoted as FB18, is parameterized using high-quality ab initio potential energy scans and is designed to be fully compatible with the AMBER-FB15 protein force field. When utilized in MD simulations together with the TIP3P-FB water model, we find that FB18 consistently enhances the prediction of experimental quantities such as 3J NMR couplings and intramolecular hydrogen-bonding propensities in comparison to previously published models. As was reported with AMBER-FB15, we also see improved agreement with the reference QM calculations in regions at and away from local minima. We thus believe that the FB18 parameter set provides a promising route for the further investigation of the varied effects of protein phosphorylation.
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Affiliation(s)
- John P Stoppelman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Tracey T Ng
- Department of Physics & Astronomy, California State University, Los Angeles, California 90032, United States
| | - Paul S Nerenberg
- Department of Physics & Astronomy, California State University, Los Angeles, California 90032, United States.,Department of Biological Sciences, California State University, Los Angeles, California 90032, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
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3
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Gruszczynska-Biegala J, Stefan A, Kasprzak AA, Dobryszycki P, Khaitlina S, Strzelecka-Gołaszewska H. Myopathy-Sensitive G-Actin Segment 227-235 Is Involved in Salt-Induced Stabilization of Contacts within the Actin Filament. Int J Mol Sci 2021; 22:ijms22052327. [PMID: 33652657 PMCID: PMC7956362 DOI: 10.3390/ijms22052327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 01/09/2023] Open
Abstract
Formation of stable actin filaments, critically important for actin functions, is determined by the ionic strength of the solution. However, not much is known about the elements of the actin fold involved in ionic-strength-dependent filament stabilization. In this work, F-actin was destabilized by Cu2+ binding to Cys374, and the effects of solvent conditions on the dynamic properties of F-actin were correlated with the involvement of Segment 227-235 in filament stabilization. The results of our work show that the presence of Mg2+ at the high-affinity cation binding site of Cu-modified actin polymerized with MgCl2 strongly enhances the rate of filament subunit exchange and promotes the filament instability. In the presence of 0.1 M KCl, the filament subunit exchange was 2-3-fold lower than that in the MgCl2-polymerized F-actin. This effect correlates with the reduced accessibility of the D-loop and Segment 227-235 on opposite filament strands, consistent with an ionic-strength-dependent conformational change that modulates involvement of Segment 227-235 in stabilization of the intermonomer interface. KCl may restrict the mobility of the α-helix encompassing part of Segment 227-235 and/or be bound to Asp236 at the boundary of Segment 227-235. These results provide experimental evidence for the involvement of Segment 227-235 in salt-induced stabilization of contacts within the actin filament and suggest that they can be weakened by mutations characteristic of actin-associated myopathies.
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Affiliation(s)
- Joanna Gruszczynska-Biegala
- Department of Muscle Biochemistry, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland; (J.G.-B.); (A.S.); (A.A.K.); (H.S.-G.)
- Molecular Biology Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Andrzej Stefan
- Department of Muscle Biochemistry, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland; (J.G.-B.); (A.S.); (A.A.K.); (H.S.-G.)
| | - Andrzej A. Kasprzak
- Department of Muscle Biochemistry, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland; (J.G.-B.); (A.S.); (A.A.K.); (H.S.-G.)
| | - Piotr Dobryszycki
- Faculty of Chemistry, Wrocław University of Technology, 50-370 Wroclaw, Poland;
| | - Sofia Khaitlina
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
- Correspondence:
| | - Hanna Strzelecka-Gołaszewska
- Department of Muscle Biochemistry, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland; (J.G.-B.); (A.S.); (A.A.K.); (H.S.-G.)
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4
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Jaswandkar SV, Faisal HMN, Katti KS, Katti DR. Dissociation Mechanisms of G-actin Subunits Govern Deformation Response of Actin Filament. Biomacromolecules 2021; 22:907-917. [PMID: 33481563 DOI: 10.1021/acs.biomac.0c01602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Actin molecules are essential structural components of the cellular cytoskeleton. Here, we report a comprehensive analysis of F-actin's deformation behavior and highlight underlying mechanisms using steered molecular dynamics simulations (SMD). The investigation of F-actin was done under tension, compression, bending, and torsion. We report that the dissociation pattern of conformational locks at intrastrand and interstrand G-actin interfaces regulates the deformation response of F-actin. The conformational locks at the G-actin interfaces are portrayed by a spheroidal joint, interlocking serrated plates' analogy. Further, the SMD simulation approach was utilized to evaluate Young's modulus, flexural rigidity, persistent length, and torsional rigidity of F-actin, and the values obtained were found to be consistent with available experimental data. The evaluation of the mechanical properties of actin and the insight into the fundamental mechanisms contributing to its resilience described here are necessary for developing accurate models of eukaryotic cells and for assessing cellular viability and mobility.
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Affiliation(s)
- Sharad V Jaswandkar
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58105, United States
| | - H M Nasrullah Faisal
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58105, United States
| | - Kalpana S Katti
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58105, United States
| | - Dinesh R Katti
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58105, United States
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5
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Jepsen L, Sept D. Effects of Nucleotide and End-Dependent Actin Conformations on Polymerization. Biophys J 2020; 119:1800-1810. [PMID: 33080221 DOI: 10.1016/j.bpj.2020.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
The regulation of actin is key for controlled cellular function. Filaments are regulated by actin-binding proteins, but the nucleotide state of actin is also an important factor. From extended molecular dynamics simulations, we find that both nucleotide states of the actin monomer have significantly less twist than their crystal structures and that the ATP monomer is flatter than the ADP form. We also find that the filament's pointed end is flatter than the remainder of the filament and has a conformation distinct from G-actin, meaning that incoming monomers would need to undergo isomerization that would weaken the affinity and slow polymerization. Conversely, the barbed end of the filament takes on a conformation nearly identical to the ATP monomer, enhancing ATP G-actin's ability to polymerize as compared with ADP G-actin. The thermodynamic penalty imposed by differences in isomerization for the ATP and ADP growth at the barbed end exactly matches experimental results.
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Affiliation(s)
- Lauren Jepsen
- Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - David Sept
- Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.
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6
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Khan MI, Hasan F, Mahmud KAHA, Adnan A. Recent Computational Approaches on Mechanical Behavior of Axonal Cytoskeletal Components of Neuron: A Brief Review. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s42493-020-00043-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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Viswanathan MC, Schmidt W, Franz P, Rynkiewicz MJ, Newhard CS, Madan A, Lehman W, Swank DM, Preller M, Cammarato A. A role for actin flexibility in thin filament-mediated contractile regulation and myopathy. Nat Commun 2020; 11:2417. [PMID: 32415060 PMCID: PMC7229152 DOI: 10.1038/s41467-020-15922-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
Striated muscle contraction is regulated by the translocation of troponin-tropomyosin strands over the thin filament surface. Relaxation relies partly on highly-favorable, conformation-dependent electrostatic contacts between actin and tropomyosin, which position tropomyosin such that it impedes actomyosin associations. Impaired relaxation and hypercontractile properties are hallmarks of various muscle disorders. The α-cardiac actin M305L hypertrophic cardiomyopathy-causing mutation lies near residues that help confine tropomyosin to an inhibitory position along thin filaments. Here, we investigate M305L actin in vivo, in vitro, and in silico to resolve emergent pathological properties and disease mechanisms. Our data suggest the mutation reduces actin flexibility and distorts the actin-tropomyosin electrostatic energy landscape that, in muscle, result in aberrant contractile inhibition and excessive force. Thus, actin flexibility may be required to establish and maintain interfacial contacts with tropomyosin as well as facilitate its movement over distinct actin surface features and is, therefore, likely necessary for proper regulation of contraction. The α-cardiac actin M305L hypertrophic cardiomyopathy-causing mutation is located near residues that help confine tropomyosin to an inhibitory position along thin filaments. Here the authors assessed M305L actin in vivo, in vitro, and in silico to characterize emergent pathological properties and define the mechanistic basis of disease.
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Affiliation(s)
- Meera C Viswanathan
- Department of Medicine, Division of Cardiology, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - William Schmidt
- Department of Medicine, Division of Cardiology, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Peter Franz
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Michael J Rynkiewicz
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street St, Boston, MA, 02118, USA
| | - Christopher S Newhard
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, 12180-3590, USA
| | - Aditi Madan
- Department of Medicine, Division of Cardiology, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street St, Boston, MA, 02118, USA
| | - Douglas M Swank
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, 12180-3590, USA
| | - Matthias Preller
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.
| | - Anthony Cammarato
- Department of Medicine, Division of Cardiology, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD, 21205, USA. .,Department of Physiology, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, MD, 21205, USA.
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8
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Frank D, Rangrez AY, Friedrich C, Dittmann S, Stallmeyer B, Yadav P, Bernt A, Schulze-Bahr E, Borlepawar A, Zimmermann WH, Peischard S, Seebohm G, Linke WA, Baba HA, Krüger M, Unger A, Usinger P, Frey N, Schulze-Bahr E. Cardiac α-Actin (
ACTC1
) Gene Mutation Causes Atrial-Septal Defects Associated With Late-Onset Dilated Cardiomyopathy. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 12:e002491. [DOI: 10.1161/circgen.119.002491] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Familial atrial septal defect (ASD) has previously been attributed primarily to mutations in cardiac transcription factors. Here, we report a large, multi-generational family (78 members) with ASD combined with a late-onset dilated cardiomyopathy and further characterize the consequences of mutant α-actin.
Methods:
We combined a genome-wide linkage analysis with cell biology, microscopy, and molecular biology tools to characterize a novel
ACTC1
(cardiac α-actin) mutation identified in association with ASD and late-onset dilated cardiomyopathy in a large, multi-generational family.
Results:
Using a genome-wide linkage analysis, the ASD disease locus was mapped to chromosome 15q14 harboring the
ACTC1
gene. In 15 affected family members, a heterozygous, nonsynonymous, and fully penetrant mutation (p. Gly247Asp) was identified in exon 5 of
ACTC1
that was absent in all healthy family members (n=63). In silico tools predicted deleterious consequences of this variant that was found absent in control databases. Ultrastructural analysis of myocardial tissue of one of the mutation carriers showed sarcomeric disarray, myofibrillar degeneration, and increased apoptosis, while cardiac proteomics revealed a significant increase in extracellular matrix proteins. Consistently, structural defects and increased apoptosis were also observed in neonatal rat ventricular cardiomyocytes overexpressing the mutant, but not native human ACTC1. Molecular dynamics studies and additional mechanistic analyses in cardiomyocytes confirmed actin polymerization/turnover defects, thereby affecting contractility.
Conclusions:
A combined phenotype of ASD and late-onset heart failure was caused by a heterozygous, nonsynonymous ACTC1 mutation. Mechanistically, we found a shared molecular mechanism of defective actin signaling and polymerization in both cardiac development and contractile function. Detection of ACTC1 mutations in patients with ASD may thus have further clinical implications with regard to monitoring for (late-onset) dilated cardiomyopathy.
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Affiliation(s)
- Derk Frank
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel (D.F., A.Y.R., A. Bernt, A. Borlepawar, P.U., N.F.)
- Co-affiliated with DZHK (German Centre for Cardiovascular Research), sites Hamburg/Kiel/Lübeck and Göttingen, Germany (D.F., A.Y.R., A. Bernt, A. Borlepawar, W.H.-Z., W.A.L., N.F.)
| | - Ashraf Yusuf Rangrez
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel (D.F., A.Y.R., A. Bernt, A. Borlepawar, P.U., N.F.)
- Co-affiliated with DZHK (German Centre for Cardiovascular Research), sites Hamburg/Kiel/Lübeck and Göttingen, Germany (D.F., A.Y.R., A. Bernt, A. Borlepawar, W.H.-Z., W.A.L., N.F.)
| | - Corinna Friedrich
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
- Institute for Human Genetics (C.F), University Hospital Münster
| | - Sven Dittmann
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
| | - Birgit Stallmeyer
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
| | - Pankaj Yadav
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg (P.Y.)
| | - Alexander Bernt
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel (D.F., A.Y.R., A. Bernt, A. Borlepawar, P.U., N.F.)
- Co-affiliated with DZHK (German Centre for Cardiovascular Research), sites Hamburg/Kiel/Lübeck and Göttingen, Germany (D.F., A.Y.R., A. Bernt, A. Borlepawar, W.H.-Z., W.A.L., N.F.)
| | - Ellen Schulze-Bahr
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
| | - Ankush Borlepawar
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel (D.F., A.Y.R., A. Bernt, A. Borlepawar, P.U., N.F.)
- Co-affiliated with DZHK (German Centre for Cardiovascular Research), sites Hamburg/Kiel/Lübeck and Göttingen, Germany (D.F., A.Y.R., A. Bernt, A. Borlepawar, W.H.-Z., W.A.L., N.F.)
| | - Wolfram-Hubertus Zimmermann
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen (W.H.-Z.)
- Co-affiliated with DZHK (German Centre for Cardiovascular Research), sites Hamburg/Kiel/Lübeck and Göttingen, Germany (D.F., A.Y.R., A. Bernt, A. Borlepawar, W.H.-Z., W.A.L., N.F.)
| | - Stefan Peischard
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
| | - Guiscard Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
| | - Wolfgang A. Linke
- Institute of Physiology II (W.A.L.), University Hospital Münster
- Co-affiliated with DZHK (German Centre for Cardiovascular Research), sites Hamburg/Kiel/Lübeck and Göttingen, Germany (D.F., A.Y.R., A. Bernt, A. Borlepawar, W.H.-Z., W.A.L., N.F.)
| | - Hideo A. Baba
- Institute of Pathology, University of Duisburg-Essen (H.A.B.)
| | - Marcus Krüger
- Center for Molecular Medicine Cologne (CMMC), Proteomics Facility, University of Cologne (M.K.)
| | - Andreas Unger
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
| | - Philip Usinger
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel (D.F., A.Y.R., A. Bernt, A. Borlepawar, P.U., N.F.)
| | - Norbert Frey
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel (D.F., A.Y.R., A. Bernt, A. Borlepawar, P.U., N.F.)
- Co-affiliated with DZHK (German Centre for Cardiovascular Research), sites Hamburg/Kiel/Lübeck and Göttingen, Germany (D.F., A.Y.R., A. Bernt, A. Borlepawar, W.H.-Z., W.A.L., N.F.)
| | - Eric Schulze-Bahr
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine (C.F., S.D., B.S., Ellen Schulze-Bahr, S.P., G.S., A.U., Eric Schulze-Bahr), University Hospital Münster
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9
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Structural evidence for the roles of divalent cations in actin polymerization and activation of ATP hydrolysis. Proc Natl Acad Sci U S A 2018; 115:10345-10350. [PMID: 30254171 PMCID: PMC6187199 DOI: 10.1073/pnas.1806394115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actin polymerization is a divalent cation-dependent process. Here we identify a cation binding site on the surface of actin in a 2.0-Å resolution X-ray structure of actin and find evidence of three additional sites in published high-resolution structures. These cations are stable in molecular dynamics (MD) simulations of the filament, suggesting a functional role in polymerization or filament rigidity. Polymerization activates the ATPase activity of the incorporating actin protomers. Careful analysis of water molecules that approach the ATP in the MD simulations revealed Gln137-activated water to be in a suitable position in F-actin, to initiate attack for ATP hydrolysis, and its occupancy was dependent on bound cations. The structure of the actin filament is known at a resolution that has allowed the architecture of protein components to be unambiguously assigned. However, fully understanding the chemistry of the system requires higher resolution to identify the ions and water molecules involved in polymerization and ATP hydrolysis. Here, we find experimental evidence for the association of cations with the surfaces of G-actin in a 2.0-Å resolution X-ray structure of actin bound to a Cordon-Bleu WH2 motif and in previously determined high-resolution X-ray structures. Three of four reoccurring divalent cation sites were stable during molecular dynamics (MD) simulations of the filament, suggesting that these sites may play a functional role in stabilizing the filament. We modeled the water coordination at the ATP-bound Mg2+, which also proved to be stable during the MD simulations. Using this model of the filament with a hydrated ATP-bound Mg2+, we compared the cumulative probability of an activated hydrolytic water molecule approaching the γ-phosphorous of ATP, in comparison with G-actin, in the MD simulations. The cumulative probability increased in F-actin in line with the activation of actin’s ATPase activity on polymerization. However, inclusion of the cations in the filament lowered cumulative probability, suggesting the rate of hydrolysis may be linked to filament flexibility. Together, these data extend the possible roles of Mg2+ in polymerization and the mechanism of polymerization-induced activation of actin’s ATPase activity.
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10
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Mehrafrooz B, Shamloo A. Mechanical differences between ATP and ADP actin states: A molecular dynamics study. J Theor Biol 2018; 448:94-103. [PMID: 29634959 DOI: 10.1016/j.jtbi.2018.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/31/2018] [Accepted: 04/06/2018] [Indexed: 11/15/2022]
Abstract
This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed to assess tension of monomeric G-actin molecule under different types of mechanical loading including axial and lateral. As a result, stress-strain curves are obtained in aqueous solution, with either ATP or ADP bound in the nucleotide binding pocket. The obtained results yield evaluation of the tensile stiffness of a single actin monomer in lateral and normal direction. In order to compare the behavior of ATP and ADP G-actins, the number of hydrogen bonds and nonbonded interactions between the nucleotide and the protein are analyzed. Moreover, The effect of virtual spring of steered molecular dynamics on the mechanical behavior of actin monomer is investigated. The results reveal increasing the virtual spring constant leads to convergence of the stiffness. Moreover, in this paper, a generalized model is proposed to extend the obtained results for the monomeric G-actin scale to the actin filament. Our modeling estimated a persistence length of actin filament 15.41 µm, close to experimental measurements. Moreover, In this paper, the breaking force actin-actin bond is evaluated using steered molecular dynamics simulation. By applying a tensile force, actin-actin bond ruptured at 4197.5 pN.
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Affiliation(s)
- Behzad Mehrafrooz
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
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11
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Shamloo A, Mehrafrooz B. Nanomechanics of actin filament: A molecular dynamics simulation. Cytoskeleton (Hoboken) 2018; 75:118-130. [PMID: 29272080 DOI: 10.1002/cm.21429] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 11/08/2022]
Abstract
Actin is known as the most abundant essentially protein in eukaryotic cells. Actin plays a crucial role in many cellular processes involving mechanical forces such as cell motility, adhesion, muscle contraction, and intracellular transport. However, little is known about the mechanical properties of this protein when subjected to mechanical forces in cellular processes. In this article, a series of large-scale molecular dynamics simulations are carried out to elucidate nanomechanical behavior such as elastic and viscoelastic properties of a single actin filament. Here, we used two individual methods namely, all-atoms and coarse-grained molecular dynamics, to evaluate elastic properties of a single actin filament. In the other word, based on Brownian motions of the filament and using the principle of the equipartition theorem, in aqueous solution, tensile stiffness, torsional rigidity, and bending rigidity of the single actin filament are studied. The results revealed that increasing the sampling window time leads to convergence of obtained mechanical properties to the experimental values. Moreover, in order to investigate viscoelastic properties of a single actin filament, constant force steered molecular dynamics method is used to apply different external tensile loads and perform five individual creep tests on the molecule. The strain-time response of the filament for each creep test is obtained. Based on the Kelvin-Voigt model, the results reveal that a single actin filament shows a nonlinear viscoelastic behavior, with a Young's modulus of 2.85 GPa, a viscosity of 4.06 GPa.ns, and a relaxation time in the range of 1.42 ns which were measured here for the first time at the single filament level. The findings of this article suggest that molecular dynamics simulations could also be a useful tool for investigating the mechanical behavior of bio-nanomaterials.
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Affiliation(s)
- Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
| | - Behzad Mehrafrooz
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
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12
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Abstract
Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.
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Affiliation(s)
- Marcus Thomas
- Computational Biology Department, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States of America. Joint Carnegie Mellon University/University of Pittsburgh Ph.D. Program in Computational Biology, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States of America
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13
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Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. J Phys Chem B 2017; 121:4023-4039. [PMID: 28306259 DOI: 10.1021/acs.jpcb.7b02320] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.
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Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Keri A McKiernan
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Joseph Gomes
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Kyle A Beauchamp
- Counsyl, Inc. , South San Francisco, California 94080, United States
| | - Teresa Head-Gordon
- Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, and Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley , Berkeley, California 94720, United States.,Chemical Sciences Division, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Julia E Rice
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - William C Swope
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - Todd J Martínez
- Department of Chemistry, Stanford University , Stanford, California 94305, United States.,PULSE Institute, Stanford University , Stanford, California 94305, United States.,SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Vijay S Pande
- Department of Chemistry, Stanford University , Stanford, California 94305, United States.,Departments of Computer Science, Structural Biology, and Program in Biophysics, Stanford University , Stanford, California 94305, United States
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14
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Popov K, Komianos J, Papoian GA. MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks. PLoS Comput Biol 2016; 12:e1004877. [PMID: 27120189 PMCID: PMC4847874 DOI: 10.1371/journal.pcbi.1004877] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
Active matter systems, and in particular the cell cytoskeleton, exhibit complex mechanochemical dynamics that are still not well understood. While prior computational models of cytoskeletal dynamics have lead to many conceptual insights, an important niche still needs to be filled with a high-resolution structural modeling framework, which includes a minimally-complete set of cytoskeletal chemistries, stochastically treats reaction and diffusion processes in three spatial dimensions, accurately and efficiently describes mechanical deformations of the filamentous network under stresses generated by molecular motors, and deeply couples mechanics and chemistry at high spatial resolution. To address this need, we propose a novel reactive coarse-grained force field, as well as a publicly available software package, named the Mechanochemical Dynamics of Active Networks (MEDYAN), for simulating active network evolution and dynamics (available at www.medyan.org). This model can be used to study the non-linear, far from equilibrium processes in active matter systems, in particular, comprised of interacting semi-flexible polymers embedded in a solution with complex reaction-diffusion processes. In this work, we applied MEDYAN to investigate a contractile actomyosin network consisting of actin filaments, alpha-actinin cross-linking proteins, and non-muscle myosin IIA mini-filaments. We found that these systems undergo a switch-like transition in simulations from a random network to ordered, bundled structures when cross-linker concentration is increased above a threshold value, inducing contraction driven by myosin II mini-filaments. Our simulations also show how myosin II mini-filaments, in tandem with cross-linkers, can produce a range of actin filament polarity distributions and alignment, which is crucially dependent on the rate of actin filament turnover and the actin filament’s resulting super-diffusive behavior in the actomyosin-cross-linker system. We discuss the biological implications of these findings for the arc formation in lamellipodium-to-lamellum architectural remodeling. Lastly, our simulations produce force-dependent accumulation of myosin II, which is thought to be responsible for their mechanosensation ability, also spontaneously generating myosin II concentration gradients in the solution phase of the simulation volume. Active matter systems have the distinct ability to convert energy from their surroundings into mechanical work, which gives rise to them having highly dynamic properties. Modeling active matter systems and capturing their complex behavior has been a great challenge in past years due to the many coupled interactions between their constituent parts, including not only distinct chemical and mechanical properties, but also feedback between them. One of the most intriguing biological active matter systems is the cell cytoskeleton, which can dynamically respond to chemical and mechanical cues to control cell structure and shape, playing a central role in many higher-order cellular processes. To model these systems and reproduce their behavior, we present a new modeling approach which combines the chemical, mechanical, and molecular transport aspects of active matter systems, all represented with equivalent complexity, while also allowing for various forms of mechanochemical feedback. This modeling approach, named MEDYAN, and software implementation is flexible so that a wide range of active matter systems can be simulated with a high level of detail, and ultimately can help to describe active matter phenomena, and in particular, the dynamics of the cell cytoskeleton. In this work, we have used MEDYAN to simulate a cytoskeletal network consisting of actin filaments, cross-linking proteins, and myosin II molecular motors. We found that these systems show rich dynamical behaviors, undergoing alignment and bundling transitions, with an emergent contractility, as the concentrations of myosin II and cross-linking proteins, as well as actin filament turnover rates, are varied.
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Affiliation(s)
- Konstantin Popov
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
| | - James Komianos
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Biophysics Graduate Program, University of Maryland, College Park, Maryland, United States of America
| | - Garegin A. Papoian
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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15
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Kudryashov DS, Reisler E. ATP and ADP actin states. Biopolymers 2016; 99:245-56. [PMID: 23348672 DOI: 10.1002/bip.22155] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/07/2012] [Indexed: 11/06/2022]
Abstract
This minireview is dedicated to the memory of Henryk Eisenberg and honors his major contributions to many areas of biophysics and to the analysis of macromolecular states and interactions in particular. This work reviews the ATP and ADP states of a ubiquitous protein, actins, and considers the present evidence for and against unique, nucleotide-dependent conformations of this protein. The effects of ATP and ADP on specific structural elements of actins, its loops and clefts, as revealed by mutational, crosslinking, spectroscopic, and EPR methods are discussed. It is concluded that the existing evidence points to dynamic equilibria of these structural elements among various conformational states in both ATP- and ADP-actins, with the nucleotides impacting the equilibria distributions.
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Affiliation(s)
- Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, the Ohio State University, Columbus, OH 43210.
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16
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Kumar RP, Roopa L, Nongthomba U, Sudheer Mohammed MM, Kulkarni N. Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin. J Mol Graph Model 2015; 63:29-37. [PMID: 26615469 DOI: 10.1016/j.jmgm.2015.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 10/29/2015] [Accepted: 11/06/2015] [Indexed: 11/30/2022]
Abstract
CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the β-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable "tense" state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin.
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Affiliation(s)
- R Pravin Kumar
- Research and Development Centre, Bharathiar University, Coimbatore, India; Polyclone Bioservices, Bangalore, India
| | - L Roopa
- Research and Development Centre, Bharathiar University, Coimbatore, India
| | - Upendra Nongthomba
- Department of Molecular Reproduction Development and Genetics, Indian Institute of Science, Bangalore, India.
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17
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Schmeiser C, Winkler C. The flatness of Lamellipodia explained by the interaction between actin dynamics and membrane deformation. J Theor Biol 2015; 380:144-55. [PMID: 26002996 DOI: 10.1016/j.jtbi.2015.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 11/28/2022]
Abstract
The crawling motility of many cell types relies on lamellipodia, flat protrusions spreading on flat substrates but (on cells in suspension) also growing into three-dimensional space. Lamellipodia consist of a plasma membrane wrapped around an oriented actin filament meshwork. It is well known that the actin density is controlled by coordinated polymerization, branching, and capping processes, but the mechanisms producing the small aspect ratios of lamellipodia (hundreds of nm thickness vs. several μm lateral and inward extension) remain unclear. The main hypothesis of this work is a strong influence of the local geometry of the plasma membrane on the actin dynamics. This is motivated by observations of co-localization of proteins with I-BAR domains (like IRSp53) with polymerization and branching agents along the membrane. The I-BAR domains are known to bind to the membrane and to prefer and promote membrane curvature. This hypothesis is translated into a stochastic mathematical model where branching and capping rates, and polymerization speeds depend on the local membrane geometry and branching directions are influenced by the principal curvature directions. This requires the knowledge of the deformation of the membrane, being described in a quasi-stationary approximation by minimization of a modified Helfrich energy, subject to the actin filaments acting as obstacles. Simulations with this model predict pieces of flat lamellipodia without any prescribed geometric restrictions.
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Affiliation(s)
- Christian Schmeiser
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria; Johann Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences, Altenberger Straße 69, 4040 Linz, Austria
| | - Christoph Winkler
- Johann Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences, Altenberger Straße 69, 4040 Linz, Austria.
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18
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Cryo-EM reveals different coronin binding modes for ADP- and ADP-BeFx actin filaments. Nat Struct Mol Biol 2014; 21:1075-81. [PMID: 25362487 PMCID: PMC4388421 DOI: 10.1038/nsmb.2907] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 09/29/2014] [Indexed: 11/16/2022]
Abstract
Essential cellular processes involving the actin cytoskeleton are regulated by auxiliary proteins which can sense the nucleotide state of actin. Here we report cryo electron microscopy (cryoEM) structures at 8.6 Å resolution for ADP- and ADP-BeFx- (mimicking ADP-Pi) bound actin filaments in complex with the β-propeller domain (residues 1–600) of yeast coronin 1 (crn1). Our structures identify the main differences in the interaction of coronin with the two nucleotide states of F-actin. We derived pseudo-atomic models by fitting the atomic structures of actin and coronin into these structures. The identified binding interfaces on actin were confirmed by chemical crosslinking, fluorescence spectroscopy and actin mutagenesis. Importantly, the structures of actin and coronin mapped in this study offer a structural explanation for the nucleotide-dependent effects of coronin on cofilin-assisted remodeling of F-actin.
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19
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Sousa DR, Stagg SM, Stroupe ME. Cryo-EM structures of the actin:tropomyosin filament reveal the mechanism for the transition from C- to M-state. J Mol Biol 2013; 425:4544-55. [PMID: 24021812 PMCID: PMC3845445 DOI: 10.1016/j.jmb.2013.08.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 12/18/2022]
Abstract
Tropomyosin (Tm) is a key factor in the molecular mechanisms that regulate the binding of myosin motors to actin filaments (F-Actins) in most eukaryotic cells. This regulation is achieved by the azimuthal repositioning of Tm along the actin (Ac):Tm:troponin (Tn) thin filament to block or expose myosin binding sites on Ac. In striated muscle, including involuntary cardiac muscle, Tm regulates muscle contraction by coupling Ca(2+) binding to Tn with myosin binding to the thin filament. In smooth muscle, the switch is the posttranslational modification of the myosin. Depending on the activation state of Tn and the binding state of myosin, Tm can occupy the blocked, closed, or open position on Ac. Using native cryogenic 3DEM (three-dimensional electron microscopy), we have directly resolved and visualized cardiac and gizzard muscle Tm on filamentous Ac in the position that corresponds to the closed state. From the 8-Å-resolution structure of the reconstituted Ac:Tm filament formed with gizzard-derived Tm, we discuss two possible mechanisms for the transition from closed to open state and describe the role Tm plays in blocking myosin tight binding in the closed-state position.
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Affiliation(s)
- Duncan R. Sousa
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL, 32306 USA
- Department of Physiology and Biophysics, Boston University School of Medicine, 72 East Concord Street Boston MA 02118-2526 USA
| | - Scott M. Stagg
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL, 32306 USA
| | - M. Elizabeth Stroupe
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL, 32306 USA
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20
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Carlier MF, Pernier J, Avvaru BS. Control of actin filament dynamics at barbed ends by WH2 domains: From capping to permissive and processive assembly. Cytoskeleton (Hoboken) 2013; 70:540-9. [DOI: 10.1002/cm.21124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 01/01/2023]
Affiliation(s)
| | - Julien Pernier
- Cytoskeleton Dynamics and Motility Team; LEBS; CNRS; Gif-Sur-Yvette France
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21
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Globisch C, Krishnamani V, Deserno M, Peter C. Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation. PLoS One 2013; 8:e60582. [PMID: 23613730 PMCID: PMC3628857 DOI: 10.1371/journal.pone.0060582] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 02/28/2013] [Indexed: 11/18/2022] Open
Abstract
The major protective coat of most viruses is a highly symmetric protein capsid that forms spontaneously from many copies of identical proteins. Structural and mechanical properties of such capsids, as well as their self-assembly process, have been studied experimentally and theoretically, including modeling efforts by computer simulations on various scales. Atomistic models include specific details of local protein binding but are limited in system size and accessible time, while coarse grained (CG) models do get access to longer time and length scales but often lack the specific local interactions. Multi-scale models aim at bridging this gap by systematically connecting different levels of resolution. Here, a CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical protein monomers, is developed, where parameters are derived from atomistic simulations of capsid protein dimers in aqueous solution. In particular, a new method is introduced to combine the MARTINI CG model with a supportive elastic network based on structural fluctuations of individual monomers. In the parametrization process, both network connectivity and strength are optimized. This elastic-network optimized CG model, which solely relies on atomistic data of small units (dimers), is able to correctly predict inter-protein conformational flexibility and properties of larger capsid fragments of 20 and more subunits. Furthermore, it is shown that this CG model reproduces experimental (Atomic Force Microscopy) indentation measurements of the entire viral capsid. Thus it is shown that one obvious goal for hierarchical modeling, namely predicting mechanical properties of larger protein complexes from models that are carefully parametrized on elastic properties of smaller units, is achievable.
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Affiliation(s)
| | - Venkatramanan Krishnamani
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Christine Peter
- Max Planck Institute for Polymer Research (MPIP), Mainz, Germany
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22
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Fan J, Saunders MG, Haddadian EJ, Freed KF, De La Cruz EM, Voth GA. Molecular origins of cofilin-linked changes in actin filament mechanics. J Mol Biol 2013; 425:1225-40. [PMID: 23352932 DOI: 10.1016/j.jmb.2013.01.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/14/2013] [Accepted: 01/16/2013] [Indexed: 10/27/2022]
Abstract
The actin regulatory protein cofilin plays a central role in actin assembly dynamics by severing filaments and increasing the concentration of ends from which subunits add and dissociate. Cofilin binding modifies the average structure and mechanical properties of actin filaments, thereby promoting fragmentation of partially decorated filaments at boundaries of bare and cofilin-decorated segments. Despite extensive evidence for cofilin-dependent changes in filament structure and mechanics, it is unclear how the two processes are linked at the molecular level. Here, we use molecular dynamics simulations and coarse-grained analyses to evaluate the molecular origins of the changes in filament compliance due to cofilin binding. Filament subunits with bound cofilin are less flat and maintain a significantly more open nucleotide cleft than bare filament subunits. Decorated filament segments are less twisted, thinner (considering only actin), and less connected than their bare counterparts, which lowers the filament bending persistence length and torsional stiffness. Using coarse-graining as an analysis method reveals that cofilin binding increases the average distance between the adjacent long-axis filament subunit, thereby weakening their interaction. In contrast, a fraction of lateral filament subunit contacts are closer and presumably stronger with cofilin binding. A cofilactin interface contact identified by cryo-electron microscopy is unstable during simulations carried out at 310K, suggesting that this particular interaction may be short lived at ambient temperatures. These results reveal the molecular origins of cofilin-dependent changes in actin filament mechanics that may promote filament severing.
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Affiliation(s)
- Jun Fan
- Department of Chemistry, James Franck Institute, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
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23
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Yogurtcu ON, Kim JS, Sun SX. A mechanochemical model of actin filaments. Biophys J 2013; 103:719-27. [PMID: 22947933 DOI: 10.1016/j.bpj.2012.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/21/2012] [Accepted: 07/18/2012] [Indexed: 11/19/2022] Open
Abstract
In eukaryotic cells, actin filaments are involved in important processes such as motility, division, cell shape regulation, contractility, and mechanosensation. Actin filaments are polymerized chains of monomers, which themselves undergo a range of chemical events such as ATP hydrolysis, polymerization, and depolymerization. When forces are applied to F-actin, in addition to filament mechanical deformations, the applied force must also influence chemical events in the filament. We develop an intermediate-scale model of actin filaments that combines actin chemistry with filament-level deformations. The model is able to compute mechanical responses of F-actin during bending and stretching. The model also describes the interplay between ATP hydrolysis and filament deformations, including possible force-induced chemical state changes of actin monomers in the filament. The model can also be used to model the action of several actin-associated proteins, and for large-scale simulation of F-actin networks. All together, our model shows that mechanics and chemistry must be considered together to understand cytoskeletal dynamics in living cells.
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Affiliation(s)
- Osman N Yogurtcu
- Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland, USA
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24
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Düttmann M, Mittnenzweig M, Togashi Y, Yanagida T, Mikhailov AS. Complex intramolecular mechanics of G-actin--an elastic network study. PLoS One 2012; 7:e45859. [PMID: 23077498 PMCID: PMC3471905 DOI: 10.1371/journal.pone.0045859] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/17/2012] [Indexed: 11/30/2022] Open
Abstract
Systematic numerical investigations of conformational motions in single actin molecules were performed by employing a simple elastic-network (EN) model of this protein. Similar to previous investigations for myosin, we found that G-actin essentially behaves as a strain sensor, responding by well-defined domain motions to mechanical perturbations. Several sensitive residues within the nucleotide-binding pocket (NBP) could be identified, such that the perturbation of any of them can induce characteristic flattening of actin molecules and closing of the cleft between their two mobile domains. Extending the EN model by introduction of a set of breakable links which become effective only when two domains approach one another, it was observed that G-actin can possess a metastable state corresponding to a closed conformation and that a transition to this state can be induced by appropriate perturbations in the NBP region. The ligands were roughly modeled as a single particle (ADP) or a dimer (ATP), which were placed inside the NBP and connected by elastic links to the neighbors. Our approximate analysis suggests that, when ATP is present, it stabilizes the closed conformation of actin. This may play an important role in the explanation why, in the presence of ATP, the polymerization process is highly accelerated.
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Affiliation(s)
- Markus Düttmann
- Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Berlin, Germany.
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25
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Behrmann E, Müller M, Penczek PA, Mannherz HG, Manstein DJ, Raunser S. Structure of the rigor actin-tropomyosin-myosin complex. Cell 2012; 150:327-38. [PMID: 22817895 DOI: 10.1016/j.cell.2012.05.037] [Citation(s) in RCA: 267] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/13/2012] [Accepted: 05/20/2012] [Indexed: 01/13/2023]
Abstract
Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions within the complex and the trajectory of tropomyosin movement between its "open" and "closed" positions on the actin filament. Here, we report the 8 Å resolution structure of the rigor (nucleotide-free) actin-tropomyosin-myosin complex determined by cryo-electron microscopy. The pseudoatomic model of the complex, obtained from fitting crystal structures into the map, defines the large interface involving two adjacent actin monomers and one tropomyosin pseudorepeat per myosin contact. Severe forms of hereditary myopathies are linked to mutations that critically perturb this interface. Myosin binding results in a 23 Å shift of tropomyosin along actin. Complex domain motions occur in myosin, but not in actin. Based on our results, we propose a structural model for the tropomyosin-dependent modulation of myosin binding to actin.
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Affiliation(s)
- Elmar Behrmann
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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Grantham J, Lassing I, Karlsson R. Controlling the cortical actin motor. PROTOPLASMA 2012; 249:1001-1015. [PMID: 22526202 PMCID: PMC3459087 DOI: 10.1007/s00709-012-0403-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 03/21/2012] [Indexed: 05/31/2023]
Abstract
Actin is the essential force-generating component of the microfilament system, which powers numerous motile processes in eukaryotic cells and undergoes dynamic remodeling in response to different internal and external signaling. The ability of actin to polymerize into asymmetric filaments is the inherent property behind the site-directed force-generating capacity that operates during various intracellular movements and in surface protrusions. Not surprisingly, a broad variety of signaling pathways and components are involved in controlling and coordinating the activities of the actin microfilament system in a myriad of different interactions. The characterization of these processes has stimulated cell biologists for decades and has, as a consequence, resulted in a huge body of data. The purpose here is to present a cellular perspective on recent advances in our understanding of the microfilament system with respect to actin polymerization, filament structure and specific folding requirements.
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Affiliation(s)
- Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ingrid Lassing
- Department of Cell Biology, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Roger Karlsson
- Department of Cell Biology, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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27
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Freedman H, Laino T, Curioni A. Reaction Dynamics of ATP Hydrolysis in Actin Determined by ab Initio Molecular Dynamics Simulations. J Chem Theory Comput 2012; 8:3373-83. [PMID: 26605743 DOI: 10.1021/ct3003282] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Energy released by the hydrolysis of the high-energy phosphate bond of nucleoside triphosphate (NTP) cofactors is the driving force behind most biological processes. To understand how this energy is used to induce differences in protein structure and function, we examine the transfer of vibrational energy into the nucleotide-bound actin active site immediately after reaction activation. To this end, we perform Born-Oppenheimer molecular dynamics simulations of the active site at the level of density functional theory (DFT) starting at the calculated transition state (TS) structure. Similarly to the mechanism determined in many nucleotide-bound protein systems, the Os-Pγ bond is first elongated. Then, nucleophilic attack of the lytic water on Pγ occurs. Subsequently, protons are transferred in a cycle formed by water molecules, a protein residue, Asp154, and the γ-phosphate group, resulting in the formation of H2PO4(-). To investigate the possible creation of excited vibrational states in the products, power spectra of bond-length autocorrelation functions for relevant bonds within the active site are compared for simulations that start at the TS, at reactants, and at reaction end products. The hydroxyl bond formed in the final proton transfer to the phosphate molecule is observed to exhibit relatively high kinetic energies and large oscillations during reaction. It is also likely that some of the energy released by the reaction is captured by the low-energy stretching vibrations of the phosphoryl bonds of orthophosphate, which oscillate with large amplitudes in nonequilibrium simulations of end products.
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Affiliation(s)
- Holly Freedman
- CCMAR, FCT, University of Algarve, Campus de Gambelas, Faro, Portugal
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28
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Rennebaum S, Caflisch A. Inhibition of interdomain motion in g-actin by the natural product latrunculin: a molecular dynamics study. Proteins 2012; 80:1998-2008. [PMID: 22488806 DOI: 10.1002/prot.24088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/22/2012] [Accepted: 03/30/2012] [Indexed: 11/09/2022]
Abstract
As part of the cytoskeleton, actin is essential for the morphology, motility, and division of eukaryotic cells. Recent X-ray fiber diffraction studies have shown that the conformation of monomeric actin is flattened upon incorporation into the filament by a relative rotation of its two major domains. The antiproliferative activity of latrunculin, a macrolide toxin produced by sponges, seems to be related to its binding to monomeric actin and inhibition of polymerization. Yet, the mechanism of inhibition is not known in detail. Here, multiple explicit water molecular dynamics simulations show that latrunculin binding hinders the conformational transition related to actin polymerization. In particular, the presence of latrunculin at the interface of the two major domains of monomeric actin reduces the correlated displacement of Domain 2 with respect to Domain 1. Moreover, higher rotational flexibility between the two major domains is observed in the absence of ATP as compared to ATP-bound actin, offering a possible explanation as to why actin polymerizes more favorably in the absence of nucleotides.
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Affiliation(s)
- Sandra Rennebaum
- Department of Biochemistry, University of Zürich, Zürich 8057, Switzerland
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29
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Saunders MG, Voth GA. Comparison between actin filament models: coarse-graining reveals essential differences. Structure 2012; 20:641-53. [PMID: 22483111 DOI: 10.1016/j.str.2012.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 02/06/2012] [Accepted: 02/08/2012] [Indexed: 10/28/2022]
Abstract
The interconversion of actin between monomeric and polymeric forms is a fundamental process in cell biology that is incompletely understood, in part because there is no high-resolution structure for filamentous actin. Several models have been proposed recently; identifying structural and dynamic differences between them is an essential step toward understanding actin dynamics. We compare three of these models, using coarse-grained analysis of molecular dynamics simulations to analyze the differences between them and evaluate their relative stability. Based on this analysis, we identify key motions that may be associated with polymerization, including a potential energetic barrier in the process. We also find that actin subunits are polymorphic; during simulations they assume a range of configurations remarkably similar to those seen in recent cryoEM images.
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Affiliation(s)
- Marissa G Saunders
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
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30
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Deriu MA, Shkurti A, Paciello G, Bidone TC, Morbiducci U, Ficarra E, Audenino A, Acquaviva A. Multiscale modeling of cellular actin filaments: from atomistic molecular to coarse-grained dynamics. Proteins 2012; 80:1598-609. [PMID: 22411308 DOI: 10.1002/prot.24053] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 01/11/2012] [Accepted: 01/29/2012] [Indexed: 11/06/2022]
Abstract
In this article, we present a computational multiscale model for the characterization of subcellular proteins. The model is encoded inside a simulation tool that builds coarse-grained (CG) force fields from atomistic simulations. Equilibrium molecular dynamics simulations on an all-atom model of the actin filament are performed. Then, using the statistical distribution of the distances between pairs of selected groups of atoms at the output of the MD simulations, the force field is parameterized using the Boltzmann inversion approach. This CG force field is further used to characterize the dynamics of the protein via Brownian dynamics simulations. This combination of methods into a single computational tool flow enables the simulation of actin filaments with length up to 400 nm, extending the time and length scales compared to state-of-the-art approaches. Moreover, the proposed multiscale modeling approach allows to investigate the relationship between atomistic structure and changes on the overall dynamics and mechanics of the filament and can be easily (i) extended to the characterization of other subcellular structures and (ii) used to investigate the cellular effects of molecular alterations due to pathological conditions.
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Affiliation(s)
- Marco A Deriu
- Department of Mechanics, Politecnico di Torino, Torino, Italy.
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31
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Saunders MG, Voth GA. Water molecules in the nucleotide binding cleft of actin: effects on subunit conformation and implications for ATP hydrolysis. J Mol Biol 2011; 413:279-91. [PMID: 21856312 DOI: 10.1016/j.jmb.2011.07.068] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 11/15/2022]
Abstract
In the monomeric actin crystal structure, the positions of a highly organized network of waters are clearly visible within the active site. However, the recently proposed models of filamentous actin (F-actin) did not extend to including these waters. Since the water network is important for ATP hydrolysis, information about water position is critical to understanding the increased rate of catalysis upon filament formation. Here, we show that waters in the active site are essential for intersubdomain rotational flexibility and that they organize the active-site structure. Including the crystal structure waters during simulation setup allows us to observe distinct changes in the active-site structure upon the flattening of the actin subunit, as proposed in the Oda model for F-actin. We identify changes in both protein position and water position relative to the phosphate tail that suggest a mechanism for accelerating the rate of nucleotide hydrolysis in F-actin by stabilizing charge on the β-phosphate and by facilitating deprotonation of catalytic water.
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Affiliation(s)
- Marissa G Saunders
- Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
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