1
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Singh AP, Kumar R, Gupta D. Structural insights into the mechanism of human methyltransferase hPRMT4. J Biomol Struct Dyn 2022; 40:10821-10834. [PMID: 34308797 DOI: 10.1080/07391102.2021.1950567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Human PRMT4, also known as CARM1, is a type I arginine methyltransferase protein that catalyse the formation of asymmetrical dimethyl arginine product. Structural studies done to date on PRMT4 have shown that the N-terminal region, Rossmann fold and dimerization arm play an important role in PRMT4 activity. Elucidating the functions of these regions in catalysis remains to be explored. Studies have shown the existence of communication pathways in PRMT4, which need further elucidation. The molecular dynamics (MD) simulations performed in this study show differences in different monomeric and dimeric forms of hPRMT4, revealing the role of the N-terminal region, Rossmann fold and dimerization arm. The study shows the conformational changes that occur during dimerization and SAM binding. Our cross-correlation analysis showed a correlation between these regions. Further, we performed PSN and network analysis to establish the existence of communication networks and an allosteric pathway. This study shows the use of MD simulations and network analysis to explore the aspects of PRMT4 dimerization, SAM binding and demonstrates the existence of an allosteric network. These findings shed novel insights into the conformational changes associated with hPRMT4, the mechanism of its dimerization, SAM binding and clues for better inhibitor designs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amar Pratap Singh
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rakesh Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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2
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Sperti M, Malavolta M, Ciniero G, Borrelli S, Cavaglià M, Muscat S, Tuszynski JA, Afeltra A, Margiotta DPE, Navarini L. JAK inhibitors in immune-mediated rheumatic diseases: From a molecular perspective to clinical studies. J Mol Graph Model 2021; 104:107789. [DOI: 10.1016/j.jmgm.2020.107789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022]
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3
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Khan MI, Ferdous SF, Adnan A. Mechanical behavior of actin and spectrin subjected to high strain rate: A molecular dynamics simulation study. Comput Struct Biotechnol J 2021; 19:1738-1749. [PMID: 33897978 PMCID: PMC8050423 DOI: 10.1016/j.csbj.2021.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
Recent nanoscopy and super-resolution microscopy studies have substantiated the structural contribution of periodic actin-spectrin lattice to the axonal cytoskeleton of neuron. However, sufficient mechanical insight is not present for spectrin and actin-spectrin network, especially in high strain rate scenario. To quantify the mechanical behavior of actin-spectrin cytoskeleton in such conditions, this study determines individual stretching characteristics of actin and spectrin at high strain rate by molecular dynamics (MD) simulation. The actin-spectrin separation criteria are also determined. It is found that both actin and spectrin have high stiffness when susceptible to high strain rate and show strong dependence on applied strain rate. The stretching stiffness of actin and forced unfolding mechanism of spectrin are in harmony with the current literature. Actin-spectrin model provides novel insight into their interaction and separation stretch. It is shown that the region vulnerable to failure is the actin-spectrin interface at lower strain rate, while it is the inter-repeat region of spectrin at higher strain rate.
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Affiliation(s)
- Md Ishak Khan
- Department of Mechanical and Aerospace Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sheikh Fahad Ferdous
- Department of Applied Engineering and Technology Management, Indiana State University, Terre Haute, IN 47809, USA
| | - Ashfaq Adnan
- Department of Mechanical and Aerospace Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
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4
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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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5
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Horan BG, Hall AR, Vavylonis D. Insights into Actin Polymerization and Nucleation Using a Coarse-Grained Model. Biophys J 2020; 119:553-566. [PMID: 32668234 DOI: 10.1016/j.bpj.2020.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the Cα atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, x-ray diffraction, and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at an angle with respect to the polymerizable bound structure, and the angle range depended on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G-actin form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to the antiparallel (lower) dimer. Individual monomers bound each other in a short-pitch helix complex in addition to other configurations, with several of them apparently nonproductive for polymerization. Simulations with multiple monomers in the F-actin form show assembly into filaments as well as transient aggregates at the barbed end. We discuss the implications of these observations on the kinetic pathway of actin filament nucleation and polymerization and possibilities for future improvements of the coarse-grained model.
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Affiliation(s)
- Brandon G Horan
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
| | - Aaron R Hall
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
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6
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Gaetani R, Zizzi EA, Deriu MA, Morbiducci U, Pesce M, Messina E. When Stiffness Matters: Mechanosensing in Heart Development and Disease. Front Cell Dev Biol 2020; 8:334. [PMID: 32671058 PMCID: PMC7326078 DOI: 10.3389/fcell.2020.00334] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
During embryonic morphogenesis, the heart undergoes a complex series of cellular phenotypic maturations (e.g., transition of myocytes from proliferative to quiescent or maturation of the contractile apparatus), and this involves stiffening of the extracellular matrix (ECM) acting in concert with morphogenetic signals. The maladaptive remodeling of the myocardium, one of the processes involved in determination of heart failure, also involves mechanical cues, with a progressive stiffening of the tissue that produces cellular mechanical damage, inflammation, and ultimately myocardial fibrosis. The assessment of the biomechanical dependence of the molecular machinery (in myocardial and non-myocardial cells) is therefore essential to contextualize the maturation of the cardiac tissue at early stages and understand its pathologic evolution in aging. Because systems to perform multiscale modeling of cellular and tissue mechanics have been developed, it appears particularly novel to design integrated mechano-molecular models of heart development and disease to be tested in ex vivo reconstituted cells/tissue-mimicking conditions. In the present contribution, we will discuss the latest implication of mechanosensing in heart development and pathology, describe the most recent models of cell/tissue mechanics, and delineate novel strategies to target the consequences of heart failure with personalized approaches based on tissue engineering and induced pluripotent stem cell (iPSC) technologies.
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Affiliation(s)
- Roberto Gaetani
- Department of Molecular Medicine, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome, Italy.,Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, San Diego, CA, United States
| | - Eric Adriano Zizzi
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Agostino Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Umberto Morbiducci
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Maurizio Pesce
- Tissue Engineering Research Unit, "Centro Cardiologico Monzino," IRCCS, Milan, Italy
| | - Elisa Messina
- Department of Maternal, Infantile, and Urological Sciences, "Umberto I" Hospital, Sapienza University of Rome, Rome, Italy
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7
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Schroer CFE, Baldauf L, van Buren L, Wassenaar TA, Melo MN, Koenderink GH, Marrink SJ. Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. Proc Natl Acad Sci U S A 2020; 117:5861-5872. [PMID: 32123101 PMCID: PMC7084070 DOI: 10.1073/pnas.1914884117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed that direct interactions between actin filaments and lipid bilayers are possible and that the net charge of the bilayer as well as the presence of divalent ions in the buffer play an important role. In vivo, colocalization of actin filaments and divalent ions are suppressed, and cells rely on linker proteins to connect the plasma membrane to the actin network. Little is known, however, about why this is the case and what microscopic interactions are important. A deeper understanding is highly beneficial, first, to obtain understanding in the biological design of cells and, second, as a possible basis for the building of artificial cortices for the stabilization of synthetic cells. Here, we report the results of coarse-grained molecular dynamics simulations of monomeric and filamentous actin in the vicinity of differently charged lipid bilayers. We observe that charges on the lipid head groups strongly determine the ability of actin to adsorb to the bilayer. The inclusion of divalent ions leads to a reversal of the binding affinity. Our in silico results are validated experimentally by reconstitution assays with actin on lipid bilayer membranes and provide a molecular-level understanding of the actin-membrane interaction.
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Affiliation(s)
- Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Lucia Baldauf
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica, New University of Lisbon, 2780-157, Oeiras, Portugal
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands;
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands;
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
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8
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Stojceski F, Grasso G, Pallante L, Danani A. Molecular and Coarse-Grained Modeling to Characterize and Optimize Dendrimer-Based Nanocarriers for Short Interfering RNA Delivery. ACS OMEGA 2020; 5:2978-2986. [PMID: 32095720 PMCID: PMC7033960 DOI: 10.1021/acsomega.9b03908] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Dendrimer nanocarriers are unique hyper-branched polymers with biomolecule-like properties, representing a promising prospect as a nucleic acid delivery system. The design of effective dendrimer-based gene carriers requires considering several parameters, such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity. In detail, the rational design of the dendrimer surface chemistry has been ascertained to play a crucial role on the efficiency of interaction with nucleic acids. Within this framework, advances in the field of organic chemistry have allowed us to design dendrimers with even small difference in the chemical structure of their surface terminals. In this study, we have selected two different cationic phosphorus dendrimers of generation 3 functionalized, respectively, with pyrrolidinium (DP) and morpholinium (DM) surface groups, which have demonstrated promising potential for short interfering RNA (siRNA) delivery. Despite DP and DM differing only for one atom in their chemical structure, in vitro and in vivo experiments have highlighted several differences between them in terms of siRNA complexation properties. In this context, we have employed coarse-grained molecular dynamics simulation techniques to shed light on the supramolecular characteristics of dendrimer-siRNA complexation, the so-called dendriplex formations. Our data provide important information on self-assembly dynamics driven by surface chemistry and competition mechanisms.
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Affiliation(s)
- Filip Stojceski
- Istituto
Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera
Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Gianvito Grasso
- Istituto
Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera
Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Lorenzo Pallante
- PolitoBIOMed
Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy
| | - Andrea Danani
- Istituto
Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera
Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland
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9
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Grasso G, Rebella M, Morbiducci U, Tuszynski JA, Danani A, Deriu MA. The Role of Structural Polymorphism in Driving the Mechanical Performance of the Alzheimer's Beta Amyloid Fibrils. Front Bioeng Biotechnol 2019; 7:83. [PMID: 31106199 PMCID: PMC6499180 DOI: 10.3389/fbioe.2019.00083] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/03/2019] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's Disease (AD) is related with the abnormal aggregation of amyloid β-peptides Aβ1−40 and Aβ1−42, the latter having a polymorphic character which gives rise to U- or S-shaped fibrils. Elucidating the role played by the nanoscale-material architecture on the amyloid fibril stability is a crucial breakthrough to better understand the pathological nature of amyloid structures and to support the rational design of bio-inspired materials. The computational study here presented highlights the superior mechanical behavior of the S-architecture, characterized by a Young's modulus markedly higher than the U-shaped architecture. The S-architecture showed a higher mechanical resistance to the enforced deformation along the fibril axis, consequence of a better interchain hydrogen bonds' distribution. In conclusion, this study, focusing the attention on the pivotal multiscale relationship between molecular phenomena and material properties, suggests the S-shaped Aβ1−42 species as a target of election in computational screen/design/optimization of effective aggregation modulators.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Martina Rebella
- Polito BioMEDLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Umberto Morbiducci
- Polito BioMEDLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Jack A Tuszynski
- Polito BioMEDLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy.,Department of Physics, University of Alberta, Edmonton AB, Canada
| | - Andrea Danani
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
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10
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Mu Y, Li N, Hang L, Zhao G, Gao J, Niu Z. Investigation of the Rheological Behaviors of Polymeric Materials in the Film Casting Process through Multiscale Modeling and Simulation Method. MACROMOL THEOR SIMUL 2019. [DOI: 10.1002/mats.201900001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yue Mu
- Key Laboratory for Liquid‐Solid Structural Evolution and Processing of Materials (Ministry of Education)Shandong University Jinan Shandong 250061 P. R. China
- Engineering Research Center for Mould and Die TechnologiesShandong University Jinan Shandong 250061 P. R. China
| | - Na Li
- Key Laboratory for Liquid‐Solid Structural Evolution and Processing of Materials (Ministry of Education)Shandong University Jinan Shandong 250061 P. R. China
- Engineering Research Center for Mould and Die TechnologiesShandong University Jinan Shandong 250061 P. R. China
| | - Lianqiang Hang
- Key Laboratory for Liquid‐Solid Structural Evolution and Processing of Materials (Ministry of Education)Shandong University Jinan Shandong 250061 P. R. China
- Engineering Research Center for Mould and Die TechnologiesShandong University Jinan Shandong 250061 P. R. China
| | - Guoqun Zhao
- Key Laboratory for Liquid‐Solid Structural Evolution and Processing of Materials (Ministry of Education)Shandong University Jinan Shandong 250061 P. R. China
- Engineering Research Center for Mould and Die TechnologiesShandong University Jinan Shandong 250061 P. R. China
| | - Jiacheng Gao
- Key Laboratory for Liquid‐Solid Structural Evolution and Processing of Materials (Ministry of Education)Shandong University Jinan Shandong 250061 P. R. China
- Engineering Research Center for Mould and Die TechnologiesShandong University Jinan Shandong 250061 P. R. China
| | - Zhiyuan Niu
- Key Laboratory for Liquid‐Solid Structural Evolution and Processing of Materials (Ministry of Education)Shandong University Jinan Shandong 250061 P. R. China
- Engineering Research Center for Mould and Die TechnologiesShandong University Jinan Shandong 250061 P. R. China
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11
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Bidone TC, Polley A, Jin J, Driscoll T, Iwamoto DV, Calderwood DA, Schwartz MA, Voth GA. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys J 2019; 116:1000-1010. [PMID: 30851876 DOI: 10.1016/j.bpj.2019.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/25/2018] [Accepted: 02/13/2019] [Indexed: 01/01/2023] Open
Abstract
Integrin conformational dynamics are critical to their receptor and signaling functions in many cellular processes, including spreading, adhesion, and migration. However, assessing integrin conformations is both experimentally and computationally challenging because of limitations in resolution and dynamic sampling. Thus, structural changes that underlie transitions between conformations are largely unknown. Here, focusing on integrin αvβ3, we developed a modified form of the coarse-grained heterogeneous elastic network model (hENM), which allows sampling conformations at the onset of activation by formally separating local fluctuations from global motions. Both local fluctuations and global motions are extracted from all-atom molecular dynamics simulations of the full-length αvβ3 bent integrin conformer, but whereas the former are incorporated in the hENM as effective harmonic interactions between groups of residues, the latter emerge by systematically identifying and treating weak interactions between long-distance domains with flexible and anharmonic connections. The new hENM model allows integrins and single-point mutant integrins to explore various conformational states, including the initiation of separation between α- and β-subunit cytoplasmic regions, headpiece extension, and legs opening.
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Affiliation(s)
- Tamara C Bidone
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Anirban Polley
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Jaehyeok Jin
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Tristan Driscoll
- Yale Cardiovascular Research Center and Department of Internal Medicine (Section of Cardiovascular Medicine), Yale School of Medicine, New Haven, Connecticut
| | | | - David A Calderwood
- Department of Pharmacology, New Haven, Connecticut; Department of Cell Biology, Yale University, New Haven, Connecticut
| | - Martin A Schwartz
- Departments of Cell Biology and Biomedical Engineering, Yale University, New Haven, Connecticut; Yale Cardiovascular Research Center and Department of Internal Medicine (Section of Cardiovascular Medicine), Yale School of Medicine, New Haven, Connecticut
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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12
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Grasso G, Morbiducci U, Massai D, Tuszynski JA, Danani A, Deriu MA. Destabilizing the AXH Tetramer by Mutations: Mechanisms and Potential Antiaggregation Strategies. Biophys J 2019; 114:323-330. [PMID: 29401430 DOI: 10.1016/j.bpj.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/03/2017] [Accepted: 11/20/2017] [Indexed: 01/12/2023] Open
Abstract
The AXH domain of protein Ataxin 1 is thought to play a key role in the misfolding and aggregation pathway responsible for Spinocerebellar ataxia 1. For this reason, a molecular level understanding of AXH oligomerization pathway is crucial to elucidate the aggregation mechanism, which is thought to trigger the disease. This study employs classical and enhanced molecular dynamics to identify the structural and energetic basis of AXH tetramer stability. Results of this work elucidate molecular mechanisms behind the destabilizing effect of protein mutations, which consequently affect the AXH tetramer assembly. Moreover, results of the study draw attention for the first time, to our knowledge, to the R638 protein residue, which is shown to play a key role in AXH tetramer stability. Therefore, R638 might be also implicated in the AXH oligomerization pathway and stands out as a target for future experimental studies focused on self-association mechanisms and fibril formation of full-length ATX1.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Diana Massai
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Andrea Danani
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland.
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13
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Wijerathne WDCC, Rathnayaka CM, Karunasena HCP, Senadeera W, Sauret E, Turner IW, Gu YT. A coarse-grained multiscale model to simulate morphological changes of food-plant tissues undergoing drying. SOFT MATTER 2019; 15:901-916. [PMID: 30543256 DOI: 10.1039/c8sm01593g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Numerical modelling has emerged as a powerful and effective tool to study various dynamic behaviours of biological matter. Such numerical modelling tools have contributed to the optimisations of food drying parameters leading to higher quality end-products in the field of food engineering. In this context, one of the most recent developments is the meshfree-based numerical models, which have demonstrated enhanced capabilities to model cellular deformations during drying, providing many benefits compared to conventional grid-based modelling approaches. However, the potential extension of this method for simulating bulk level tissues has been a challenge due to the increased requirement for higher computational time and resources. As a solution for this, by incorporating meshfree features, a novel coarse-grained multiscale numerical model is proposed in this work to predict bulk level (macroscale) deformations of food-plant tissues during drying. Accordingly, realistic simulation of morphological changes of apple tissues can now be performed with just 2% of the previous computational time in microscale and macroscale simulations can also be conducted. Compared to contemporary multiscale models, this modelling approach provides more convenient computational implementation as well. Thus, this novel approach can be recommended for efficiently and accurately simulating morphological changes of cellular materials undergoing drying processes, while confirming its potential future expansion to efficiently and accurately predict morphological changes of heterogeneous plant tissues in different spatial scales.
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Affiliation(s)
- W D C C Wijerathne
- School of Chemistry, Physics, and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, 2 George St, Brisbane, 4001, Australia.
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14
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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: 11] [Impact Index Per Article: 1.8] [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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Deriu MA, Grasso G, Tuszynski JA, Massai D, Gallo D, Morbiducci U, Danani A. Characterization of the AXH domain of Ataxin-1 using enhanced sampling and functional mode analysis. Proteins 2016; 84:666-73. [DOI: 10.1002/prot.25017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/25/2016] [Accepted: 02/02/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Marco A. Deriu
- Istituto Dalle Molle Di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI); Centro Galleria 2 Manno CH-6928 Switzerland
| | - Gianvito Grasso
- Istituto Dalle Molle Di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI); Centro Galleria 2 Manno CH-6928 Switzerland
| | - Jack A. Tuszynski
- Department of Physics; University of Alberta; Edmonton Alberta Canada
| | - Diana Massai
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
- Department of Cardiothoracic; Transplantation, and Vascular Surgery (HTTG), Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School; Carl-Neuberg-Strabe 1 Hannover 30625 Germany
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
| | - Andrea Danani
- Istituto Dalle Molle Di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI); Centro Galleria 2 Manno CH-6928 Switzerland
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Deriu MA, Grasso G, Tuszynski JA, Gallo D, Morbiducci U, Danani A. Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates. PLoS Comput Biol 2016; 12:e1004699. [PMID: 26745628 PMCID: PMC4706304 DOI: 10.1371/journal.pcbi.1004699] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023] Open
Abstract
The Josephin Domain (JD), i.e. the N-terminal domain of Ataxin 3 (At3) protein, is an interesting example of competition between physiological function and aggregation risk. In fact, the fibrillogenesis of Ataxin 3, responsible for the spinocerebbellar ataxia 3, is strictly related to the JD thermodynamic stability. Whereas recent NMR studies have demonstrated that different JD conformations exist, the likelihood of JD achievable conformational states in solution is still an open issue. Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states. In this work we have carried out an investigation on the JD conformational arrangement by means of both classical molecular dynamics (MD) and Metadynamics employing essential coordinates as collective variables. We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation. Findings of our in silico study strongly point to the closed-like conformation as the most likely for a Josephin Domain in water.
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Affiliation(s)
- Marco A. Deriu
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
- * E-mail:
| | - Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
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Grasso G, Deriu MA, Prat M, Rimondini L, Vernè E, Follenzi A, Danani A. Cell Penetrating Peptide Adsorption on Magnetite and Silica Surfaces: A Computational Investigation. J Phys Chem B 2015; 119:8239-46. [PMID: 26042722 DOI: 10.1021/jp512782e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Magnetic nanoparticles (MNPs) represent one of the most promising materials as they can act as a versatile platform in the field of bionanotechnology for enhanced imaging, diagnosis, and treatment of various diseases. Silica is the most common compound for preparing coated iron oxide NPs since it improves colloidal stability and the binding affinity for various organic molecules. Biomolecules such as cell penetrating peptides (CPPs) might be employed to decorate MNPs, combining their promising physicochemical properties with a cell penetrating ability. In this work, a computational investigation on adsorption of Antennapedia homeodomain-derived penetrating peptide (pAntp) on silica and magnetite (MAG) surfaces is presented. By employing umbrella sampling molecular dynamics, we provided a quantitative estimation of the pAntp-surface adsorption free energy to highlight the influence of surface hydroxylation state on the adsorption mechanism. The interaction between peptide and surface has shown to be mainly driven by electrostatics. In case of MAG surface, also an important contribution of van der Waals (VdW) attraction was observed. Our data suggest that a competitive mechanism between MNPs and cell membrane might partially inhibit the CPP to carry out its membrane penetrating function.
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Affiliation(s)
- Gianvito Grasso
- †Department of Innovative Technologies, University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno CH-6928, Switzerland.,‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Marco A Deriu
- †Department of Innovative Technologies, University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Maria Prat
- ‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Lia Rimondini
- ‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Enrica Vernè
- §Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino IT-10129, Italy
| | - Antonia Follenzi
- ‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Andrea Danani
- †Department of Innovative Technologies, University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno CH-6928, Switzerland
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Bidone TC, Kim T, Deriu MA, Morbiducci U, Kamm RD. Multiscale impact of nucleotides and cations on the conformational equilibrium, elasticity and rheology of actin filaments and crosslinked networks. Biomech Model Mechanobiol 2015; 14:1143-55. [PMID: 25708806 DOI: 10.1007/s10237-015-0660-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 01/01/2023]
Abstract
Cells are able to respond to mechanical forces and deformations. The actin cytoskeleton, a highly dynamic scaffolding structure, plays an important role in cell mechano-sensing. Thus, understanding rheological behaviors of the actin cytoskeleton is critical for delineating mechanical behaviors of cells. The actin cytoskeleton consists of interconnected actin filaments (F-actin) that form via self-assembly of actin monomers. It has been shown that molecular changes of the monomer subunits impact the rigidity of F-actin. However, it remains inconclusive whether or not the molecular changes can propagate to the network level and thus alter the rheological properties of actin networks. Here, we focus on how cation binding and nucleotide state tune the molecular conformation and rigidity of F-actin and a representative rheological behavior of actin networks, strain-stiffening. We employ a multiscale approach by combining established computational techniques: molecular dynamics, normal mode analysis and Brownian dynamics. Our findings indicate that different combinations of nucleotide (ATP, ADP or ADP-Pi) and cation [Formula: see text] or [Formula: see text] at one or multiple sites) binding change the molecular conformation of F-actin by varying inter- and intra-strand interactions which bridge adjacent subunits between and within F-actin helical strands. This is reflected in the rigidity of actin filaments against bending and stretching. We found that differences in extension and bending rigidity of F-actin induced by cation binding to the low-, intermediate- and high-affinity sites vary the strain-stiffening response of actin networks crosslinked by rigid crosslinkers, such as scruin, whereas they minimally impact the strain-stiffening response when compliant crosslinkers, such as filamin A or [Formula: see text]-actinin, are used.
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Affiliation(s)
- Tamara Carla Bidone
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, corso Duca degli Abruzzi 24, 10129, Turin, Italy
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Deriu MA, Grasso G, Licandro G, Danani A, Gallo D, Tuszynski JA, Morbiducci U. Investigation of the Josephin Domain protein-protein interaction by molecular dynamics. PLoS One 2014; 9:e108677. [PMID: 25268243 PMCID: PMC4182536 DOI: 10.1371/journal.pone.0108677] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/23/2014] [Indexed: 11/18/2022] Open
Abstract
Spinocerebellar ataxia (SCA) 3, the most common form of SCA, is a neurodegenerative rare disease characterized by polyglutamine tract expansion and self-assembly of Ataxin3 (At3) misfolded proteins into highly organized fibrillar aggregates. The At3 N-terminal Josephin Domain (JD) has been suggested as being responsible for mediating the initial phase of the At3 double-step fibrillogenesis. Several issues concerning the residues involved in the JD's aggregation and, more generally, the JD clumping mechanism have not been clarified yet. In this paper we present an investigation focusing on the JD protein-protein interaction by means of molecular modeling. Our results suggest possible aminoacids involved in JD contact together with local and non-local effects following JD dimerization. Surprisingly, JD conformational changes following the binding may involve ubiquitin binding sites and hairpin region even though they do not pertain to the JD interaction surfaces. Moreover, the JD binding event has been found to alter the hairpin open-like conformation toward a closed-like arrangement over the simulated timescale. Finally, our results suggest that the JD aggregation might be a multi-step process, with an initial fast JD-JD binding mainly driven by Arg101, followed by slower structural global rearrangements involving the exposure to the solvent of Leu84-Trp87, which might play a role in a second step of JD aggregation.
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Affiliation(s)
- Marco A. Deriu
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
- * E-mail:
| | - Gianvito Grasso
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Ginevra Licandro
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Andrea Danani
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
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20
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Genchev GZ, Kobayashi T, Lu H. Calcium induced regulation of skeletal troponin--computational insights from molecular dynamics simulations. PLoS One 2013; 8:e58313. [PMID: 23554884 PMCID: PMC3598806 DOI: 10.1371/journal.pone.0058313] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/01/2013] [Indexed: 01/11/2023] Open
Abstract
The interaction between calcium and the regulatory site(s) of striated muscle regulatory protein troponin switches on and off muscle contraction. In skeletal troponin binding of calcium to sites I and II of the TnC subunit results in a set of structural changes in the troponin complex, displaces tropomyosin along the actin filament and allows myosin-actin interaction to produce mechanical force. In this study, we used molecular dynamics simulations to characterize the calcium dependent dynamics of the fast skeletal troponin molecule and its TnC subunit in the calcium saturated and depleted states. We focused on the N-lobe and on describing the atomic level events that take place subsequent to removal of the calcium ion from the regulatory sites I and II. A main structural event - a closure of the A/B helix hydrophobic pocket results from the integrated effect of the following conformational changes: the breakage of H-bond interactions between the backbone nitrogen atoms of the residues at positions 2, 9 and sidechain oxygen atoms of the residue at position 12 (N2-OE12/N9-OE12) in sites I and II; expansion of sites I and II and increased site II N-terminal end-segment flexibility; strengthening of the β-sheet scaffold; and the subsequent re-packing of the N-lobe hydrophobic residues. Additionally, the calcium release allows the N-lobe to rotate relative to the rest of the Tn molecule. Based on the findings presented herein we propose a novel model of skeletal thin filament regulation.
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Affiliation(s)
- Georgi Z. Genchev
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Tomoyoshi Kobayashi
- Department of Physiology and Biophysics and Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (HL); (TK)
| | - Hui Lu
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Shanghai Institute of Medical Genetics, Children’s Hospital of Shanghai, Shanghai, China
- Key Lab of Embryo Molecular Biology, Ministry of Health, Shanghai, China
- Shanghai Lab of Embryo and Reproduction Engineering, Shanghai, China
- * E-mail: (HL); (TK)
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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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