1
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Wang Y, Wu J, Zsolnay V, Pollard TD, Voth GA. Mechanism of phosphate release from actin filaments. Proc Natl Acad Sci U S A 2024; 121:e2408156121. [PMID: 38980907 PMCID: PMC11260136 DOI: 10.1073/pnas.2408156121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
After ATP-actin monomers assemble filaments, the ATP's [Formula: see text]-phosphate is hydrolyzedwithin seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to sample the release of phosphate from filaments and study residues that gate release. Dissociation of phosphate from Mg2+ is rate limiting and associated with an energy barrier of 20 kcal/mol, consistent with experimental rates of phosphate release. Phosphate then diffuses within an internal cavity toward a gate formed by R177, as suggested in prior computational studies and cryo-EM structures. The gate is closed when R177 hydrogen bonds with N111 and is open when R177 forms a salt bridge with D179. Most of the time, interactions of R177 with other residues occlude the phosphate release pathway. Machine learning analysis reveals that the occluding interactions fluctuate rapidly, underscoring the secondary role of backdoor gate opening in Pi release, in contrast with the previous hypothesis that gate opening is the primary event.
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Affiliation(s)
- Yihang Wang
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL60637
| | - Jiangbo Wu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL60637
| | - Vilmos Zsolnay
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL60637
| | - Thomas D. Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT06511
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
- Department of Cell Biology, Yale University, New Haven, CT06510
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL60637
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2
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Wang Y, Wu J, Zsolnay V, Pollard TD, Voth GA. Mechanism of Phosphate Release from Actin Filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.03.551904. [PMID: 37577500 PMCID: PMC10418243 DOI: 10.1101/2023.08.03.551904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
After ATP-actin monomers assemble filaments, the ATP's γ-phosphate is hydrolyzed within seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to sample the release of phosphate from filaments and study residues that gate release. Dissociation of phosphate from Mg2+ is rate limiting and associated with an energy barrier of 20 kcal/mol, consistent with experimental rates of phosphate release. Phosphate then diffuses in an internal cavity toward a gate formed by R177 suggested in prior computational studies and cryo-EM structures. The gate is closed when R177 hydrogen bonds with N111 and is open when R177 forms a salt bridge with D179. Most of the time interactions of R177 with other residues occludes the phosphate release pathway. Machine learning analysis reveals that the occluding interactions fluctuate rapidly, underscoring the secondary role of backdoor gate opening in Pi release, in contrast with the previous hypothesis that gate opening is the primary event.
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Affiliation(s)
- Yihang Wang
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL
| | - Jiangbo Wu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL
| | - Vilmos Zsolnay
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL
| | - Thomas D. Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
- Department of Cell Biology, Yale University, New Haven, CT
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL
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3
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Mukadum F, Ccoa WJP, Hocky GM. Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton. Cytoskeleton (Hoboken) 2024:10.1002/cm.21837. [PMID: 38334204 PMCID: PMC11310368 DOI: 10.1002/cm.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
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Affiliation(s)
- Fatemah Mukadum
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | | - Glen M. Hocky
- Department of Chemistry, New York University, New York, NY 10003, USA
- Simons Center for Computational Physical Chemistry, New York, NY 10003, USA
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4
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Galata AA, Kröger M. Globular Proteins and Where to Find Them within a Polymer Brush-A Case Study. Polymers (Basel) 2023; 15:polym15102407. [PMID: 37242983 DOI: 10.3390/polym15102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Protein adsorption by polymerized surfaces is an interdisciplinary topic that has been approached in many ways, leading to a plethora of theoretical, numerical and experimental insight. There is a wide variety of models trying to accurately capture the essence of adsorption and its effect on the conformations of proteins and polymers. However, atomistic simulations are case-specific and computationally demanding. Here, we explore universal aspects of the dynamics of protein adsorption through a coarse-grained (CG) model, that allows us to explore the effects of various design parameters. To this end, we adopt the hydrophobic-polar (HP) model for proteins, place them uniformly at the upper bound of a CG polymer brush whose multibead-spring chains are tethered to a solid implicit wall. We find that the most crucial factor affecting the adsorption efficiency appears to be the polymer grafting density, while the size of the protein and its hydrophobicity ratio come also into play. We discuss the roles of ligands and attractive tethering surfaces to the primary adsorption as well as secondary and ternary adsorption in the presence of attractive (towards the hydrophilic part of the protein) beads along varying spots of the backbone of the polymer chains. The percentage and rate of adsorption, density profiles and the shapes of the proteins, alongside with the respective potential of mean force are recorded to compare the various scenarios during protein adsorption.
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Affiliation(s)
- Aikaterini A Galata
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Kröger
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
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5
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Anand DV, Wei RKJ, Xia K. Coarse-Grained Models for Vault Normal Model Analysis. Methods Mol Biol 2023; 2671:307-318. [PMID: 37308652 DOI: 10.1007/978-1-0716-3222-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent experiments have shown that the molecular complex of vault has large conformational changes at its shoulder and cap regions in solution. From the comparison of two configuration structures, it has been found that the shoulder region can twist and move outward, while the cap region will rotate and push upward correspondingly. To further understand these experimental results, in this paper, we study the vault dynamics for the first time. Since vault has an extremely large-sized structure with around 63,336 Cα atoms, traditional normal mode method with the Cα coarse-grained representation will fall short. We employ a newly invented multiscale virtual particle-based anisotropic network model (MVP-ANM). To reduce the complexity, the 39-folder vault structure is coarse-grained to about 6000 virtual particles, which significantly reduces the computational cost while still maintaining the basic structure information. Among the 14 low frequency eigenmodes from Mode 7 to Mode 20, two eigenmodes, i.e., Mode 9 and Mode 20, are found to be directly associated with the experimental observations. In Mode 9, shoulder region undergoes a significant expansion while the cap part is lifted upward. In Mode 20, a clear rotation of both shoulder and cap regions is well observed. Our results are consistent with the experimental observations. More importantly, these low frequency eigenmodes indicate that the vault waist, shoulder and lower cap regions are the most likely regions for the opening of the vault particle. And the opening mechanism is highly likely to be rotation and expansion at these regions. As far as we know, this is the first work to provide the normal mode analysis for the vault complex.
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Affiliation(s)
- D Vijay Anand
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ronald Koh Joon Wei
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelin Xia
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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6
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Sun X, Alushin GM. Cellular force-sensing through actin filaments. FEBS J 2022; 290:2576-2589. [PMID: 35778931 PMCID: PMC9945651 DOI: 10.1111/febs.16568] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 02/05/2023]
Abstract
The actin cytoskeleton orchestrates cell mechanics and facilitates the physical integration of cells into tissues, while tissue-scale forces and extracellular rigidity in turn govern cell behaviour. Here, we discuss recent evidence that actin filaments (F-actin), the core building blocks of the actin cytoskeleton, also serve as molecular force sensors. We delineate two classes of proteins, which interpret forces applied to F-actin through enhanced binding interactions: 'mechanically tuned' canonical actin-binding proteins, whose constitutive F-actin affinity is increased by force, and 'mechanically switched' proteins, which bind F-actin only in the presence of force. We speculate mechanically tuned and mechanically switched actin-binding proteins are biophysically suitable for coordinating cytoskeletal force-feedback and mechanical signalling processes, respectively. Finally, we discuss potential mechanisms mediating force-activated actin binding, which likely occurs both through the structural remodelling of F-actin itself and geometric rearrangements of higher-order actin networks. Understanding the interplay of these mechanisms will enable the dissection of force-activated actin binding's specific biological functions.
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Affiliation(s)
- Xiaoyu Sun
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University. New York, NY, USA.,Correspondence: ;
| | - Gregory M. Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University. New York, NY, USA.,Correspondence: ;
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7
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Yu CC, Raj N, Chu JW. Edge weights in a protein elastic network reorganize collective motions and render long-range sensitivity responses. J Chem Phys 2022; 156:245105. [DOI: 10.1063/5.0095107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effects of inter-residue interactions on protein collective motions are analyzed by comparing two elastic network models (ENM)—structural contact ENM (SC-ENM) and molecular dynamics (MD)-ENM—with the edge weights computed from an all-atom MD trajectory by structure-mechanics statistical learning. A theoretical framework is devised to decompose the eigenvalues of ENM Hessian into contributions from individual springs and to compute the sensitivities of positional fluctuations and covariances to spring constant variation. Our linear perturbation approach quantifies the response mechanisms as softness modulation and orientation shift. All contacts of C α positions in SC-ENM have an identical spring constant by fitting the profile of root-of-mean-squared-fluctuation calculated from an all-atom MD simulation, and the same trajectory data are also used to compute the specific spring constant of each contact as an MD-ENM edge weight. We illustrate that the soft-mode reorganization can be understood in terms of gaining weights along the structural contacts of low elastic strengths and loosing magnitude along those of high rigidities. With the diverse mechanical strengths encoded in protein dynamics, MD-ENM is found to have more pronounced long-range couplings and sensitivity responses with orientation shift identified as a key player in driving the specific residues to have high sensitivities. Furthermore, the responses of perturbing the springs of different residues are found to have asymmetry in the action–reaction relationship. In understanding the mutation effects on protein functional properties, such as long-range communications, our results point in the directions of collective motions as a major effector.
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Affiliation(s)
- Chieh Cheng Yu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, 75 Bo-Ai Street, Hsinchu 30010, Taiwan
| | - Nixon Raj
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, 75 Bo-Ai Street, Hsinchu 30010, Taiwan
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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8
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Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092785. [PMID: 35566140 PMCID: PMC9104776 DOI: 10.3390/molecules27092785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022]
Abstract
Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation; that is, the target distribution function and the PMF potential energy are extracted, and then, the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have been through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.
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9
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Hernández-Del-Valle M, Valencia-Expósito A, López-Izquierdo A, Casanova-Ferrer P, Tarazona P, Martín-Bermudo MD, Míguez DG. A coarse-grained approach to model the dynamics of the actomyosin cortex. BMC Biol 2022; 20:90. [PMID: 35459165 PMCID: PMC9034637 DOI: 10.1186/s12915-022-01279-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 03/11/2022] [Indexed: 01/21/2023] Open
Abstract
Background The dynamics of the actomyosin machinery is at the core of many important biological processes. Several relevant cellular responses such as the rhythmic compression of the cell cortex are governed, at a mesoscopic level, by the nonlinear interaction between actin monomers, actin crosslinkers, and myosin motors. Coarse-grained models are an optimal tool to study actomyosin systems, since they can include processes that occur at long time and space scales, while maintaining the most relevant features of the molecular interactions. Results Here, we present a coarse-grained model of a two-dimensional actomyosin cortex, adjacent to a three-dimensional cytoplasm. Our simplified model incorporates only well-characterized interactions between actin monomers, actin crosslinkers and myosin, and it is able to reproduce many of the most important aspects of actin filament and actomyosin network formation, such as dynamics of polymerization and depolymerization, treadmilling, network formation, and the autonomous oscillatory dynamics of actomyosin. Conclusions We believe that the present model can be used to study the in vivo response of actomyosin networks to changes in key parameters of the system, such as alterations in the attachment of actin filaments to the cell cortex. Supplementary Information The online version contains supplementary material available at (10.1186/s12915-022-01279-2).
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Affiliation(s)
- Miguel Hernández-Del-Valle
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,IFIMAC, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Instituto Nicolás Cabrera, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Fisica de la Materia Condensada, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Andrea Valencia-Expósito
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Carretera de Utrera km 1, Seville, 41013, Spain
| | - Antonio López-Izquierdo
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,IFIMAC, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Instituto Nicolás Cabrera, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Fisica de la Materia Condensada, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pau Casanova-Ferrer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,IFIMAC, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Instituto Nicolás Cabrera, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Fisica de la Materia Condensada, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pedro Tarazona
- IFIMAC, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Instituto Nicolás Cabrera, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.,Fisica Teórica de la Materia Condensada, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Maria D Martín-Bermudo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Carretera de Utrera km 1, Seville, 41013, Spain
| | - David G Míguez
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Madrid, 28049, Spain. .,IFIMAC, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain. .,Instituto Nicolás Cabrera, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain. .,Fisica de la Materia Condensada, Fac. de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain.
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10
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Tan C, Jung J, Kobayashi C, Torre DUL, Takada S, Sugita Y. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PLoS Comput Biol 2022; 18:e1009578. [PMID: 35381009 PMCID: PMC9012402 DOI: 10.1371/journal.pcbi.1009578] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/15/2022] [Accepted: 03/26/2022] [Indexed: 12/28/2022] Open
Abstract
Residue-level coarse-grained (CG) models have become one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. To investigate large-scale biological phenomena in molecular dynamics (MD) simulations with CG models, unified treatments of proteins and nucleic acids, as well as efficient parallel computations, are indispensable. In the GENESIS MD software, we implement several residue-level CG models, covering structure-based and context-based potentials for both well-folded biomolecules and intrinsically disordered regions. An amino acid residue in protein is represented as a single CG particle centered at the Cα atom position, while a nucleotide in RNA or DNA is modeled with three beads. Then, a single CG particle represents around ten heavy atoms in both proteins and nucleic acids. The input data in CG MD simulations are treated as GROMACS-style input files generated from a newly developed toolbox, GENESIS-CG-tool. To optimize the performance in CG MD simulations, we utilize multiple neighbor lists, each of which is attached to a different nonbonded interaction potential in the cell-linked list method. We found that random number generations for Gaussian distributions in the Langevin thermostat are one of the bottlenecks in CG MD simulations. Therefore, we parallelize the computations with message-passing-interface (MPI) to improve the performance on PC clusters or supercomputers. We simulate Herpes simplex virus (HSV) type 2 B-capsid and chromatin models containing more than 1,000 nucleosomes in GENESIS as examples of large-scale biomolecular simulations with residue-level CG models. This framework extends accessible spatial and temporal scales by multi-scale simulations to study biologically relevant phenomena, such as genome-scale chromatin folding or phase-separated membrane-less condensations.
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Affiliation(s)
- Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Diego Ugarte La Torre
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
- * E-mail:
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11
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Raj N, Click TH, Yang H, Chu JW. Structure-mechanics statistical learning uncovers mechanical relay in proteins. Chem Sci 2022; 13:3688-3696. [PMID: 35432911 PMCID: PMC8966636 DOI: 10.1039/d1sc06184d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/10/2022] [Indexed: 12/31/2022] Open
Abstract
A protein's adaptive response to its substrates is one of the key questions driving molecular physics and physical chemistry. This work employs the recently developed structure-mechanics statistical learning method to establish a mechanical perspective. Specifically, by mapping all-atom molecular dynamics simulations onto the spring parameters of a backbone-side-chain elastic network model, the chemical moiety specific force constants (or mechanical rigidity) are used to assemble the rigidity graph, which is the matrix of inter-residue coupling strength. Using the S1A protease and the PDZ3 signaling domain as examples, chains of spatially contiguous residues are found to exhibit prominent changes in their mechanical rigidity upon substrate binding or dissociation. Such a mechanical-relay picture thus provides a mechanistic underpinning for conformational changes, long-range communication, and inter-domain allostery in both proteins, where the responsive mechanical hotspots are mostly residues having important biological functions or significant mutation sensitivity. Protein residues exhibit specific routes of mechanical relay as the adaptive responses to substrate binding or dissociation. On such physically contiguous connections, residues experience prominent changes in their coupling strengths.![]()
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Affiliation(s)
- Nixon Raj
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| | - Timothy H Click
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
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12
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Wang C, Li S, Ademiloye AS, Nithiarasu P. Biomechanics of cells and subcellular components: A comprehensive review of computational models and applications. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2021; 37:e3520. [PMID: 34390323 DOI: 10.1002/cnm.3520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
Cells are a fundamental structural, functional and biological unit for all living organisms. Up till now, considerable efforts have been made to study the responses of single cells and subcellular components to an external load, and understand the biophysics underlying cell rheology, mechanotransduction and cell functions using experimental and in silico approaches. In the last decade, computational simulation has become increasingly attractive due to its critical role in interpreting experimental data, analysing complex cellular/subcellular structures, facilitating diagnostic designs and therapeutic techniques, and developing biomimetic materials. Despite the significant progress, developing comprehensive and accurate models of living cells remains a grand challenge in the 21st century. To understand current state of the art, this review summarises and classifies the vast array of computational biomechanical models for cells. The article covers the cellular components at multi-spatial levels, that is, protein polymers, subcellular components, whole cells and the systems with scale beyond a cell. In addition to the comprehensive review of the topic, this article also provides new insights into the future prospects of developing integrated, active and high-fidelity cell models that are multiscale, multi-physics and multi-disciplinary in nature. This review will be beneficial for the researchers in modelling the biomechanics of subcellular components, cells and multiple cell systems and understanding the cell functions and biological processes from the perspective of cell mechanics.
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Affiliation(s)
- Chengyuan Wang
- Zienkiewicz Centre for Computational Engineering, Faculty of Science and Engineering, Swansea University, Bay Campus, Swansea, UK
| | - Si Li
- Zienkiewicz Centre for Computational Engineering, Faculty of Science and Engineering, Swansea University, Bay Campus, Swansea, UK
| | - Adesola S Ademiloye
- Zienkiewicz Centre for Computational Engineering, Faculty of Science and Engineering, Swansea University, Bay Campus, Swansea, UK
| | - Perumal Nithiarasu
- Zienkiewicz Centre for Computational Engineering, Faculty of Science and Engineering, Swansea University, Bay Campus, Swansea, UK
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13
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Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function. Comput Struct Biotechnol J 2021; 19:5309-5320. [PMID: 34765086 PMCID: PMC8554173 DOI: 10.1016/j.csbj.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/02/2021] [Accepted: 09/05/2021] [Indexed: 11/23/2022] Open
Abstract
Statistical learning from protein dynamics unravels rigidities in interaction network. Backbone and side-chain mechanical couplings exhibit scale-free network properties. Graphical depiction of network rigidities captures sequence co-evolution patterns. Functional sites at secondary structure peripheries are mechanical hotspots. Our rigidity scores are compelling metrics for residue biological significance.
A backbone-side-chain elastic network model (bsENM) is devised in this contribution to decipher the network of molecular interactions during protein dynamics. The chemical details in 5 μs all-atom molecular dynamics (MD) simulation are mapped onto the bsENM spring constants by self-consistent iterations. The elastic parameters obtained by this structure-mechanics statistical learning are then used to construct inter-residue rigidity graphs for the chemical components in protein amino acids. A key discovery is that the mechanical coupling strengths of both backbone and side chains exhibit heavy-tailed distributions and scale-free network properties. In both rat trypsin and PDZ3 proteins, the statistically prominent modes of rigidity graphs uncover the sequence-specific coupling patterns and mechanical hotspots. Based on the contributions to graphical modes, our residue rigidity scores in backbone and side chains are found to be very useful metrics for the biological significance. Most functional sites have high residue rigidity scores in side chains while the biologically important glycines are generally next to mechanical hotspots. Furthermore, prominent modes in the rigidity graphs involving side chains oftentimes coincide with the co-evolution patterns due to evolutionary restraints. The bsENM specifically devised to resolve the protein chemical character thus provides useful means for extracting functional information from all-atom MD.
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14
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Kumar A, Zhong Y, Albrecht A, Sang PB, Maples A, Liu Z, Vinayachandran V, Reja R, Lee CF, Kumar A, Chen J, Xiao J, Park B, Shen J, Liu B, Person MD, Trybus KM, Zhang KYJ, Pugh BF, Kamm KE, Milewicz DM, Shen X, Kapoor P. Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. Cell Rep 2021; 32:108172. [PMID: 32997990 PMCID: PMC8860185 DOI: 10.1016/j.celrep.2020.108172] [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: 09/16/2019] [Revised: 07/11/2020] [Accepted: 08/27/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear actin has been elusive due to the lack of knowledge about molecular mechanisms. From actin-containing chromatin remodeling complexes, we discovered an arginine mono-methylation mark on an evolutionarily conserved R256 residue of actin (R256me1). Actin R256 mutations in yeast affect nuclear functions and cause diseases in human. Interestingly, we show that an antibody specific for actin R256me1 preferentially stains nuclear actin over cytoplasmic actin in yeast, mouse, and human cells. We also show that actin R256me1 is regulated by protein arginine methyl transferase-5 (PRMT5) in HEK293 cells. A genome-wide survey of actin R256me1 mark provides a landscape for nuclear actin correlated with transcription. Further, gene expression and protein interaction studies uncover extensive correlations between actin R256me1 and active transcription. The discovery of actin R256me1 mark suggests a fundamental mechanism to distinguish nuclear actin from cytoplasmic actin through post-translational modification (PTM) and potentially implicates an actin PTM mark in transcription and human diseases. Nuclear actin and actin PTMs are poorly understood. Kumar et al. discover a system of actin PTMs similar to histone PTMs, including a conserved mark on nuclear actin (R256me1) with potential implications for transcription and human diseases.
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Affiliation(s)
- Ashok Kumar
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA
| | - Yuan Zhong
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Amelie Albrecht
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Pau Biak Sang
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA
| | - Adrian Maples
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA
| | - Zhenan Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vinesh Vinayachandran
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rohit Reja
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chia-Fang Lee
- ICMB Proteomics Facility, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jiyuan Chen
- Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Jing Xiao
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Bongsoo Park
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Maria D Person
- ICMB Proteomics Facility, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05405, USA
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kristine E Kamm
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dianna M Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Xuetong Shen
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA.
| | - Prabodh Kapoor
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA.
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15
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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16
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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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17
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Mani S, Katkar HH, Voth GA. Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments. J Chem Theory Comput 2021; 17:1900-1913. [PMID: 33596075 DOI: 10.1021/acs.jctc.0c01186] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Actin filament networks in eukaryotic cells are constantly remodeled through nucleotide state controlled interactions with actin binding proteins, leading to macroscopic structures such as bundled filaments, branched filaments, and so on. The nucleotide (ATP) hydrolysis, phosphate release, and polymerization/depolymerization reactions that lead to the formation of these structures are correlated with the conformational fluctuations of the actin subunits at the molecular scale. The resulting structures generate and experience varying levels of force and impart cells with several functionalities such as their ability to move, divide, transport cargo, etc. Models that explicitly connect the structure to reactions are essential to elucidate a fundamental level of understanding of these processes. In this regard, a bottom-up Ultra-Coarse-Grained (UCG) model of actin filaments that can simulate ATP hydrolysis, inorganic phosphate release (Pi), and depolymerization reactions is presented in this work. In this model, actin subunits are represented using coarse-grained particles that evolve in time and undergo reactions depending on the conformations sampled. The reactions are represented through state transitions, with each state represented by a unique effective coarse-grained potential. Effects of compressive and tensile strains on the rates of reactions are then analyzed. Compressive strains tend to unflatten the actin subunits, reduce the rate of ATP hydrolysis, and increase the Pi release rate. On the other hand, tensile strain flattens subunits, increases the rate of ATP hydrolysis, and decrease the Pi release rate. Incorporating these predictions into a Markov State Model highlighted that strains alter the steady-state distribution of subunits with ADPPi and ADP nucleotide, thus identifying possible additional factors underlying the cooperative binding of regulatory proteins to actin filaments.
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Affiliation(s)
- Sriramvignesh Mani
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Harshwardhan H Katkar
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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18
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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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19
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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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20
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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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21
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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: 42] [Impact Index Per Article: 10.5] [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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22
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Chen YT, Yang H, Chu JW. Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids. Chem Sci 2020; 11:4969-4979. [PMID: 34122953 PMCID: PMC8159235 DOI: 10.1039/d0sc00480d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals. The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.![]()
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China +886 3 5712121 ext. 56996
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23
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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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24
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Wu Z, Zhang Y, Zhang JZ, Xia K, Xia F. Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes. J Comput Chem 2019; 41:14-20. [PMID: 31568566 DOI: 10.1002/jcc.26070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/15/2019] [Accepted: 08/27/2019] [Indexed: 12/30/2022]
Abstract
The development of ultracoarse-grained models for large biomolecules needs to derive the optimal number of coarse-grained (CG) sites to represent the targets. In this work, we propose to use the statistical internal cluster validation indexes to determine the optimal number of CG sites that are optimized based on the essential dynamics coarse-graining method. The calculated curves of Calinski-Harabasz and Silhouette Coefficient indexes exhibit the extrema corresponding to the similar CG numbers. The calculated ratios of the optimal CG numbers to the residue numbers of fine-grained models are in the range from 4 to 2. The comparison of the stability of index results indicates that Calinski-Harabasz index is the better choice to determine the optimal CG representation in coarse-graining. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhenliang Wu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Yuwei Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - John Zenghui Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.,School of Biological Sciences, Nanyang Technological University, 637371, Singapore
| | - Fei Xia
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
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25
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Lee M, Kang EH. Molecular dynamics study of interactions between polymorphic actin filaments and gelsolin segment-1. Proteins 2019; 88:385-392. [PMID: 31498927 DOI: 10.1002/prot.25813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/22/2019] [Accepted: 09/04/2019] [Indexed: 11/08/2022]
Abstract
The assembly of protein actin into double-helical filaments promotes many eukaryotic cellular processes that are regulated by actin-binding proteins (ABPs). Actin filaments can adopt multiple conformations, known as structural polymorphism, which possibly influences the interaction between filaments and ABPs. Gelsolin is a Ca2+ -regulated ABP that severs and caps actin filaments. Gelsolin binding modulates filament structure; however, it is not known how polymorphic actin filament structures influence an interaction of gelsolin S1 with the barbed-end of filament. Herein, we investigated how polymorphic structures of actin filaments affect the interactions near interfaces between the gelsolin segment 1 (S1) domain and the filament barbed-end. Using all-atom molecular dynamics simulations, we demonstrate that different tilted states of subunits modulate gelsolin S1 interactions with the barbed-end of polymorphic filaments. Hydrogen bonding and interaction energy at the filament-gelsolin S1 interface indicate distinct conformations of filament barbed ends, resulting in different interactions of gelsolin S1. This study demonstrates that filament's structural multiplicity plays important roles in the interactions of actin with ABPs.
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Affiliation(s)
- Myeongsang Lee
- NanoScience Technology Center, University of Central Florida, Orlando, Florida
| | - Ellen H Kang
- NanoScience Technology Center, University of Central Florida, Orlando, Florida.,Department of Physics, University of Central Florida, Orlando, Florida.,Department of Materials Science and Engineering, University of Central Florida, Orlando, Florida
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26
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Schramm AC, Hocky GM, Voth GA, Martiel JL, De La Cruz EM. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophys J 2019; 117:453-463. [PMID: 31301801 DOI: 10.1016/j.bpj.2019.06.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022] Open
Abstract
The assembly of actin filaments and filament networks generate forces that drive cell and vesicle movement. These structures and the comprising actin filaments must be mechanically stable to sustain these forces and maintain their structural integrity. Filaments in these dynamic structures must also be disassembled to recycle and replenish the pool of actin monomers available for polymerization. Actin-severing proteins such as cofilin and contractile myosin motor proteins fragment these nominally stable structures. We developed a mesoscopic-length-scale actin filament model to investigate force-induced filament fragmentation. We show that fragmentation in our model occurs at curvatures similar to previous measurements of fragmentation within (cofil)actin and actin-cofilactin boundaries. Boundaries between bare and cofilin-decorated segments are brittle and fragment at small bending and twisting deformations. Extending filaments disperses strain uniformly over subunit interfaces, and filaments fragment with no detectable partial rupture or plastic deformation. In contrast, bending or twisting filaments imposes nonuniform interface strain and leads to partial interface rupture, accelerating filament fragmentation. As a result, the rupture force under compressive loads is an order of magnitude lower than under tensile loads. Partial interface rupture may be a primary mechanism of accelerating actin filament fragmentation by other actin-destabilizing proteins.
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Affiliation(s)
- Anthony C Schramm
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, New York
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois
| | - Jean-Louis Martiel
- TIMC-IMAG Lab, UMR 5525, Inserm/CNRS/Université Grenoble-Alpes, Tronche, France.
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
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Gong B, Wei X, Qian J, Lin Y. Modeling and Simulations of the Dynamic Behaviors of Actin-Based Cytoskeletal Networks. ACS Biomater Sci Eng 2019; 5:3720-3734. [DOI: 10.1021/acsbiomaterials.8b01228] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Bo Gong
- Department of Engineering Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Xi Wei
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Jin Qian
- Department of Engineering Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Yuan Lin
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
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28
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Anand DV, Meng Z, Xia K. A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes. Phys Chem Chem Phys 2019; 21:4359-4366. [DOI: 10.1039/c8cp07442a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CMVP-ENM for virus normal mode analysis. With a special ratio parameter, CMVP-ENM can characterize the multi-material properties of biomolecular complexes and systematically enhance or suppress the modes for different components.
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Affiliation(s)
- D. Vijay Anand
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - Zhenyu Meng
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Kelin Xia
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
- School of Biological Sciences
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29
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Aydin F, Katkar HH, Voth GA. Multiscale simulation of actin filaments and actin-associated proteins. Biophys Rev 2018; 10:1521-1535. [PMID: 30382557 PMCID: PMC6297090 DOI: 10.1007/s12551-018-0474-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/21/2018] [Indexed: 02/04/2023] Open
Abstract
Actin is an important cytoskeletal protein that serves as a building block to form filament networks that span across the cell. These networks are orchestrated by a myriad of other cytoskeletal entities including the unbranched filament-forming protein formin and branched network-forming protein complex Arp2/3. Computational models have been able to provide insights into many important structural transitions that are involved in forming these networks, and into the nature of interactions essential for actin filament formation and for regulating the behavior of actin-associated proteins. In this review, we summarize a subset of such models that focus on the atomistic features and those that can integrate atomistic features into a larger picture in a multiscale fashion.
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Affiliation(s)
- Fikret Aydin
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Harshwardhan H Katkar
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Gregory A Voth
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA.
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30
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Fortoul N, Bykhovskaia M, Jagota A. Coarse-Grained Model for Zippering of SNARE from Partially Assembled States. J Phys Chem B 2018; 122:10834-10840. [PMID: 30408418 DOI: 10.1021/acs.jpcb.8b09502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the presynaptic membrane. Vesicles are attached to the membrane via the SNARE complex, comprising the vesicle associated protein synaptobrevin (Syb), the membrane associated protein syntaxin (Syx), and the cytosolic protein SNAP25, that together form a four-helical bundle. The full assembly of Syb onto the core SNARE bundle promotes vesicle fusion. We investigated SNARE assembly using a coarse-grained model of the SNARE complex that retains chemical specificity. Steered force-control simulations of SNARE unzippering were used to set up initial disassembled states of the SNARE complex. From these states, the assembly process was simulated. We find that if Syb is in helical form and proximal to the other helices, then the SNARE complex assembles rapidly, on a microsecond time-scale, which is well within in vivo synaptic vesicle fusion time scales. Assembly times grow exponentially with a separation distance between Syb and Syx C-termini. Our results indicate that for biologically relevant rapid assembly of the SNARE complex, Syb should be in helical form, and the SNARE constituent helices brought into proximity, possibly by an agent, such as a chaperone.
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31
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Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations. Curr Opin Struct Biol 2018; 56:1-10. [PMID: 30439585 DOI: 10.1016/j.sbi.2018.10.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 11/22/2022]
Abstract
While many proteins and protein regions utilize a complex repertoire of amino acids to achieve their biological function, a subset of protein sequences are enriched in a reduced set of amino acids. These so-called low complexity (LC) sequences, specifically intrinsically disordered variants of LC sequences, have been the focus of recent investigations owing to their roles in a range of biological functions, specifically phase separation. Computational studies of LC sequences have provided rich insights into their behavior both as individual proteins in dilute solutions and as the drivers and modulators of higher-order assemblies. Here, we review how simulations performed across distinct resolutions have provided different types of insights into the biological role of LC sequences.
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32
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Katkar HH, Davtyan A, Durumeric AEP, Hocky GM, Schramm AC, De La Cruz EM, Voth GA. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophys J 2018; 115:1589-1602. [PMID: 30249402 PMCID: PMC6260209 DOI: 10.1016/j.bpj.2018.08.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
Actin filaments continually assemble and disassemble within a cell. Assembled filaments "age" as a bound nucleotide ATP within each actin subunit quickly hydrolyzes followed by a slower release of the phosphate Pi, leaving behind a bound ADP. This subtle change in nucleotide state of actin subunits affects filament rigidity as well as its interactions with binding partners. We present here a systematic multiscale ultra-coarse-graining approach that provides a computationally efficient way to simulate a long actin filament undergoing ATP hydrolysis and phosphate-release reactions while systematically taking into account available atomistic details. The slower conformational changes and their dependence on the chemical reactions are simulated with the ultra-coarse-graining model by assigning internal states to the coarse-grained sites. Each state is represented by a unique potential surface of a local heterogeneous elastic network. Internal states undergo stochastic transitions that are coupled to conformations of the underlying molecular system. The model reproduces mechanical properties of the filament and allows us to study whether conformational fluctuations in actin subunits produce cooperative filament aging. We find that the nucleotide states of neighboring subunits modulate the reaction kinetics, implying cooperativity in ATP hydrolysis and Pi release. We further systematically coarse grain the system into a Markov state model that incorporates assembly and disassembly, facilitating a direct comparison with previously published models. We find that cooperativity in ATP hydrolysis and Pi release significantly affects the filament growth dynamics only near the critical G-actin concentration, whereas far from it, both cooperative and random mechanisms show similar growth dynamics. In contrast, filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights, to our knowledge, into the cooperative nature of ATP hydrolysis and Pi release and the implications it has for actin filament properties, providing novel predictions for future experimental studies.
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Affiliation(s)
- Harshwardhan H Katkar
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Aram Davtyan
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Aleksander E P Durumeric
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Glen M Hocky
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Anthony C Schramm
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois.
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33
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Adnan A, Qidwai S, Bagchi A. On the atomistic-based continuum viscoelastic constitutive relations for axonal microtubules. J Mech Behav Biomed Mater 2018; 86:375-389. [DOI: 10.1016/j.jmbbm.2018.06.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 01/04/2018] [Accepted: 06/21/2018] [Indexed: 11/25/2022]
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34
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Li S, Zhang J, Wang C, Nithiarasu P. Atomistic Modeling of F-Actin Mechanical Responses and Determination of Mechanical Properties. ACS Biomater Sci Eng 2018; 4:2794-2803. [DOI: 10.1021/acsbiomaterials.8b00640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Si Li
- Zienkiewicz Centre for Computational Engineering, College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea, Wales SA1 8EN, U.K
| | - Jin Zhang
- Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
| | - Chengyuan Wang
- Zienkiewicz Centre for Computational Engineering, College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea, Wales SA1 8EN, U.K
| | - Perumal Nithiarasu
- Zienkiewicz Centre for Computational Engineering, College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea, Wales SA1 8EN, U.K
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35
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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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36
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Xia K. Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules. Phys Chem Chem Phys 2018; 20:658-669. [PMID: 29227479 DOI: 10.1039/c7cp07177a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for the normal mode analysis of large-sized biomolecules. The multiscale virtual particle (MVP) model is proposed for the discretization of biomolecular density data. With this model, large-sized biomolecular structures can be coarse-grained into virtual particles such that a balance between model accuracy and computational cost can be achieved. An elastic network is constructed by assuming "connections" between virtual particles. The connection is described by a special harmonic potential function, which considers the influence from both the mass distributions and distance relations of the virtual particles. Two independent models, i.e., the multiscale virtual particle based Gaussian network model (MVP-GNM) and the multiscale virtual particle based anisotropic network model (MVP-ANM), are proposed. It has been found that in the Debye-Waller factor (B-factor) prediction, the results from our MVP-GNM with a high resolution are as good as the ones from GNM. Even with low resolutions, our MVP-GNM can still capture the global behavior of the B-factor very well with mismatches predominantly from the regions with large B-factor values. Further, it has been demonstrated that the low-frequency eigenmodes from our MVP-ANM are highly consistent with the ones from ANM even with very low resolutions and a coarse grid. Finally, the great advantage of MVP-ANM model for large-sized biomolecules has been demonstrated by using two poliovirus virus structures. The paper ends with a conclusion.
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Affiliation(s)
- Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371.
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37
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Schneider J, Korshunova K, Musiani F, Alfonso-Prieto M, Giorgetti A, Carloni P. Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations. Biochem Biophys Res Commun 2018; 498:366-374. [PMID: 29409902 DOI: 10.1016/j.bbrc.2018.01.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/21/2022]
Abstract
Membrane receptors constitute major targets for pharmaceutical intervention. Drug design efforts rely on the identification of ligand binding poses. However, the limited experimental structural information available may make this extremely challenging, especially when only low-resolution homology models are accessible. In these cases, the predictions may be improved by molecular dynamics simulation approaches. Here we review recent developments of multiscale, hybrid molecular mechanics/coarse-grained (MM/CG) methods applied to membrane proteins. In particular, we focus on our in-house MM/CG approach. It is especially tailored for G-protein coupled receptors, the largest membrane receptor family in humans. We show that our MM/CG approach is able to capture the atomistic details of the receptor/ligand binding interactions, while keeping the computational cost low by representing the protein frame and the membrane environment in a highly simplified manner. We close this review by discussing ongoing improvements and challenges of the current implementation of our MM/CG code.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany; VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Viet Nam.
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38
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Bore SL, Milano G, Cascella M. Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains. J Chem Theory Comput 2018; 14:1120-1130. [DOI: 10.1021/acs.jctc.7b01160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sigbjørn Løland Bore
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo, Norway
| | - Giuseppe Milano
- Department
of Organic Materials Science, University of Yamagata, 4-3-16 Jonan
Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo, Norway
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39
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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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40
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Jiang N, Bailey ME, Burke J, Ross JL, Dima RI. Modeling the effects of lattice defects on microtubule breaking and healing. Cytoskeleton (Hoboken) 2017; 74:3-17. [PMID: 27935245 DOI: 10.1002/cm.21346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/29/2016] [Accepted: 11/29/2016] [Indexed: 12/19/2022]
Abstract
Microtubule reorganization often results from the loss of polymer induced through breakage or active destruction by energy-using enzymes. Pre-existing defects in the microtubule lattice likely lower structural integrity and aid filament destruction. Using large-scale molecular simulations, we model diverse microtubule fragments under forces generated at specific positions to locally crush the filament. We show that lattices with 2% defects are crushed and severed by forces three times smaller than defect-free ones. We validate our results with direct comparisons of microtubule kinking angles during severing. We find a high statistical correlation between the angle distributions from experiments and simulations indicating that they sample the same population of structures. Our simulations also indicate that the mechanical environment of the filament affects breaking: local mechanical support inhibits healing after severing, especially in the case of filaments with defects. These results recall reports of microtubule healing after flow-induced bending and corroborate prior experimental studies that show severing is more likely at locations where microtubules crossover in networks. Our results shed new light on mechanisms underlying the ability of microtubules to be destroyed and healed in the cell, either by external forces or by severing enzymes wedging dimers apart. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221
| | - Megan E Bailey
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Jessica Burke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221
| | - Jennifer L Ross
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts, 01003.,Department of Physics, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221
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41
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Bope CD, Tong D, Li X, Lu L. Fluctuation matching approach for elastic network model and structure-based model of biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:100-112. [DOI: 10.1016/j.pbiomolbio.2016.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/25/2016] [Accepted: 12/19/2016] [Indexed: 10/24/2022]
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42
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Combining experimental and simulation data of molecular processes via augmented Markov models. Proc Natl Acad Sci U S A 2017; 114:8265-8270. [PMID: 28716931 DOI: 10.1073/pnas.1704803114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.
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43
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Chang HJ, Lee M, Kim JI, Yoon G, Na S. Mechanical and vibrational characterization of amyloid-like HET-s nanosheets based on the skewed plate theory. Phys Chem Chem Phys 2017; 19:11492-11501. [PMID: 28425516 DOI: 10.1039/c7cp01418j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pathological amyloidogenic prion proteins have a toxic effect on functional cells in the human cerebrum because of poor degradability and the tendency to accumulate in an uncontrolled manner under physiological conditions. HET-s, a fungal prion protein, is known to undergo conformational variations from fibrillar to nanosheet structures during a change from low to high pH conditions. It has been said that this conformational change can lead to self-propagation by nucleating on the lateral surface of singlet fibrils. Efforts have been made toward the mechanical characterization of fibrillar amyloids, but a global understanding of amyloid-like HET-s nanosheet structures is lacking. In this study, we analyzed the mechanical and vibrational characteristics of the skewed HET-s nanosheet structures that developed under neutral pH conditions by performing various molecular dynamics simulations. By applying the skewed plate theory to HET-s nanosheets for various length scales with numerous pores inside the structures, we found that the skewed HET-s nanosheet structure has mechanical properties comparable to those of previously reported biological film materials and nanomaterials. Considering the inherent characteristics of structural stability, our observation provides valuable and detailed structural information on skewed amyloid-like HET-s nanosheets.
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Affiliation(s)
- Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea.
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44
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Zhang Y, Cao Z, Zhang JZ, Xia F. Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules. J Chem Inf Model 2017; 57:214-222. [PMID: 28128949 DOI: 10.1021/acs.jcim.6b00683] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Construction of coarse-grained (CG) models for large biomolecules used for multiscale simulations demands a rigorous definition of CG sites for them. Several coarse-graining methods such as the simulated annealing and steepest descent (SASD) based on the essential dynamics coarse-graining (ED-CG) or the stepwise local iterative optimization (SLIO) based on the fluctuation maximization coarse-graining (FM-CG), were developed to do it. However, the practical applications of these methods such as SASD based on ED-CG are subject to limitations because they are too expensive. In this work, we extend the applicability of ED-CG by combining it with the SLIO algorithm. A comprehensive comparison of optimized results and accuracy of various algorithms based on ED-CG show that SLIO is the fastest as well as the most accurate algorithm among them. ED-CG combined with SLIO could give converged results as the number of CG sites increases, which demonstrates that it is another efficient method for coarse-graining large biomolecules. The construction of CG sites for Ras protein by using MD fluctuations demonstrates that the CG sites derived from FM-CG can reflect the fluctuation properties of secondary structures in Ras accurately.
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Affiliation(s)
- Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University , Xiamen 361005, China.,School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University , Xiamen 361005, China
| | - John Zenghui Zhang
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry, NYU Shanghai , Shanghai 200062, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry, NYU Shanghai , Shanghai 200062, China
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45
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Kim JI, Kwon J, Baek I, Na S. Steered molecular dynamics analysis of the role of cofilin in increasing the flexibility of actin filaments. Biophys Chem 2016; 218:27-35. [PMID: 27589672 DOI: 10.1016/j.bpc.2016.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 08/25/2016] [Accepted: 08/27/2016] [Indexed: 12/14/2022]
Abstract
Cofilin is one of the most essential regulatory proteins and participates in the process of disassembling actin filaments. Cofilin induces conformational changes to actin filaments, and both the bending and torsional rigidity of the filament. In this study, we investigate the effects of cofilin on the mechanical properties of actin filaments using computational methods. Three models defined by their number of bound cofilins are constructed using coarse-grained MARTINI force field, and they are then extended with steered molecular dynamics simulation. After obtaining the stress-strain curves of the models, we calculate their Young's moduli and other mechanical properties that have not yet been determined for actin filaments. We analyze the cause of the different behaviors of the three models based on their atomistic geometrical differences. Finally, it is demonstrated that cofilin binding causes changes in the distances, angles, and stabilities of the residues in actin filaments.
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Affiliation(s)
- Jae In Kim
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea
| | - Junpyo Kwon
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea
| | - Inchul Baek
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea.
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46
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Click TH, Raj N, Chu JW. Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation. Methods Enzymol 2016; 578:327-42. [PMID: 27497173 DOI: 10.1016/bs.mie.2016.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
In this work, a computational framework is presented to compute the time evolution of force constants for a coarse grained (CG) elastic network model along an all-atom molecular dynamics trajectory of a protein system. Obtained via matching distance fluctuations, these force constants represent strengths of mechanical coupling between CG beads. Variation of coupling strengths with time is hence termed the fluctuogram of protein dynamics. In addition to the schematic procedure and implementation considerations, several ways of combining force constants and data analysis are presented to illustrate the potential application of protein fluctuograms. The unique angle provided by the fluctuogram expands the scope of atomistic simulations and is expected to impact upon fundamental understanding of protein dynamics as well as protein engineering technologies.
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Affiliation(s)
- T H Click
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC
| | - N Raj
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC
| | - J-W Chu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, ROC; Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan, ROC.
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47
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A coarse-grained model for polylactide: glass transition temperature and conformational properties. JOURNAL OF POLYMER RESEARCH 2016. [DOI: 10.1007/s10965-016-1037-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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48
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Mahalik JP, Brown KA, Cheng X, Fuentes-Cabrera M. Theoretical Study of the Initial Stages of Self-Assembly of a Carboxysome's Facet. ACS NANO 2016; 10:5751-8. [PMID: 26906087 DOI: 10.1021/acsnano.5b07805] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bacterial microcompartments, BMCs, are organelles that exist within wide variety of bacteria and act as nanofactories. Among the different types of known BMCs, the carboxysome has been studied the most. The carboxysome plays an important role in the light-independent part of the photosynthesis process, where its icosahedral-like proteinaceous shell acts as a membrane that controls the transport of metabolites. Although a structural model exists for the carboxysome shell, it remains largely unknown how the shell proteins self-assemble. Understanding the self-assembly process can provide insights into how the shell affects the carboxysome's function and how it can be modified to create new functionalities, such as artificial nanoreactors and artificial protein membranes. Here, we describe a theoretical framework that employs Monte Carlo simulations with a coarse-grain potential that reproduces well the atomistic potential of mean force; employing this framework, we are able to capture the initial stages of the 2D self-assembly of CcmK2 hexamers, a major protein-shell component of the carboxysome's facet. The simulations reveal that CcmK2 hexamers self-assemble into clusters that resemble what was seen experimentally in 2D layers. Further analysis of the simulation results suggests that the 2D self-assembly of carboxysome's facets is driven by a nucleation-growth process, which in turn could play an important role in the hierarchical self-assembly of BMC shells in general.
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Affiliation(s)
| | - Kirsten A Brown
- Chemistry Department, Mercer University , 1501 Mercer University Drive, Macon, Georgia 31207, United States
| | - Xiaolin Cheng
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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50
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Multiscale simulations of protein-facilitated membrane remodeling. J Struct Biol 2016; 196:57-63. [PMID: 27327264 DOI: 10.1016/j.jsb.2016.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.
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