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Fuchigami S, Takada S. Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations. Front Mol Biosci 2022; 9:882989. [PMID: 35573735 PMCID: PMC9100425 DOI: 10.3389/fmolb.2022.882989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022] Open
Abstract
High-speed atomic force microscopy (HS-AFM) is a powerful technique to image the structural dynamics of biomolecules. We can obtain atomic-resolution structural information from the measured AFM image by superimposing a structural model on the image. We previously developed a flexible fitting molecular dynamics (MD) simulation method that allows for modest conformational changes when superimposed on an AFM image. In this study, for a molecular motor, myosin V (which changes its chemical state), we examined whether the conformationally distinct state in each HS-AFM image could be inferred via flexible fitting MD simulation. We first built models of myosin V bound to the actin filament in two conformational states, the “down-up” and “down-down” states. Then, for the previously obtained HS-AFM image of myosin bound to the actin filament, we performed flexible-fitting MD simulations using the two states. By comparing the fitting results, we inferred the conformational and chemical states from the AFM image.
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Affiliation(s)
| | - Shoji Takada
- *Correspondence: Sotaro Fuchigami, ; Shoji Takada,
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Zhang PF, Su JG. Identification of key sites controlling protein functional motions by using elastic network model combined with internal coordinates. J Chem Phys 2019; 151:045101. [PMID: 31370540 DOI: 10.1063/1.5098542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The elastic network model (ENM) is an effective method to extract the intrinsic dynamical properties encoded in protein tertiary structures. We have proposed a new ENM-based analysis method to reveal the motion modes directly responsible for a specific protein function, in which an internal coordinate related to the specific function was introduced to construct the internal/Cartesian hybrid coordinate space. In the present work, the function-related internal coordinates combined with a linear perturbation method were applied to identify the key sites controlling specific protein functional motions. The change in the fluctuations of the internal coordinate in response to residue perturbation was calculated in the hybrid coordinate space by using the linear response theory. The residues with the large fluctuation changes were identified to be the key sites that allosterically control the specific protein function. Two proteins, i.e., human DNA polymerase β and the chaperonin from Methanococcus maripaludis, were investigated as case studies, in which several collective and local internal coordinates were applied to identify the functionally key residues of these two studied proteins. The calculation results are consistent with the experimental observations. It is found that different collective internal coordinates lead to similar results, where the predicted functionally key sites are located at similar positions in the protein structure. While for the local internal coordinates, the predicted key sites tend to be situated at the region near to the coordinate-involving residues. Our studies provide a starting point for further exploring other function-related internal coordinates for other interesting proteins.
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Affiliation(s)
- Peng Fei Zhang
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Ji Guo Su
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
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Kežar A, Kavčič L, Polák M, Nováček J, Gutiérrez-Aguirre I, Žnidarič MT, Coll A, Stare K, Gruden K, Ravnikar M, Pahovnik D, Žagar E, Merzel F, Anderluh G, Podobnik M. Structural basis for the multitasking nature of the potato virus Y coat protein. SCIENCE ADVANCES 2019; 5:eaaw3808. [PMID: 31328164 PMCID: PMC6636993 DOI: 10.1126/sciadv.aaw3808] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/10/2019] [Indexed: 05/02/2023]
Abstract
Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
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Affiliation(s)
- Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Martin Polák
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- University of Nova Gorica, Vipavska cesta, 5000 Nova Gorica, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Corresponding author.
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Abstract
While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold.
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Affiliation(s)
- Holger Flechsig
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan
| | - Alexander S Mikhailov
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan.,2 Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin , Germany
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Fujisaki H, Shiga M, Moritsugu K, Kidera A. Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer. J Chem Phys 2014; 139:054117. [PMID: 23927253 DOI: 10.1063/1.4817209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling technique suggested by Moritsugu and co-workers [J. Chem. Phys. 133, 224105 (2010)]. The basic idea of this method is that the system we want to study (for example, some molecular system described by molecular mechanics) is coupled to a coarse-grained (CG) system, which can move more quickly and can be computed more efficiently than the original system. We simulate this combined system (original + CG system) using Langevin dynamics where different heat baths are coupled to the two systems. When the coupling is strong enough, the original system is guided by the CG system, and is able to sample the configuration and path space with more efficiency. We need to correct the bias caused by the coupling, however, by employing the Hamiltonian replica exchange, where we prepare many path replicas with different coupling strengths. As a result, an unbiased path ensemble for the original system can be found in the weakest coupling path ensemble. This strategy is easily implemented because a weight for a path calculated by the OM action is formally the same as the Boltzmann weight if we properly define the path "Hamiltonian." We apply this method to a model polymer with Asakura-Oosawa interaction, and compare the results with the conventional transition path sampling method.
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Affiliation(s)
- Hiroshi Fujisaki
- Department of Physics, Nippon Medical School, Nakahara, Kawasaki 211-0063, Japan.
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Terada T, Kidera A. Comparative molecular dynamics simulation study of crystal environment effect on protein structure. J Phys Chem B 2012; 116:6810-8. [PMID: 22397704 DOI: 10.1021/jp2125558] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Crystal structures of proteins are under the influence from the crystal environment. In this study, we used molecular dynamics (MD) simulations to explore the possibility of eliminating the effect of the crystal packing and recovering the structure in solution. Ten representative proteins were chosen from the Protein Structural Change Database as the target systems, and 50 ns MD stimulations starting from two crystal structures having different domain arrangements were performed for each. The MD trajectories of the relaxation processes upon the release from the crystal environment revealed that the behaviors of the proteins were classified into three groups: "single domain linker", "harmonic motion", and "large barrier". We discuss the structural features common to the proteins in each group.
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Affiliation(s)
- Tohru Terada
- Molecular Scale Team, Computational Science Research Program, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.
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