The Experts below are selected from a list of 327 Experts worldwide ranked by ideXlab platform
Ayori Mitsutake - One of the best experts on this subject based on the ideXlab platform.
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folding pathways of nug2 a designed mutant of protein g using relaxation Mode Analysis
Journal of Chemical Physics, 2019Co-Authors: Ayori Mitsutake, Hiroshi TakanoAbstract:Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After the early folding process, the fourth β strand formed along the first β strand in the same or opposite direction as the native structure; two characteristic intermediate states were identified. Finally, the intermediate structures folded to the native structure in the folding process. Relaxation Mode Analysis can be applied to folding simulations of complex proteins to investigate their folding processes.Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After t...
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Folding pathways of NuG2—a designed mutant of protein G—using relaxation Mode Analysis
Journal of Chemical Physics, 2019Co-Authors: Ayori Mitsutake, Hiroshi TakanoAbstract:Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After the early folding process, the fourth β strand formed along the first β strand in the same or opposite direction as the native structure; two characteristic intermediate states were identified. Finally, the intermediate structures folded to the native structure in the folding process. Relaxation Mode Analysis can be applied to folding simulations of complex proteins to investigate their folding processes.Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After t...
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relaxation Mode Analysis and markov state relaxation Mode Analysis for chignolin in aqueous solution near a transition temperature
Journal of Chemical Physics, 2015Co-Authors: Ayori Mitsutake, Hiroshi TakanoAbstract:It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component Analysis, which extracts Modes of large conformational fluctuations around an average structure. We recently applied relaxation Mode Analysis for protein systems, which approximately estimates the slow relaxation Modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation Mode Analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component Analysis and relaxation Mode Analysis to the system. In the relaxation Mode Analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new Analysis method called Markov state relaxation Mode Analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation Mode Analysis. Finally, the relaxation times of the states obtained with a simple Markov state Model and the proposed Markov state relaxation Mode Analysis are compared and discussed.
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Relaxation Mode Analysis for a Peptide
Biophysical Journal, 2014Co-Authors: Ayori MitsutakeAbstract:Biopolymers have flexible structures and several varieties of functions. The functions are derived from not only structures but also the structural fluctuations. Therefore, the properties of structural fluctuations of biopolymers are important for understanding the interrelationship between its movement and functions. Principle component Analysis is one of the most popular methods for analyzing the static properties of structural fluctuations. The method treats “static” information although it is applied in many simulations of protein systems. Relaxation Mode Analysis developed to investigate “dynamic” properties of polymer, homo-polymer, systems [1,2]. In the case of liner polymers, the relaxation phenomena have been studied systematically in terms of the relaxation Modes and rates.In RMA, the time correlation matrices of structural fluctuations for two different times are calculated. Then, by solving a generalized eigenvalue problem for these matrices, the relaxation rates and Modes are estimated from the eigenvalues and eigenvectors, respectively. Recently, relaxation Mode Analysis has been applied to protein, hetero-polymer, systems to investigate dynamic properties of structural fluctuations[3,4]. In this poster, we explain relaxation Mode Analysis for hetero-polymer systems and show the obtained results.[1] H. Takano and S. Miyashita, J. Phys. Soc. Jpn. 64, 3688 (1995).[2] H. Hirao, S. Koseki, H. Takano, J. Phys. Soc. Jpn. 66, 3399 (1997).[3] A. Mitsutake, H. Iijima, H. Takano, J. Chem. Phys.135, 164102 (2011).[4] T. Nagai, A. Mitsutake, and H. Takano, J. Phys. Soc. Jpn. 82, 023803 (2013); T. Nagai, A. Mitsutake, H. Takano, Seibutsu Butsuri (Biophysics), 49, Supplement S75, (Abstracts for the 47st annual meeting, The Biophysical Society of Japan) (2009).
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principal component relaxation Mode Analysis of an all atom molecular dynamics simulation of human lysozyme
Journal of the Physical Society of Japan, 2013Co-Authors: Toshiki Nagai, Ayori Mitsutake, Hiroshi TakanoAbstract:A new relaxation Mode Analysis method, which is referred to as the principal component relaxation Mode Analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component Analysis is carried out first and then relaxation Mode Analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation Modes in these principal components efficiently, we have also proposed a relaxation Mode Analysis method using multiple evolution times. The principal component relaxation Mode Analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation Modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.
Hiroshi Takano - One of the best experts on this subject based on the ideXlab platform.
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folding pathways of nug2 a designed mutant of protein g using relaxation Mode Analysis
Journal of Chemical Physics, 2019Co-Authors: Ayori Mitsutake, Hiroshi TakanoAbstract:Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After the early folding process, the fourth β strand formed along the first β strand in the same or opposite direction as the native structure; two characteristic intermediate states were identified. Finally, the intermediate structures folded to the native structure in the folding process. Relaxation Mode Analysis can be applied to folding simulations of complex proteins to investigate their folding processes.Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After t...
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Folding pathways of NuG2—a designed mutant of protein G—using relaxation Mode Analysis
Journal of Chemical Physics, 2019Co-Authors: Ayori Mitsutake, Hiroshi TakanoAbstract:Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After the early folding process, the fourth β strand formed along the first β strand in the same or opposite direction as the native structure; two characteristic intermediate states were identified. Finally, the intermediate structures folded to the native structure in the folding process. Relaxation Mode Analysis can be applied to folding simulations of complex proteins to investigate their folding processes.Dynamic Analysis methods are important for analyzing long simulations such as folding simulations. Relaxation Mode Analysis, which approximately extracts slow Modes and rates, has been applied in molecular dynamics (MD) simulations of protein systems. Previously, we showed that slow Modes are suitable for analyzing simulations in which large conformational changes occur. Here, we applied relaxation Mode Analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways. The folding simulations of NuG2 were previously performed for this mutant with Anton. In the present study, the free energy surfaces were calculated by projecting the coordinates on the axis of the slow relaxation Modes obtained from relaxation Mode Analysis. We classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways. In the early folding process, the first and second β strands formed an N-terminal β-sheet. After t...
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relaxation Mode Analysis and markov state relaxation Mode Analysis for chignolin in aqueous solution near a transition temperature
Journal of Chemical Physics, 2015Co-Authors: Ayori Mitsutake, Hiroshi TakanoAbstract:It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component Analysis, which extracts Modes of large conformational fluctuations around an average structure. We recently applied relaxation Mode Analysis for protein systems, which approximately estimates the slow relaxation Modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation Mode Analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component Analysis and relaxation Mode Analysis to the system. In the relaxation Mode Analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new Analysis method called Markov state relaxation Mode Analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation Mode Analysis. Finally, the relaxation times of the states obtained with a simple Markov state Model and the proposed Markov state relaxation Mode Analysis are compared and discussed.
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principal component relaxation Mode Analysis of an all atom molecular dynamics simulation of human lysozyme
Journal of the Physical Society of Japan, 2013Co-Authors: Toshiki Nagai, Ayori Mitsutake, Hiroshi TakanoAbstract:A new relaxation Mode Analysis method, which is referred to as the principal component relaxation Mode Analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component Analysis is carried out first and then relaxation Mode Analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation Modes in these principal components efficiently, we have also proposed a relaxation Mode Analysis method using multiple evolution times. The principal component relaxation Mode Analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation Modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.
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relaxation Mode Analysis of a peptide system comparison with principal component Analysis
Journal of Chemical Physics, 2011Co-Authors: Ayori Mitsutake, Hiromitsu Iijima, Hiroshi TakanoAbstract:This article reports the first attempt to apply the relaxation Mode Analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component Analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation Mode Analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component Analysis and relaxation Mode Analysis methods. We compare the results of both methods and show the effectiveness of the relaxation Mode Analysis.
Tsuneyoshi Nakayama - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Approach to the Mode Analysis of Optical Waveguides
Japanese Journal of Applied Physics, 1996Co-Authors: Haruhito Noro, Kouji Fukushi, Tsuneyoshi NakayamaAbstract:A novel numerical method, based on a molecular dynamics algorithm for coupled harmonic oscillators, is applied to the Mode Analysis of arbitrary-shaped optical waveguides. We describe in detail the relationships between the vibrational equation of motion for lattice dynamics and the discretized form of the wave equation for light. This mapping is useful for the Analysis of the characteristics of optical waveguides. The efficiency of the method is demonstrated by application of the method to the Mode Analysis of a semiconductor rib-waveguide.
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Mode Analysis of optical waveguides: a new approach.
Optics letters, 1995Co-Authors: Haruhito Noro, Tsuneyoshi NakayamaAbstract:We propose a new numerical method for extracting extreme eigenvalues and the corresponding eigenModes for very large Hermitian matrices. The method is applied, for what we believe is the first time, to the Mode Analysis of arbitrarily shaped optical waveguides. Compared with results obtained by other numerical methods, it is shown that our method is powerful with respect to the Analysis, Modeling, and optimum design of lossless optical waveguides.
Haruhito Noro - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Approach to the Mode Analysis of Optical Waveguides
Japanese Journal of Applied Physics, 1996Co-Authors: Haruhito Noro, Kouji Fukushi, Tsuneyoshi NakayamaAbstract:A novel numerical method, based on a molecular dynamics algorithm for coupled harmonic oscillators, is applied to the Mode Analysis of arbitrary-shaped optical waveguides. We describe in detail the relationships between the vibrational equation of motion for lattice dynamics and the discretized form of the wave equation for light. This mapping is useful for the Analysis of the characteristics of optical waveguides. The efficiency of the method is demonstrated by application of the method to the Mode Analysis of a semiconductor rib-waveguide.
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Mode Analysis of optical waveguides: a new approach.
Optics letters, 1995Co-Authors: Haruhito Noro, Tsuneyoshi NakayamaAbstract:We propose a new numerical method for extracting extreme eigenvalues and the corresponding eigenModes for very large Hermitian matrices. The method is applied, for what we believe is the first time, to the Mode Analysis of arbitrarily shaped optical waveguides. Compared with results obtained by other numerical methods, it is shown that our method is powerful with respect to the Analysis, Modeling, and optimum design of lossless optical waveguides.
D. Orobengoa - One of the best experts on this subject based on the ideXlab platform.
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ampliModes symmetry Mode Analysis on the bilbao crystallographic server
Journal of Applied Crystallography, 2009Co-Authors: D. Orobengoa, C. Capillas, Mois I. Aroyo, Manuel J PerezmatoAbstract:AMPLIModeS is a computer program available on the Bilbao Crystallographic Server that can perform a symmetry-Mode Analysis of any distorted structure of displacive type. The Analysis consists in decomposing the symmetry-breaking distortion present in the distorted structure into contributions from different symmetry-adapted Modes. Given the high- and the low-symmetry structures, AMPLIModeS determines the atomic displacements that relate them, defines a basis of symmetry-adapted Modes, and calculates the amplitudes and polarization vectors of the distortion Modes of different symmetry frozen in the structure. The program uses a Mode parameterization that is as close as possible to the crystallographic conventions, expressing all quantities for the asymmetric unit of the low-symmetry structure. Distorted structures are often related to their higher-symmetry counterparts by temperature- and/or pressure-driven phase transitions, ferroic phase transitions being a particular example. The automatic symmetry-Mode Analysis performed by AMPLIModeS can be very useful for establishing the driving mechanisms of such structural phase transitions or the fundamental instabilities at the origin of the distorted phases.
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AMPLIModeS: symmetry‐Mode Analysis on the Bilbao Crystallographic Server
Journal of Applied Crystallography, 2009Co-Authors: D. Orobengoa, C. Capillas, Mois I. Aroyo, J. Manuel Perez-matoAbstract:AMPLIModeS is a computer program available on the Bilbao Crystallographic Server that can perform a symmetry-Mode Analysis of any distorted structure of displacive type. The Analysis consists in decomposing the symmetry-breaking distortion present in the distorted structure into contributions from different symmetry-adapted Modes. Given the high- and the low-symmetry structures, AMPLIModeS determines the atomic displacements that relate them, defines a basis of symmetry-adapted Modes, and calculates the amplitudes and polarization vectors of the distortion Modes of different symmetry frozen in the structure. The program uses a Mode parameterization that is as close as possible to the crystallographic conventions, expressing all quantities for the asymmetric unit of the low-symmetry structure. Distorted structures are often related to their higher-symmetry counterparts by temperature- and/or pressure-driven phase transitions, ferroic phase transitions being a particular example. The automatic symmetry-Mode Analysis performed by AMPLIModeS can be very useful for establishing the driving mechanisms of such structural phase transitions or the fundamental instabilities at the origin of the distorted phases.
