1
|
Hirata F. Structural Fluctuation, Relaxation, and Folding of Protein: An Approach Based on the Combined Generalized Langevin and RISM/3D-RISM Theories. Molecules 2023; 28:7351. [PMID: 37959769 PMCID: PMC10647392 DOI: 10.3390/molecules28217351] [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] [Received: 09/04/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 11/15/2023] Open
Abstract
In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto the two dynamic variables: the structural fluctuation defined by the displacement of atoms from their equilibrium positions, and the solvent density fluctuation. The equation has an expression similar to the classical Langevin equation (CLE) for a harmonic oscillator, possessing terms corresponding to the restoring force proportional to the structural fluctuation, as well as the frictional and random forces. However, there is a distinct difference between the two expressions that touches on the essential physics of the structural fluctuation, that is, the force constant, or Hessian, in the restoring force. In the CLE, this is given by the second derivative of the potential energy among atoms in a protein. So, the quadratic nature or the harmonicity is only valid at the minimum of the potential surface. On the contrary, the linearity of the restoring force in the GLE originates from the projection of the water's degrees of freedom onto the protein's degrees of freedom. Taking this into consideration, Kim and Hirata proposed an ansatz for the Hessian matrix. The ansatz is used to equate the Hessian matrix with the second derivative of the free-energy surface or the potential of the mean force of a protein in water, defined by the sum of the potential energy among atoms in a protein and the solvation free energy. Since the free energy can be calculated from the molecular mechanics and the RISM/3D-RISM theory, one can perform an analysis similar to the normal mode analysis (NMA) just by diagonalizing the Hessian matrix of the free energy. This method is referred to as the Generalized Langevin Mode Analysis (GLMA). This theory may be realized to explore a variety of biophysical processes, including protein folding, spectroscopy, and chemical reactions. The present article is devoted to reviewing the development of this theory, and to providing perspective in exploring life phenomena.
Collapse
Affiliation(s)
- Fumio Hirata
- Institute for Molecular Science, National Institute of Natural Sciences, Okazaki 444-8585, Japan
| |
Collapse
|
2
|
Varadi M, Velankar S. The impact of AlphaFold Protein Structure Database on the fields of life sciences. Proteomics 2023; 23:e2200128. [PMID: 36382391 DOI: 10.1002/pmic.202200128] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 09/06/2023]
Abstract
Arguably, 2020 was the year of high-accuracy protein structure predictions, with AlphaFold 2.0 achieving previously unseen accuracy in the Critical Assessment of Protein Structure Prediction (CASP). In 2021, DeepMind and EMBL-EBI developed the AlphaFold Protein Structure Database to make an unprecedented number of reliable protein structure predictions easily accessible to the broad scientific community. We provide a brief overview and describe the latest developments in the AlphaFold database. We highlight how the fields of data services, bioinformatics, structural biology, and drug discovery are directly affected by the influx of protein structure data. We also show examples of cutting-edge research that took advantage of the AlphaFold database. It is apparent that connections between various fields through protein structures are now possible, but the amount of data poses new challenges. Finally, we give an outlook regarding the future direction of the database, both in terms of data sets and new functionalities.
Collapse
Affiliation(s)
- Mihaly Varadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| |
Collapse
|
3
|
Hirata F. A theory of chemical reactions in biomolecules in solution: Generalized Langevin mode analysis (GLMA). J Chem Phys 2023; 158:144108. [PMID: 37061466 DOI: 10.1063/5.0143849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
The generalized Langevin mode analysis (GLMA) is applied to chemical reactions in biomolecules in solution. The theory sees a chemical reaction in solution as a barrier-crossing process, similar to the Marcus theory. The barrier is defined as the crossing point of two free-energy surfaces that are attributed to the reactant and product of the reaction. It is assumed that both free-energy surfaces are quadratic or harmonic. The assumption is based on the Kim-Hirata theory of structural fluctuation of protein, which proves that the fluctuation around an equilibrium structure is quadratic with respect to the structure or atomic coordinates. The quadratic surface is a composite of many harmonic functions with different modes or frequencies. The height of the activation barrier will be dependent on the mode or frequency-the less the frequency, the lower the barrier. Hence, it is essential to decouple the fluctuational modes into a hierarchical order. GLMA is impeccable for this purpose. It is essential for a theoretical study of chemical reactions to choose a reaction coordinate along which the reaction proceeds. We suppose that the mode whose center of coordinate and/or the frequency changes most before and after the reaction is the one relevant to the chemical reaction and choose the coordinate as the reaction coordinate. The rate of reaction along the reaction coordinate is krate=νexp-ΔF(†)/kBT, which is similar to the Marcus expression for the electron transfer reaction. In the equation, ΔF(†) is the activation barrier defined by ΔF(†)≡F(r)Q†-F(r)(Qeq (r)), where F(r)(Qeq (r)) and F(r)Q† denote the free energies at equilibrium Qeq (r) and the crossing point Q†, respectively, both on the free energy surface of the reactant.
Collapse
Affiliation(s)
- Fumio Hirata
- National Insistitutes of Natural Sciencees, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
4
|
Hirata F. Generalized Langevin Mode Analysis (GLMA) for Local Density Fluctuation of Water in an Inhomogeneous Field of a Biomolecule. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
|
5
|
Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [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: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
Collapse
Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| |
Collapse
|
6
|
Varadi M, Nair S, Sillitoe I, Tauriello G, Anyango S, Bienert S, Borges C, Deshpande M, Green T, Hassabis D, Hatos A, Hegedus T, Hekkelman ML, Joosten R, Jumper J, Laydon A, Molodenskiy D, Piovesan D, Salladini E, Salzberg SL, Sommer MJ, Steinegger M, Suhajda E, Svergun D, Tenorio-Ku L, Tosatto S, Tunyasuvunakool K, Waterhouse AM, Žídek A, Schwede T, Orengo C, Velankar S. 3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources. Gigascience 2022; 11:6854872. [PMID: 36448847 PMCID: PMC9709962 DOI: 10.1093/gigascience/giac118] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/20/2022] [Accepted: 11/11/2022] [Indexed: 12/02/2022] Open
Abstract
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank.
Collapse
Affiliation(s)
- Mihaly Varadi
- Correspondence address. Mihaly Varadi, PDBe team, Wellcome Trust Genome Campus, Saffron Walden CB10 1SA, UK. E-mail:
| | | | | | | | - Stephen Anyango
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
| | - Stefan Bienert
- Biozentrum, University of Basel, Basel 4056, Switzerland,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Clemente Borges
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany
| | - Mandar Deshpande
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
| | | | | | - Andras Hatos
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy,Department of Oncology, Lausanne University Hospital, Lausanne 1015, Switzerland,Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland,Swiss Cancer Center Leman, Lausanne 1005, Switzerland
| | - Tamas Hegedus
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
| | | | - Robbie Joosten
- Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | | | | | - Dmitry Molodenskiy
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | - Edoardo Salladini
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | - Steven L Salzberg
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Markus J Sommer
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Martin Steinegger
- School of Biology, Seoul National University, Seoul 82-2-880-6971, 6977, South Korea
| | - Erzsebet Suhajda
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
| | - Dmitri Svergun
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany
| | - Luiggi Tenorio-Ku
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | - Silvio Tosatto
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | | | - Andrew Mark Waterhouse
- Biozentrum, University of Basel, Basel 4056, Switzerland,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | | | - Torsten Schwede
- Biozentrum, University of Basel, Basel 4056, Switzerland,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Christine Orengo
- Department of Structural and Molecular Biology, UCL, London WC1E 6BT, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
| |
Collapse
|
7
|
Akasaka K, Maeno A. Proteins in Wonderland: The Magical World of Pressure. BIOLOGY 2021; 11:6. [PMID: 35053003 PMCID: PMC8772990 DOI: 10.3390/biology11010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/03/2023]
Abstract
Admitting the "Native", "Unfolded" and "Fibril" states as the three basic generic states of proteins in nature, each of which is characterized with its partial molar volume, here we predict that the interconversion among these generic states N, U, F may be performed simply by making a temporal excursion into the so called "the high-pressure regime", created artificially by putting the system under sufficiently high hydrostatic pressure, where we convert N to U and F to U, and then back to "the low-pressure regime" (the "Anfinsen regime"), where we convert U back to N (U→N). Provided that the solution conditions (temperature, pH, etc.) remain largely the same, the idea provides a general method for choosing N, U, or F of a protein, to a great extent at will, assisted by the proper use of the external perturbation pressure. A successful experiment is demonstrated for the case of hen lysozyme, for which the amyloid fibril state F prepared at 1 bar is turned almost fully back into its original native state N at 1 bar by going through the "the high-pressure regime". The outstanding simplicity and effectiveness of pressure in controlling the conformational state of a protein are expected to have a wide variety of applications both in basic and applied bioscience in the future.
Collapse
Affiliation(s)
- Kazuyuki Akasaka
- Keihanna Academy of Science & Culture, Kansai Science City, Keihanna Interaction Plaza, Lab. Wing, Kyoto 619-0237, Japan
| | - Akihiro Maeno
- Lab of Medical Chemistry, Kansai Medical University, 2-5-1 Shin-machi, Osaka 573-1010, Japan;
| |
Collapse
|
8
|
Tanimoto S, Tamura K, Hayashi S, Yoshida N, Nakano H. A computational method to simulate global conformational changes of proteins induced by cosolvent. J Comput Chem 2021; 42:552-563. [PMID: 33433010 DOI: 10.1002/jcc.26481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/09/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022]
Abstract
A computational method to investigate the global conformational change of a protein is proposed by combining the linear response path following (LRPF) method and three-dimensional reference interaction site model (3D-RISM) theory, which is referred to as the LRPF/3D-RISM method. The proposed method makes it possible to efficiently simulate protein conformational changes caused by either solutions of varying concentrations or the presence of cosolvent species by taking advantage of the LRPF and 3D-RISM. The proposed method is applied to the urea-induced denaturation of ubiquitin. The LRPF/3D-RISM trajectories successfully simulate the early stage of the denaturation process within the simulation time of 300 ns, whereas no significant structural change is observed even in the 1 μs standard MD simulation. The obtained LRPF/3D-RISM trajectories reproduce the mechanism of the urea denaturation of ubiquitin reported in previous studies, and demonstrate the high efficiency of the method.
Collapse
Affiliation(s)
- Shoichi Tanimoto
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Koichi Tamura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| |
Collapse
|
9
|
Sugita M, Onishi I, Irisa M, Yoshida N, Hirata F. Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory. Molecules 2021; 26:E271. [PMID: 33430461 PMCID: PMC7826681 DOI: 10.3390/molecules26020271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022] Open
Abstract
There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.
Collapse
Affiliation(s)
- Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1, Ookayama Meguro-ku, Tokyo 152-8550, Japan;
| | - Itaru Onishi
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Masayuki Irisa
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Norio Yoshida
- Department of Chemistry, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan;
| | - Fumio Hirata
- Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
10
|
Zhang BW, Matubayasi N, Levy RM. Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. J Phys Chem B 2020; 124:5220-5237. [PMID: 32469519 DOI: 10.1021/acs.jpcb.0c02721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Endpoints density functional theory (DFT) provides a framework for calculating the excess chemical potential of a solute in solution using solvent distribution functions obtained from both physical endpoints of a hypothetical charging process which transforms the solvent density from that of the pure liquid to the solution state. In this work, the endpoints DFT equations are formulated in terms of the indirect (solvent-mediated) contribution ω(x) to the solute-solvent potential of mean force, and their connections are established with the conventional DFT expressions which are based on the use of direct correlation functions. ω actually corresponds to the free-energy cost to move a cavity particle (a tagged solvent molecule which interacts with the other solvent molecules but not the solute) from the bulk to the configuration x of a solvent molecule relative to the solute and is a suitable variable to describe the solvent effects on the solute-solvent interactions. HNC and PY type approximations are then used to integrate the DFT charging integral involved in the exact expression for the excess chemical potential. With these approximations, molecular simulations are to be performed at the two endpoints of solute insertion: pure solvent without the solute and the solution system with the fully coupled solute-solvent interaction. An endpoints method thus utilizes the ensembles of intermolecular configurations of physical interest, which are often readily accessible with MD simulations given the present computational power. To illustrate properties of the formulation, we perform simulations of model systems consisting of a cavity particle in an aqueous solution containing a spherical hydrophobic solute of three different sizes from which ω(x) and the solute chemical potential can be calculated using endpoints DFT expressions. These are compared with corresponding results obtained using the approximations needed in order to evaluate the endpoints DFT charging integral when cavity particle simulation data is not available. We analyze a new approximation (two-points quadratic HNC) to the DFT charging integral which captures the correct behavior of the cavity distributions at both endpoints of the solute insertion. The behavior of the cavity particle in simple and complex liquids plays an important role in various theoretical treatments of the solute chemical potential. For pure Lennard-Jones fluids, the free energy to bring a cavity particle from the bulk to the center of a fluid particle is negative. However, for solutes of varying size, this is not generally true for Lennard-Jones fluids or the systems studied in this work. We carry out energetic and structural analyses of the cavity particle in aqueous solution with hydrophobic solutes of varying size and discuss the results in the context of the hydrophobic effect.
Collapse
Affiliation(s)
- Bin W Zhang
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| |
Collapse
|
11
|
Nishimura T, Shishi S, Sasaki Y, Akiyoshi K. Thermoresponsive Polysaccharide Graft Polymer Vesicles with Tunable Size and Structural Memory. J Am Chem Soc 2020; 142:11784-11790. [PMID: 32506909 DOI: 10.1021/jacs.0c02290] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Controlling polymer vesicle size is difficult and a major obstacle for their potential use in biomedical applications, such as drug-delivery carriers and nanoreactors. Herein, we report size-tunable polymer vesicles based on self-assembly of a thermoresponsive amphiphilic graft copolymer. Unilamellar polymer vesicles form upon heating chilled polymer solutions, and vesicle size can be tuned in the range of 40-70 nm by adjusting the initial polymer concentration. Notably, the polymer can reversibly switch between a monomer state and a vesicle state in accordance with a cooling/heating cycle, which changes neither the size nor the size distribution of the vesicles. This lack of change suggests that the polymer memorizes a particular vesicle conformation. Given our vesicles' size tunability and structural memory, our research considerably expands the fundamental and practical scope of thermoresponsive amphiphilic graft copolymers and renders amphiphilic graft copolymers useful tools for synthesizing functional self-assembled materials.
Collapse
Affiliation(s)
- Tomoki Nishimura
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shen Shishi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| |
Collapse
|
12
|
The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins. Molecules 2019; 24:molecules24234395. [PMID: 31816829 PMCID: PMC6930452 DOI: 10.3390/molecules24234395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/18/2023] Open
Abstract
Selected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: Aβ (1-42), which is listed as Aβ (15-40) and carries the D23N mutation, and Aβ (11-42) and Aβ (1-40), both of which carry the E22Δ mutation, tau amyloid, and α-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as "globular micelles," emerging as a result of interactions between the proteins' constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril's long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.
Collapse
|
13
|
Matyushov DV, Newton MD. Thermodynamics of Reactions Affected by Medium Reorganization. J Phys Chem B 2018; 122:12302-12311. [PMID: 30514079 DOI: 10.1021/acs.jpcb.8b08865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a thermodynamic analysis of the activation barrier for reactions which can be monitored through the difference in the energies of reactants and products defined as the reaction coordinate (electron and atom transfer, enzyme catalysis, etc.). The free-energy surfaces along the reaction coordinate are separated into the enthalpy and entropy surfaces. For the Gaussian statistics of the reaction coordinate, the free-energy surfaces are parabolas, and the entropy surface is an inverted parabola. Its maximum coincides with the transition state for reactions with zero value of the reaction free energy. Maximum entropic depression of the activation barrier, anticipated by the concept of transition-state ensembles, can be achieved for such reactions. From Onsager's reversibility, the entropy of equilibrium fluctuations encodes the entropic component of the activation barrier. The reorganization entropy thus becomes the critical parameter of the theory reducing the problem of activation entropy to the problem of reorganization entropy. Standard solvation theories do not allow reorganization entropy sufficient for the barrier depression. Complex media, characterized by many relaxation processes, need to be involved. Proteins provide several routes for achieving large entropic effects through incomplete (nonergodic) sampling of the complex energy landscape and by facilitating an active role of water in the reaction mechanism.
Collapse
Affiliation(s)
- Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences , Arizona State University , PO Box 871504, Tempe , Arizona 85287 , United States
| | - Marshall D Newton
- Brookhaven National Laboratory , Chemistry Department , Box 5000, Upton , New York 11973-5000 , United States
| |
Collapse
|
14
|
On the interpretation of the temperature dependence of the mean square displacement (MSD) of protein, obtained from the incoherent neutron scattering. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.01.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|