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Wang T, Yamato T, Sugiura W. Thermal Energy Transport through Nonbonded Native Contacts in Protein. J Phys Chem B 2024. [PMID: 39197018 DOI: 10.1021/acs.jpcb.4c03475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.
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Affiliation(s)
- Tingting Wang
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Wataru Sugiura
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Poudel H, Wales DJ, Leitner DM. Vibrational Energy Landscapes and Energy Flow in GPCRs. J Phys Chem B 2024; 128:7568-7576. [PMID: 39058920 DOI: 10.1021/acs.jpcb.4c04513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
We construct and analyze disconnectivity graphs to provide the first graphical representation of the vibrational energy landscape of a protein, in this study β2AR, a G-protein coupled receptor (GPCR), in active and inactive states. The graphs, which indicate the relative free energy of each residue and the minimum free energy barriers for energy transfer between them, reveal important composition, structural and dynamic properties that mediate the flow of energy. Prolines and glycines, which contribute to GPCR plasticity and function, are identified as bottlenecks to energy transport along the backbone from which alternative pathways for energy transport via nearby noncovalent contacts emerge, seen also in the analysis of first passage time (FPT) distributions presented here. Striking differences between the disconnectivity graphs and FPT distributions for the inactive and active states of β2AR are found where structural and dynamic changes occur upon activation, contributing to allosteric regulation.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David J Wales
- Yusuf Hamied Department of Chemistry, Cambridge University, Cambridge CB2 1EW, U.K
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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Ma YS, Kuo FM, Liu TH, Lin YT, Yu J, Wei Y. Exploring keratin composition variability for sustainable thermal insulator design. Int J Biol Macromol 2024; 275:133690. [PMID: 38971280 DOI: 10.1016/j.ijbiomac.2024.133690] [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: 03/10/2024] [Revised: 06/18/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
In pursuing sustainable thermal insulation solutions, this study explores the integration of human hair and feather keratin with alginate. The aim is to assess its potential in thermal insulation materials, focusing on the resultant composites' thermal and mechanical characteristics. The investigation uncovers that the type and proportion of keratin significantly influence the composites' porosity and thermal conductivity. Specifically, higher feather keratin content is associated with lesser sulfur and reduced crosslinking due to shorter amino acids, leading to increased porosity and pore sizes. This, in turn, results in a decrease in β-structured hydrogen bond networks, raising non-ordered protein structures and diminishing thermal conductivity from 0.044 W/(m·K) for pure alginate matrices to between 0.033 and 0.038 W/(m·K) for keratin-alginate composites, contingent upon the specific ratio of feather to hair keratin used. Mechanical evaluations further indicate that composites with a higher ratio of hair keratin exhibit an enhanced compressive modulus, ranging from 60 to 77 kPa, demonstrating the potential for tailored mechanical properties to suit various applications. The research underscores the critical role of sulfur content and the crosslinking index within keratin's structures, significantly impacting the thermal and mechanical properties of the matrices. The findings position keratin-based composites as environmentally friendly alternatives to traditional insulation materials.
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Affiliation(s)
- Yu-Shuan Ma
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology (Taipei Tech), Taipei 106, Taiwan
| | - Fang-Mei Kuo
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology (Taipei Tech), Taipei 106, Taiwan
| | - Tai-Hung Liu
- Department of Chemical Engineering, College of Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Ting Lin
- Department of Chemical Engineering, College of Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Jiashing Yu
- Department of Chemical Engineering, College of Engineering, National Taiwan University, Taipei 106, Taiwan.
| | - Yang Wei
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology (Taipei Tech), Taipei 106, Taiwan; High-value Biomaterials Research and Commercialization Center, National Taipei University of Technology, Taipei, 10608, Taiwan.
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Tanaka M, Sawada T, Numata K, Serizawa T. Tunable thermal diffusivity of silk protein assemblies based on their structural control and photo-induced chemical cross-linking. RSC Adv 2024; 14:12449-12453. [PMID: 38633499 PMCID: PMC11022280 DOI: 10.1039/d3ra06473e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
Silk, which has excellent mechanical properties and is lightweight, serves as a structural material in natural systems. However, the structural and functional applications of silk in artificial systems have been limited due to the difficulty in controlling its properties. In this study, we demonstrate the tunable thermal diffusivity of silk-based assemblies (films) based on secondary structural control and subsequent cross-linking. We found that the thermal diffusivity of the silk film is increased by the formation of β-sheet structures and dityrosine between Tyr residues adjacent to the β-sheet structures. Our results demonstrate the applicability of silk proteins as material components for thermally conductive biopolymer-based materials.
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Affiliation(s)
- Michihiro Tanaka
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
| | - Toshiki Sawada
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
| | - Keiji Numata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University Kyoto-Daigaku-Katsura, Nishikyo-ku Kyoto 615-8510 Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa, Wako-shi Saitama 351-0198 Japan
| | - Takeshi Serizawa
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
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Kurisaki I, Tanaka S, Mori I, Umegaki T, Mori Y, Tanaka S. Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape. J Comput Chem 2023; 44:857-868. [PMID: 36468822 PMCID: PMC10107505 DOI: 10.1002/jcc.27048] [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: 09/10/2022] [Revised: 11/10/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
Considering the importance of elucidating the heat transfer in living cells, we evaluated the thermal conductivity κ and conductance G of hydrated protein through all-atom non-equilibrium molecular dynamics simulation. Extending the computational scheme developed in earlier studies for spherical protein to cylindrical one under the periodic boundary condition, we enabled the theoretical analysis of anisotropic thermal conduction and also discussed the effects of protein size correction on the calculated results. While the present results for myoglobin and green fluorescent protein (GFP) by the spherical model were in fair agreement with previous computational and experimental results, we found that the evaluations for κ and G by the cylindrical model, in particular, those for the longitudinal direction of GFP, were enhanced substantially, but still keeping a consistency with experimental data. We also studied the influence by salt addition of physiological concentration, finding insignificant alteration of thermal conduction of protein in the present case.
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Affiliation(s)
- Ikuo Kurisaki
- Graduate School of System Informatics, Kobe University, Kobe, Japan
| | - Seiya Tanaka
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Ichiro Mori
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Toshihito Umegaki
- Graduate School of System Informatics, Kobe University, Kobe, Japan.,Center for Mathematical Modeling and Data Science, Osaka University, Osaka, Japan
| | - Yoshiharu Mori
- Graduate School of System Informatics, Kobe University, Kobe, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, Kobe, Japan
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Poudel H, Leitner DM. Locating dynamic contributions to allostery via determining rates of vibrational energy transfer. J Chem Phys 2023; 158:015101. [PMID: 36610954 DOI: 10.1063/5.0132089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relationship between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β2-adrenergic receptor, a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist-bound active state. From structures sampled during molecular dynamics (MD) simulations, we find the active state to have, on average, a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in the rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after the transition between states thereby provides information about dynamic contributions to activation and allostery.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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Kurisaki I, Suzuki M. Simulation toolkits at the molecular scale for trans-scale thermal signaling. Comput Struct Biotechnol J 2023; 21:2547-2557. [PMID: 37102156 PMCID: PMC10123322 DOI: 10.1016/j.csbj.2023.03.040] [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: 02/19/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/28/2023] Open
Abstract
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.
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Affiliation(s)
- Ikuo Kurisaki
- Waseda Research Institute for Science and Engineering, Waseda University, Bldg. No.55, S Tower, 4th Floor, 3–4-1 Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Corresponding authors.
| | - Madoka Suzuki
- Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka 565–0871, Japan
- Corresponding authors.
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Poudel H, Leitner DM. Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation. J Phys Chem B 2022; 126:8362-8373. [PMID: 36256609 DOI: 10.1021/acs.jpcb.2c03960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
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