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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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2
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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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Yamato T, Wang T, Sugiura W, Laprévote O, Katagiri T. Computational Study on the Thermal Conductivity of a Protein. J Phys Chem B 2022; 126:3029-3036. [PMID: 35416670 DOI: 10.1021/acs.jpcb.2c00958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein molecules are thermally fluctuating and tightly packed amino acid residues strongly interact with each other. Such interactions are characterized in terms of heat current at the atomic level. We calculated the thermal conductivity of a small globular protein, villin headpiece subdomain, based on the linear response theory using equilibrium molecular dynamics simulation. The value of its thermal conductivity was 0.3 ± 0.01 [W m-1 K-1], which is in good agreement with experimental and computational studies on the other proteins in the literature. Heat current along the main chain was dominated by local vibrations in the polypeptide bonds, with amide I, II, III, and A bands on the Fourier transform of the heat current autocorrelation function.
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Affiliation(s)
- Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tingting Wang
- 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
| | - Olivier Laprévote
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takahiro Katagiri
- Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Chalopin Y, Sparfel J. Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins. Front Mol Biosci 2022; 8:736376. [PMID: 35004841 PMCID: PMC8733615 DOI: 10.3389/fmolb.2021.736376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Julien Sparfel
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
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Sladek V, Yamamoto Y, Harada R, Shoji M, Shigeta Y, Sladek V. pyProGA-A PyMOL plugin for protein residue network analysis. PLoS One 2021; 16:e0255167. [PMID: 34329304 PMCID: PMC8323899 DOI: 10.1371/journal.pone.0255167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/11/2021] [Indexed: 11/18/2022] Open
Abstract
The field of protein residue network (PRN) research has brought several useful methods and techniques for structural analysis of proteins and protein complexes. Many of these are ripe and ready to be used by the proteomics community outside of the PRN specialists. In this paper we present software which collects an ensemble of (network) methods tailored towards the analysis of protein-protein interactions (PPI) and/or interactions of proteins with ligands of other type, e.g. nucleic acids, oligosaccharides etc. In parallel, we propose the use of the network differential analysis as a method to identify residues mediating key interactions between proteins. We use a model system, to show that in combination with other, already published methods, also included in pyProGA, it can be used to make such predictions. Such extended repertoire of methods allows to cross-check predictions with other methods as well, as we show here. In addition, the possibility to construct PRN models from various kinds of input is so far a unique asset of our code. One can use structural data as defined in PDB files and/or from data on residue pair interaction energies, either from force-field parameters or fragment molecular orbital (FMO) calculations. pyProGA is a free open-source software available from https://gitlab.com/Vlado_S/pyproga.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Tokyo, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Vladimir Sladek
- Institute of Construction and Architecture, Slovak Academy of Sciences, Bratislava, Slovakia
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Song H, Wutthinitikornkit Y, Zhou X, Li J. Impacts of mutations on dynamic allostery of adenylate kinase. J Chem Phys 2021; 155:035101. [PMID: 34293874 DOI: 10.1063/5.0053715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Escherichia coli adenylate kinase (AK) is composed of CORE domain and two branch domains: LID and AMP-binding domain (AMPbd). AK exhibits considerable allostery in a reversible phosphoryl transfer reaction, which is largely attributed to the relative motion of LID and AMPbd with respect to CORE. Such an allosteric conformational change is also evident in the absence of ligands. Recent studies showed that the mutations in branch domains can adjust dynamic allostery and alter the substrate affinity and enzyme activity. In this work, we use all-atom molecular dynamics simulation to study the impacts of mutations in branch domains on AK's dynamic allostery by comparing two double mutants, i.e., LID mutant (Val135Gly, Val142Gly) and AMPbd mutant (Ala37Gly, Ala55Gly), with wild-type. Two mutants undergo considerable conformational fluctuation and exhibit deviation from the initially extended apo state to more compact structures. The LID domain in the LID mutant adjusts its relative position and firmly adheres to CORE. More strikingly, AMPbd mutations affect the relative positions of both the AMPbd domain and remote LID domain. Both domains undergo considerable movement, especially the inherent hinge swing motion of the flexible LID domain. In both mutants, the mutations can enhance the inter-domain interaction. The results about the conformation change of AK in both mutants are in line with the experiment of AK's affinity and activity. As revealed by our findings, the flexibility of branch domains and their inherent motions, especially LID domain, is highly relevant to dynamic allostery in the AK system.
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Affiliation(s)
- Haoyu Song
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Yanee Wutthinitikornkit
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Xiaozhou Zhou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
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Poudel H, Leitner DM. Activation-Induced Reorganization of Energy Transport Networks in the β 2 Adrenergic Receptor. J Phys Chem B 2021; 125:6522-6531. [PMID: 34106712 DOI: 10.1021/acs.jpcb.1c03412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We compute energy exchange networks (EENs) through the β2 adrenergic receptor (β2AR), a G-protein coupled receptor (GPCR), in inactive and active states, based on the results of molecular dynamics simulations of this membrane bound protein. We introduce a new definition for the reorganization of EENs upon activation that depends on the relative change in rates of energy transfer across noncovalent contacts throughout the protein. On the basis of the reorganized network that we obtain for β2AR upon activation, we identify a branched pathway between the agonist binding site and the cytoplasmic region, where a G-protein binds to the receptor when activated. The pathway includes all of the motifs containing molecular switches previously identified as contributing to the allosteric transition of β2AR upon agonist binding. EENs and their reorganization upon activation are compared with structure-based contact networks computed for the inactive and active states of β2AR.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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Abstract
After first describing the issue contents (Biophysical Reviews-Volume 12 Issue 6), this Editorial goes on to provide a short round-up of the activities of the journal in 2020. Directly following this Editorial are two obituaries marking the recent deaths of Prof. Fumio Oosawa (Japan) and Dr. Herbert Tabor (USA)-two major figures in Biophysical/Biochemical science from the last 100 years.
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Affiliation(s)
- Damien Hall
- Department of Life Sciences and Applied Chemistry, Nagoya Institute of Technology, Gokiso Showa, Nagoya, 466-8555 Japan
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Poudel H, Reid KM, Yamato T, Leitner DM. Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations. J Phys Chem B 2020; 124:9852-9861. [PMID: 33107736 DOI: 10.1021/acs.jpcb.0c08091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular dynamics simulations of the villin headpiece subdomain HP36 have been carried out to examine relations between rates of vibrational energy transfer across non-covalently bonded contacts and equilibrium structural fluctuations, with focus on van der Waals contacts. Rates of energy transfer across van der Waals contacts vary inversely with the variance of the contact length, with the same constant of proportionality for all nonpolar contacts of HP36. A similar relation is observed for hydrogen bonds, but the proportionality depends on contact pairs, with hydrogen bonds stabilizing the α-helices all exhibiting the same constant of proportionality, one that is distinct from those computed for other polar contacts. Rates of energy transfer across van der Waals contacts are found to be up to 2 orders of magnitude smaller than rates of energy transfer across polar contacts.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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Hall D. Biophysical Reviews' national biophysical society partnership program. Biophys Rev 2020; 12:187-192. [PMID: 32350823 PMCID: PMC7242517 DOI: 10.1007/s12551-020-00693-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
This Special Issue is focused on the Biophysical Society of Japan. It represents the first in a series tasked with introducing an individual national biophysical society to the wider biophysical community. In this Editorial for Volume 12 Issue 2, I first outline the nature and goals of this program before going on to describe the contents of the Special Issue that relate to the activities organized by the Biophysical Society of Japan and the scope of the research performed by its members.
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Affiliation(s)
- Damien Hall
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bld. 8, Bethesda, MD, 20892-0830, USA.
- Institute for Protein Research, Osaka University, 3-1-Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan.
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