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Nishimura C, Kikuchi T. Non-Native Structures of Apomyoglobin and Apoleghemoglobin in Folding Intermediates Related to the Protein Misfolding. Molecules 2023; 28:molecules28093970. [PMID: 37175379 PMCID: PMC10179781 DOI: 10.3390/molecules28093970] [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: 03/02/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Protein folding is essential for a polypeptide chain to acquire its proper structure and function. Globins are a superfamily of ubiquitous heme-binding α-helical proteins whose function is principally to regulate oxygen homoeostasis. In this review, we explore the hierarchical helical formation in the globin proteins apomyoglobin and leghemoglobin, and we discuss the existence of non-native and misfolded structures occurring during the course of folding to its native state. This review summarizes the research aimed at characterizing and comparing the equilibrium and kinetic intermediates, as well as delineating the complete folding pathway at a molecular level, in order to answer the following questions: "What is the mechanism of misfolding via a folding intermediate? Does the non-native structure stabilize the contemporary intermediate structure? Does the non-native structure induce slower folding?" The role of the non-native structures in the folding intermediate related to misfolding is also discussed.
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Affiliation(s)
- Chiaki Nishimura
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo 164-8530, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu 528-8577, Japan
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Fujinami D, Hayashi S, Kohda D. Retrospective study for the universal applicability of the residue-based linear free energy relationship in the two-state exchange of protein molecules. Sci Rep 2022; 12:16843. [PMID: 36207470 PMCID: PMC9546931 DOI: 10.1038/s41598-022-21226-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022] Open
Abstract
Multiprobe measurements, such as NMR and hydrogen exchange studies, can provide the equilibrium constant, K, and rate constants for forward and backward processes, k and k′, of the two-state structural changes of a polypeptide on a per-residue basis. We previously found a linear relationship between log K and log k and between log K and log k′ for the topological exchange of a 27-residue bioactive peptide. To test the general applicability of the residue-based linear free energy relationship (rbLEFR), we performed a literature search to collect residue-specific K, k, and k′ values in various exchange processes, including folding-unfolding equilibrium, coupled folding and binding of intrinsically disordered peptides, and structural fluctuations of folded proteins. The good linearity in a substantial number of the log–log plots proved that the rbLFER holds for the structural changes in a wide variety of protein-related phenomena. Among the successful cases, the hydrogen exchange study of apomyoglobin folding intermediates is particularly interesting. We found that the residues that deviated from the linear relationship corresponded to the α-helix, for which transient translocation had been identified by other experiments. Thus, the rbLFER is useful for studying the structures and energetics of the dynamic states of protein molecules.
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Affiliation(s)
- Daisuke Fujinami
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.,Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Seiichiro Hayashi
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.
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Kuwajima K, Yagi-Utsumi M, Yanaka S, Kato K. DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123748. [PMID: 35744871 PMCID: PMC9230524 DOI: 10.3390/molecules27123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. In this method, the H/D-exchange buffer is replaced by an aprotic DMSO solution, which quenches the exchange reaction. We have improved the DMSO-quenched method by using spin desalting columns, which are used for medium exchange from the H/D-exchange buffer to the DMSO solution. This improvement has allowed us to monitor the H/D exchange of proteins at a high concentration of salts or denaturants. We describe methodological details of the improved DMSO-quenched method and present a case study using the improved method on the H/D-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (K.K.); (K.K.)
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
- Correspondence: (K.K.); (K.K.)
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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Dutta S, Ghosh M, Karmakar R, Chakrabarti J. Dynamic signature of ligand binding over a protein surface. Phys Rev E 2019; 100:062411. [PMID: 31962438 DOI: 10.1103/physreve.100.062411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Indexed: 06/10/2023]
Abstract
We study the motion of Zn^{2+} in the presence of ubiquitin by all-atom molecular-dynamics simulations. We observe that unlike normal diffusive liquid, metal ions show an exponential tail in the self-van Hove function (self-vHf). Moreover, the metal ions are trapped strongly by acidic residues which form a binding pocket over the protein surface. The exponential tail disappears by mutation of trapping residues, suggesting that the tail appears due to trapped motion of the ions. The mean-squared displacements, however, in all the cases show linear dependence on time. Our model establishes that ligand binding generically results in an exponential tail of self-vHf. The self-vHf may give an approach to find binding pockets over a protein surface.
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Affiliation(s)
- Sutapa Dutta
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Rahul Karmakar
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - J Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
- Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
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Bychkova VE, Semisotnov GV, Balobanov VA, Finkelstein AV. The Molten Globule Concept: 45 Years Later. BIOCHEMISTRY (MOSCOW) 2018; 83:S33-S47. [DOI: 10.1134/s0006297918140043] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Arai M. Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins. Biophys Rev 2018; 10:163-181. [PMID: 29307002 PMCID: PMC5899706 DOI: 10.1007/s12551-017-0346-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022] Open
Abstract
Extensive experimental and theoretical studies have advanced our understanding of the mechanisms of folding and binding of globular proteins, and coupled folding and binding of intrinsically disordered proteins (IDPs). The forces responsible for conformational changes and binding are common in both proteins; however, these mechanisms have been separately discussed. Here, we attempt to integrate the mechanisms of coupled folding and binding of IDPs, folding of small and multi-subdomain proteins, folding of multimeric proteins, and ligand binding of globular proteins in terms of conformational selection and induced-fit mechanisms as well as the nucleation–condensation mechanism that is intermediate between them. Accumulating evidence has shown that both the rate of conformational change and apparent rate of binding between interacting elements can determine reaction mechanisms. Coupled folding and binding of IDPs occurs mainly by induced-fit because of the slow folding in the free form, while ligand binding of globular proteins occurs mainly by conformational selection because of rapid conformational change. Protein folding can be regarded as the binding of intramolecular segments accompanied by secondary structure formation. Multi-subdomain proteins fold mainly by the induced-fit (hydrophobic collapse) mechanism, as the connection of interacting segments enhances the binding (compaction) rate. Fewer hydrophobic residues in small proteins reduce the intramolecular binding rate, resulting in the nucleation–condensation mechanism. Thus, the folding and binding of globular proteins and IDPs obey the same general principle, suggesting that the coarse-grained, statistical mechanical model of protein folding is promising for a unified theoretical description of all mechanisms.
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Affiliation(s)
- Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
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