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Okuda M, Tsunaka Y, Nishimura Y. Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones. Biophys Rev 2022; 14:1449-1472. [PMID: 36659983 PMCID: PMC9842849 DOI: 10.1007/s12551-022-01014-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/06/2022] [Indexed: 11/19/2022] Open
Abstract
Advances in structural analysis by cryogenic electron microscopy (cryo-EM) and X-ray crystallography have revealed the tertiary structures of various chromatin-related proteins, including transcription factors, RNA polymerases, nucleosomes, and histone chaperones; however, the dynamic structures of intrinsically disordered regions (IDRs) in these proteins remain elusive. Recent studies using nuclear magnetic resonance (NMR), together with molecular dynamics (MD) simulations, are beginning to reveal dynamic structures of the general transcription factor TFIIH complexed with target proteins including the general transcription factor TFIIE, the tumor suppressor p53, the cell cycle protein DP1, the DNA repair factors XPC and UVSSA, and three RNA polymerases, in addition to the dynamics of histone tails in nucleosomes and histone chaperones. In complexes of TFIIH, the PH domain of the p62 subunit binds to an acidic string formed by the IDR in TFIIE, p53, XPC, UVSSA, DP1, and the RPB6 subunit of three RNA polymerases by a common interaction mode, namely extended string-like binding of the IDR on the positively charged surface of the PH domain. In the nucleosome, the dynamic conformations of the N-tails of histones H2A and H2B are correlated, while the dynamic conformations of the N-tails of H3 and H4 form a histone tail network dependent on their modifications and linker DNA. The acidic IDRs of the histone chaperones of FACT and NAP1 play important roles in regulating the accessibility to histone proteins in the nucleosome.
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Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
| | - Yasuo Tsunaka
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, 739-8528 Japan
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Ueda T, Imai S, Shimada I. Function-related dynamics of GPCRs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107164. [PMID: 35168190 DOI: 10.1016/j.jmr.2022.107164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors (GPCRs) include various neurotransmitters and hormones, and over 30% of modern drugs target GPCRs. The number of GPCR crystal structures has rapidly increased, and many structures of GPCRs in complexes with their binding partners are being solved by cryo-electron microscopy. However, crystallographic or cryo-electron microscopy data alone cannot fully explain the important features of GPCR signaling determined experimentally. Recent studies have suggested that GPCRs are structurally dynamic, and exchange between multiple conformations. In this respect, NMR methods provide information about the dynamics of proteins over a wide range of frequencies, in aqueous solutions at nearphysiological temperatures. Although NMR studies of GPCRs are challenging due to their innate instability and relatively large molecular weights, recent methodological advances have enabled us to observe the NMR signals of various GPCRs. These NMR studies revealed that GPCRs exist in function-related equilibria between locally different conformations that are simultaneously populated. Here we will describe solution NMR studies that have clarified the function-related conformational dynamics of two GPCRs, β2 adrenergic receptor and adenosine A2A receptor.
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Affiliation(s)
- Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shunsuke Imai
- Center for Biosystems Dynamics Research (BDR), RIKEN, Kanagawa, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Center for Biosystems Dynamics Research (BDR), RIKEN, Kanagawa, Japan.
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Higo J, Takashima H, Fukunishi Y, Yoshimori A. Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. J Comput Chem 2021; 42:956-969. [PMID: 33755222 DOI: 10.1002/jcc.26516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/30/2022]
Abstract
A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Importantly, the molecular orientation of mS-11 is ordering in a wide region around mSin3B. The resultant binding scenario is: When mS-11 is distant from the binding site of mSin3B, mS-11 descends the free-energy slope toward the binding site maintaining the molecular orientation to be advantageous for binding. Then, finally a long and flexible hydrophobic sidechain of mS-11 fits into the binding site, which is the lowest-free-energy complex structure inhibiting NRSF/REST binding to mSin3B.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Hajime Takashima
- Department of Research and Development, PRISM BioLab Co., Ltd., Fujisawa, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Atsushi Yoshimori
- Chemoinformatics & AI Research Group, Institute for Theoretical Medicine, Inc., Fujisawa, Japan
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Higo J, Kawabata T, Kusaka A, Kasahara K, Kamiya N, Fukuda I, Mori K, Hata Y, Fukunishi Y, Nakamura H. Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J Chem Inf Model 2020; 60:4867-4880. [PMID: 32910853 DOI: 10.1021/acs.jcim.0c00551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Enhanced conformational sampling, a genetic-algorithm-guided multidimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semistable complex structures and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3ε, and a flexible peptide, phosphorylated myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3ε. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3ε surface and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spot are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding constant changes resulting from the alanine mutation experiment for the residues. We also performed a simulation of nonphosphorylated peptide and 14-3-3ε, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3ε.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kentaro Mori
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Maizuru College, 234 Shiroya, Maizuru, Kyoto 625-8511 Japan
| | - Yutaka Hata
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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Higo J, Kasahara K, Nakamura H. Multi-dimensional virtual system introduced to enhance canonical sampling. J Chem Phys 2018; 147:134102. [PMID: 28987097 DOI: 10.1063/1.4986129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
When an important process of a molecular system occurs via a combination of two or more rare events, which occur almost independently to one another, computational sampling for the important process is difficult. Here, to sample such a process effectively, we developed a new method, named the "multi-dimensional Virtual-system coupled Monte Carlo (multi-dimensional-VcMC)" method, where the system interacts with a virtual system expressed by two or more virtual coordinates. Each virtual coordinate controls sampling along a reaction coordinate. By setting multiple reaction coordinates to be related to the corresponding rare events, sampling of the important process can be enhanced. An advantage of multi-dimensional-VcMC is its simplicity: Namely, the conformation moves widely in the multi-dimensional reaction coordinate space without knowledge of canonical distribution functions of the system. To examine the effectiveness of the algorithm, we introduced a toy model where two molecules (receptor and its ligand) bind and unbind to each other. The receptor has a deep binding pocket, to which the ligand enters for binding. Furthermore, a gate is set at the entrance of the pocket, and the gate is usually closed. Thus, the molecular binding takes place via the two events: ligand approach to the pocket and gate opening. In two-dimensional (2D)-VcMC, the two molecules exhibited repeated binding and unbinding, and an equilibrated distribution was obtained as expected. A conventional canonical simulation, which was 200 times longer than 2D-VcMC, failed in sampling the binding/unbinding effectively. The current method is applicable to various biological systems.
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Affiliation(s)
- Junichi Higo
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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Hayami T, Kasahara K, Nakamura H, Higo J. Molecular dynamics coupled with a virtual system for effective conformational sampling. J Comput Chem 2018; 39:1291-1299. [PMID: 29464736 DOI: 10.1002/jcc.25196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 11/12/2022]
Abstract
An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Tomonori Hayami
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Okuda M, Nakazawa Y, Guo C, Ogi T, Nishimura Y. Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways. Nucleic Acids Res 2017; 45:13043-13055. [PMID: 29069470 PMCID: PMC5727438 DOI: 10.1093/nar/gkx970] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/03/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022] Open
Abstract
Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA Polymerase II detects a lesion on the transcribed strand and recruits TFIIH by an unknown mechanism. Here, we found that the TCR initiation factor UVSSA forms a stable complex with the PH domain of p62 via a short acidic string in the central region of UVSSA, and determined the complex structure by NMR. The acidic string of UVSSA binds strongly to the basic groove of the PH domain by inserting Phe408 and Val411 into two pockets, highly resembling the interaction mechanism of XPC with p62. Mutational binding analysis validated the structure and identified residues crucial for binding. TCR activity was markedly diminished in UVSSA-deficient cells expressing UVSSA mutated at Phe408 or Val411. Thus, a common TFIIH recruitment mechanism is shared by UVSSA in TCR and XPC in GGR.
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Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuka Nakazawa
- Department of Genome Repair, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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