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Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD. Visualizing the DNA repair process by a photolyase at atomic resolution. Science 2023; 382:eadd7795. [PMID: 38033054 DOI: 10.1126/science.add7795] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.
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Affiliation(s)
- Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Po-Hsun Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Yuhei Hosokawa
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Antonia Furrer
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | | | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hans-Joachim Emmerich
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Sophie Franz-Badur
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Chao Yang
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Sylvain Engilberge
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wael Gad
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Chun Yang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Wei-Ting Lin
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Yu-Chen Chang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Dardan Gashi
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Emma Beale
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Karol Nass
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Chris Milne
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Wiktoria Zarzycka
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pavel Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maisa Alkheder Alahmad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Filipp Bezold
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Valerie Fuchs
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Petra Gnau
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Stephan Kiontke
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Lukas Korf
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Viktoria Reithofer
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Elisa Marie Seiler
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Mohamed Watad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Laura Werel
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Roberta Spadaccini
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
- Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dongping Zhong
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jörg Standfuss
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Antoine Royant
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
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10
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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11
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Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Front Mol Biosci 2022; 9:1072733. [PMID: 36699705 PMCID: PMC9868570 DOI: 10.3389/fmolb.2022.1072733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide RNA (gRNA) that serves as a binding scaffold to guide it to the target DNA duplex via a RecA-like strand-displacement mechanism but without ATP binding or hydrolysis. The target search begins with the protospacer adjacent motif or PAM-interacting domain, recognizing it at the major groove of the duplex and melting its downstream duplex where an RNA-DNA heteroduplex is formed at nanomolar affinity. The rate-limiting step is the formation of an R-loop structure where the HNH domain inserts between the target heteroduplex and the displaced non-target DNA strand. Once the R-loop structure is formed, the non-target strand is rapidly cleaved by RuvC and ejected from the active site. This event is immediately followed by cleavage of the target DNA strand by the HNH domain and product release. Within CRISPR-associated protein 9, the HNH domain is inserted into the RuvC domain near the RuvC active site via two linker loops that provide allosteric communication between the two active sites. Due to the high flexibility of these loops and active sites, biophysical techniques have been instrumental in characterizing the dynamics and mechanism of the CRISPR-associated protein 9 nucleases, aiding structural studies in the visualization of the complete active sites and relevant linker structures. Here, we review biochemical, structural, and biophysical studies on the underlying mechanism with emphasis on how CRISPR-associated protein 9 selects the target DNA duplex and rejects non-target sequences.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Mohd Ahsan
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Souvik Sinha
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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