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Wang J, Shi Y, Reiss K, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Structural Insights into Binding of Remdesivir Triphosphate within the Replication-Transcription Complex of SARS-CoV-2. Biochemistry 2022; 61:1966-1973. [PMID: 36044776 PMCID: PMC9469760 DOI: 10.1021/acs.biochem.2c00341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/18/2022] [Indexed: 01/18/2023]
Abstract
Remdesivir is an adenosine analogue that has a cyano substitution in the C1' position of the ribosyl moiety and a modified base structure to stabilize the linkage of the base to the C1' atom with its strong electron-withdrawing cyano group. Within the replication-transcription complex (RTC) of SARS-CoV-2, the RNA-dependent RNA polymerase nsp12 selects remdesivir monophosphate (RMP) over adenosine monophosphate (AMP) for nucleotide incorporation but noticeably slows primer extension after the added RMP of the RNA duplex product is translocated by three base pairs. Cryo-EM structures have been determined for the RTC with RMP at the nucleotide-insertion (i) site or at the i + 1, i + 2, or i + 3 sites after product translocation to provide a structural basis for a delayed-inhibition mechanism by remdesivir. In this study, we applied molecular dynamics (MD) simulations to extend the resolution of structures to the measurable maximum that is intrinsically limited by MD properties of these complexes. Our MD simulations provide (i) a structural basis for nucleotide selectivity of the incoming substrates of remdesivir triphosphate over adenosine triphosphate and of ribonucleotide over deoxyribonucleotide, (ii) new detailed information on hydrogen atoms involved in H-bonding interactions between the enzyme and remdesivir, and (iii) direct information on the catalytically active complex that is not easily captured by experimental methods. Our improved resolution of interatomic interactions at the nucleotide-binding pocket between remedesivir and the polymerase could help to design a new class of anti-SARS-CoV-2 inhibitors.
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Affiliation(s)
- Jimin Wang
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Yuanjun Shi
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
| | - Krystle Reiss
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
| | - Federica Maschietto
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
| | - Elias Lolis
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06520-8066, United States
| | - William H. Konigsberg
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - George P. Lisi
- Department
of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
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Geronimo I, Vidossich P, Donati E, Vivo M. Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Elisa Donati
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Marco Vivo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
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Liu Q, Ke Y, Kan Y, Tang X, Li X, He Y, Wu L. Compatibility and Fidelity of Mirror-Image Thymidine in Transcription Events by T7 RNA Polymerase. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:604-613. [PMID: 32721880 PMCID: PMC7390857 DOI: 10.1016/j.omtn.2020.06.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/15/2020] [Accepted: 06/23/2020] [Indexed: 11/16/2022]
Abstract
Due to highly enzymatic d-stereoselectivity, l-nucleotides (l-2'-deoxynucleoside 5'-triphosphates [l-dNTPs]) are not natural targets of polymerases. In this study, we synthesized series of l-thymidine (l-T)-modified DNA strands and evaluated the processivity of nucleotide incorporation for transcription by T7 RNA polymerase (RNAP) with an l-T-containing template. When single l-T was introduced into the transcribed region, transcription proceeded to afford the full-length transcript with different efficiencies. However, introduction of l-T into the non-transcribed region did not exhibit a noticeable change in the transcription efficiency. Surprisingly, when two consecutive or internal l-Ts were introduced into the transcribed region, no transcripts were detected. Compared to natural template, significant lags in NTP incorporation into the template T+4/N and T+7/N (where the number corresponds to the site of l-T position, and + means downstream of the transcribed region) were detected by kinetic analysis. Furthermore, affinity of template T+4/N was almost the same with T/N, whereas affinity of T+7/N was apparently increased. Furthermore, no mismatch opposite to l-T in the template was detected in transcription reactions via gel fidelity analysis. These results demonstrate the effects of chiral l-T in DNA on the efficiency and fidelity of RNA transcription mediated by T7 RNAP, which provides important knowledge about how mirror-image thymidine perturbs the flow of genetic information during RNA transcription and development of diseases caused by gene mutation.
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Affiliation(s)
- Qingju Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqi Ke
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhe Kan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiangjun Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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Yoon H, Zhao LN, Warshel A. Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII. ACS Catal 2019; 9:1329-1336. [PMID: 34046245 DOI: 10.1021/acscatal.8b04324] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating the nature of the gene editing mechanism of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is an important task in view of the role of this breakthrough to the advancement of human medicine. In particular, it is crucial to understand the catalytic mechanism of Cas9 (one of the CRISPR associated proteins) and its role in confirming accurate editing. Thus, we focus in this work on an attempt to analyze the catalytic mechanism of Cas9. Considering the absence of detailed structural information on the active form of Cas9, we use an empirical valence bond (EVB) which is calibrated on the closely related mechanism of T4 endonuclease VII. The calibrated EVB is then used in studying the reaction of Cas9, while trying several structural models. It is found that the catalytic activation requires a large conformational change, where K848 or other positively charged group moves from a relatively large distance toward the scissile phosphate. This conformational change leads to the change in position of the Mg2+ ion and to a major reduction in the activation barrier for the catalytic reaction. Our finding provides an important clue on the nature of the catalytic activation of CAS9 and thus should help in elucidating a key aspect of the gene editing process. For example, the approach used here should be effective in exploring the nature of off target activation and its relationship to the energetics of the unwinding process. This strategy may offer ways to improve the selectivity of Cas9.
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Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Li Na Zhao
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
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Yoon H, Kolev V, Warshel A. Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations. J Phys Chem B 2017; 121:9358-9365. [PMID: 28911225 PMCID: PMC5954165 DOI: 10.1021/acs.jpcb.7b07726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The study of the function of proteins on a quantitative level requires consideration of the water molecules in and around the protein. This requirement presents a major computational challenge due to the fact that the insertion of water molecules can have a very high activation barrier and would require a long simulation time. Recently, we developed a water flooding (WF) approach which is based on a postprocessing Monte Carlo ranking of possible water configurations. This approach appears to provide a very effective way for assessing the insertion free energies and determining the most likely configurations of the internal water molecules. Although the WF approach was used effectively in modeling challenging systems that have not been addressed reliably by other microscopic approaches, it was not validated by a comparison to the more rigorous grand canonical Monte Carlo (GCMC) method. Here we validate the WF approach by comparing its performance to that of the GCMC method. It is found that the WF approach reproduces the GCMC results in well-defined test cases but does so much faster. This established the WF approach as a useful strategy for finding correct water configurations in proteins and thus to provide a powerful way for studies of the functions of proteins.
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Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California , 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089-1062, United States
| | - Vesselin Kolev
- Department of Chemistry, University of Southern California , 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089-1062, United States
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Yoon H, Warshel A. Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis. Proteins 2017; 85:1446-1453. [PMID: 28383109 DOI: 10.1002/prot.25305] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/20/2017] [Accepted: 03/27/2017] [Indexed: 11/06/2022]
Abstract
Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8-oxo-7,8-dhyedro-2'-deoxoguanosin(8-oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446-1453. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California, 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California, 90089-1062
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