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Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. J Struct Biol 2022; 214:107902. [PMID: 36202310 DOI: 10.1016/j.jsb.2022.107902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/23/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20-30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA.
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | | | - Shenping Wu
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | | | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA; Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
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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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Pata JD, Yin YW, Lahiri I. Editorial: Nucleic Acid Polymerases: The Two-Metal-Ion Mechanism and Beyond. Front Mol Biosci 2022; 9:948326. [PMID: 35911968 PMCID: PMC9332193 DOI: 10.3389/fmolb.2022.948326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Janice D. Pata
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
- *Correspondence: Janice D. Pata,
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Indrajit Lahiri
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
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