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Li Z, Hirst JD. Computed optical spectra of SARS-CoV-2 proteins. Chem Phys Lett 2020; 758:137935. [PMID: 33518776 PMCID: PMC7836526 DOI: 10.1016/j.cplett.2020.137935] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 02/03/2023]
Abstract
Calculated circular dichroism spectra in the far- and near-UV spectra. Calculated infra-red (IR) spectra in the amide I region. Based on experimental structures and computational models of SARS-CoV-2 proteins. Near-UV CD spectra offer greatest sensitivity to conformation.
Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined easily or quickly. Herein, we provide calculated circular dichroism (CD) spectra in the far- and near-UV, and infra-red (IR) spectra in the amide I region for experimental structures and computational models of SARS-CoV-2 proteins. The near-UV CD spectra offer greatest sensitivity in assessing the accuracy of models.
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Affiliation(s)
- Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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Uporov IV, Forlemu NY, Nori R, Aleksandrov T, Sango BA, Mbote YEB, Pothuganti S, Thomasson KA. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. Int J Mol Sci 2015; 16:21237-76. [PMID: 26370961 PMCID: PMC4613251 DOI: 10.3390/ijms160921237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/09/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023] Open
Abstract
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.
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Affiliation(s)
- Igor V Uporov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Faculty of Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia.
| | - Neville Y Forlemu
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA.
| | - Rahul Nori
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Tsvetan Aleksandrov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Boris A Sango
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Yvonne E Bongfen Mbote
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- James E. Hurley College of Science & Mathematics, Oklahoma Baptist University, OBU Box 61772, 500 W. University, Shawnee, OK 74804, USA.
| | - Sandeep Pothuganti
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Kathryn A Thomasson
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
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Individual contributions of the aromatic chromophores to the near-UV Circular Dichroism in class A β-lactamases: A comparative computational analysis. Biophys Chem 2010; 151:39-45. [DOI: 10.1016/j.bpc.2010.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 05/06/2010] [Accepted: 05/08/2010] [Indexed: 11/20/2022]
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Karabencheva T, Christov C. Mechanisms of protein circular dichroism: insights from computational modeling. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 80:85-115. [DOI: 10.1016/b978-0-12-381264-3.00003-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Christov CZ, Karabencheva TG, Lodola A. Relationship between chiroptical properties, structural changes and interactions in enzymes: A computational study on β-lactamases from class A. Comput Biol Chem 2008; 32:167-75. [DOI: 10.1016/j.compbiolchem.2008.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/06/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
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Christov C, Karabencheva T, Lodola A. Aromatic interactions and rotational strengths within protein environment: An electronic structural study on β-lactamases from class A. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Christov C, Kantardjiev A, Karabencheva T, Tielens F. Mechanisms of generation of the rotational strengths in TEM-1 β-lactamase. Part II: theoretical study of the effects of the electrostatic interactions in the near-UV. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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