Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus
Abstract
Sequence data are available for the coat proteins of seven tobamoviruses, with homologies ranging from at least 26% to 82%, and atomic co-ordinates are known for tobacco mosaic virus (TMV) vulgare. A significant spatial relationship has been found between groups of residues with identical amino acid substitution patterns. This strongly suggest that their location is linked to a particular function, at least in viruses identical with the wild-type for these residues. The most conserved feature of TMV is the RNA binding region. Core residues are conserved in all viruses or show mutations complementary in volume. The specificity of inter-subunit contacts is achieved in different ways in the three more distantly related viruses.
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The premise of methods to infer structure based on evolutionary couplings is that amino acids co-evolve in patterns reflective of the underlying structure because they exist and evolve in the context of 3D structure.
“The premise of methods to infer structure based on evolutionary couplings is that, because amino acids exist and evolve in the context of 3D structure, they are not free to evolve independently, but instead co-evolve in patterns reflective of the underlying structure.”
From Predicting multiple conformations via sequence clustering and AlphaFold2 (2024) · cites this paper as [7]
Cites
The interpretation of protein structures: Estimation of static accessibility
Lee, B., & Richards, F. M. (1971) · Journal of Molecular Biology · doi:10.1016/0022-2836(71)90324-x · Cited by 5,884 · see citing works
Solvent accessible surface area and excluded volume in proteins
Richmond, T. J. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90231-6 · Cited by 760 · see citing works
Lesk, A. M., & Chothia, C. (1980) · Journal of Molecular Biology · doi:10.1016/0022-2836(80)90373-3 · Cited by 712 · see citing works
Self-citationPRINCIPLES THAT DETERMINE THE STRUCTURE OF PROTEINS
Chothia, C. (1984) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.53.070184.002541 · Cited by 644 · see citing works
Structure and function of haemoglobin
Perutz, M. F., Kendrew, J. C., & WATSON, H. C. (1965) · Journal of Molecular Biology · doi:10.1016/s0022-2836(65)80134-6 · Cited by 608 · see citing works
Assembly and Stability of the Tobacco Mosaic Virus Particle
Caspar, D. L. D. (1964) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60268-5 · Cited by 556 · see citing works
Bloomer, A. C., Champness, J. N., Bricogne, G., et al. (1978) · Nature · doi:10.1038/276362a0 · Cited by 410 · see citing works
Self-citationStructure of Tobacco Mosaic Virus at 3.6 Å Resolution: Implications for Assembly
Namba, K., & Stubbs, G. (1986) · Science · doi:10.1126/science.3952490 · Cited by 344 · see citing works
Stubbs, G., Warren, S., & Holmes, K. C. (1977) · Nature · doi:10.1038/267216a0 · Cited by 244 · see citing works
The Current Picture of the Structure and Assembly of Tobacco Mosaic Virus
Butler, P. J. G. (1984) · Journal of General Virology · doi:10.1099/0022-1317-65-2-253 · Cited by 216 · see citing works
The structure of the protein disk of tobacco mosaic virus to 5 Å resolution
Champness, J. N., Bloomer, A. C., Bricogne, G., et al. (1976) · Nature · doi:10.1038/259020a0 · Cited by 195 · see citing works
Self-citationEvolution and the Tertiary Structure of Proteins
Bajaj, M., & Blundell, T. L. (1984) · Annual Review of Biophysics and Bioengineering · doi:10.1146/annurev.bb.13.060184.002321 · Cited by 180 · see citing works
Structural aspects of recognition and assembly in biological macromolecules
Correspondent, A. (1980) · Nature · doi:10.1038/285287a0 · Cited by 129 · see citing works
Structures and roles of the polymorphic forms of tobacco mosaic virus protein
Butler, P. J. G., Durham, A. C. H., & Klug, A. (1972) · Journal of Molecular Biology · doi:10.1016/0022-2836(72)90063-0 · Cited by 81 · see citing works
Self-citationAntigenic relationships between strains of tobacco mosaic virus
Regenmortel, M. H. V. V. (1975) · Virology · doi:10.1016/0042-6822(75)90118-x · Cited by 79 · see citing works
Takamatsu, N., Ohno, T., Meshi, T., et al. (1983) · Nucleic Acids Research · doi:10.1093/nar/11.11.3767 · Cited by 68 · see citing works
Chothia, C., & Lesk, A. M. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90033-6 · Cited by 65 · see citing works
Self-citationMeshi, T., Kiyama, R., Ohno, T., et al. (1983) · Virology · doi:10.1016/0042-6822(83)90370-7 · Cited by 58 · see citing works
Namba, K., & Stubbs, G. (1985) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s010876738500054x · Cited by 51 · see citing works
VIRAL TAXONOMY FOR THE NONVIROLOGIST
Matthews, R. E. F. (1985) · Annual Review of Microbiology · doi:10.1146/annurev.mi.39.100185.002315 · Cited by 46 · see citing works
The radial density distribution in some strains of tobacco mosaic virus
Holmes, K. C., & FRANKLIN, R. E. (1958) · Virology · doi:10.1016/0042-6822(58)90086-2 · Cited by 43 · see citing works
How Ancient Are the Tobamoviruse
Gibbs, A. J. (1980) · Intervirology · doi:10.1159/000149169 · Cited by 40 · see citing works
Otsuki, Y., & Takebe, I. (1978) · Virology · doi:10.1016/0042-6822(78)90228-3 · Cited by 33 · see citing works
Protein‐RNA interactions during TMV assembly
Holmes, K. C. (1979) · Journal of Supramolecular Structure · doi:10.1002/jss.400120304 · Cited by 32 · see citing works
Interaction and mixed aggregation of proteins from Tobacco mosaic virus strains
Sarkar, S. (1960) · Zeitschrift für Naturforschung B · doi:10.1515/znb-1960-1206 · Cited by 25 · see citing works
Taliansky, M. E., Атабекова, Т. И., & Atabekov, J. G. (1977) · Virology · doi:10.1016/0042-6822(77)90252-5 · Cited by 22 · see citing works
Altschuh, D., Reinbolt, J., & Regenmortel, M. H. V. V. (1981) · Journal of General Virology · doi:10.1099/0022-1317-52-2-363 · Cited by 9 · see citing works
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2016239118 · Cited by 3,286 · see citing works
Improved protein structure prediction using potentials from deep learning
Senior, A. W., Evans, R., Jumper, J., Kirkpatrick, J., Sifre, L., Green, T., Qin, C., Žídek, A., Nelson, A. W. R., Bridgland, A., et al. (2020) · Nature · doi:10.1038/s41586-019-1923-7 · Cited by 3,378 · see citing works
Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D. S., Sander, C., Zecchina, R., Onuchic, J. N., Hwa, T., & Weigt, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111471108 · Cited by 1,434 · see citing works
Identification of direct residue contacts in protein–protein interaction by message passing
Weigt, M., White, R. A., Szurmant, H., Hoch, J. A., & Hwa, T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805923106 · Cited by 1,025 · see citing works
Protein 3D Structure Computed from Evolutionary Sequence Variation
Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028766 · Cited by 1,144 · see citing works
Correlated mutations and residue contacts in proteins
Göbel, U., Sander, C., Schneider, R., & Valencia, A. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180402 · Cited by 863 · see citing works
Language models enable zero-shot prediction of the effects of mutations on protein function
Meier, J., Rao, R., Verkuil, R., Liu, J., Sercu, T., & Rives, A. (2021) · doi:10.1101/2021.07.09.450648 · Cited by 635 · see citing works
Protein structure prediction from sequence variation
Marks, D. S., Hopf, T. A., & Sander, C. (2012) · Nature Biotechnology · doi:10.1038/nbt.2419 · Cited by 622 · see citing works
Emerging methods in protein co-evolution
de Juan, D., Pazos, F., & Valencia, A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3414 · Cited by 607 · see citing works
Predicting multiple conformations via sequence clustering and AlphaFold2
Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature · doi:10.1038/s41586-023-06832-9 · Cited by 545 · see citing works
Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2019) · doi:10.1101/622803 · Cited by 3,280 · see citing works
“The idea that biological function and structure are recorded in the statistics of protein sequences selected through evolution has a long history (Yanofsky et al., 1964; Altschuh et al., 1987; 1988).”
BackgroundLanguage models generalize beyond natural proteins
Verkuil, R., Kabeli, O., Du, Y., Wicky, B. I. M., Milles, L. F., Dauparas, J., Baker, D., Ovchinnikov, S., Sercu, T., & Rives, A. (2022) · doi:10.1101/2022.12.21.521521 · Cited by 181 · see citing works
- Authors
- Altschuh, D., Lesk, A. M., Bloomer, A. C., & Klug, A.
- Affiliations
- MRC Laboratory of Molecular Biology (GB)
- Corresponding author
- Bloomer, A.C.
- ORCID
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1987-02
- Volume
- 193
- Issue
- 4
- Pages
- 693-707
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W1976666280
- Cited by
- 284
- References
- 27
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 3 · 2023: 11 · 2022: 7 · 2021: 27 · 2020: 5 · 2019: 13 · 2018: 9 · 2017: 8 · 2016: 5 · 2015: 7 · 2014: 12 · 2013: 14 · 2012: 12
- FWCI
- 5.56
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Virus Research Studies
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- tobacco mosaic virus, tobamovirus, capsid protein, amino acid substitutions, RNA-binding domain, protein structure, sequence conservation, complementarity
- MeSH terms
- Amino Acid Sequence, Binding Sites, Protein Conformation, RNA, Viral, Tobacco Mosaic Virus, Viral Proteins
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