The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Evolutionary biochemistry: revealing the historical and physical causes of protein properties
Open accessAbstract
The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry. Explanations of these two kinds of causality — the purviews of evolutionary biology and biochemistry, respectively — are typically pursued in isolation, but many fundamental questions fall squarely at the interface of fields. Here we articulate the paradigm of evolutionary biochemistry, which aims to dissect the physical mechanisms and evolutionary processes by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution. We show how an integration of evolution with biochemistry moves us towards a more complete understanding of why biological molecules have the properties that they do.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme
Gould, S. J., & Lewontin, R. C. (1979) · Proceedings of the Royal Society of London. Series B. Biological Sciences · doi:10.1098/rspb.1979.0086 · Cited by 7,770
Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.
Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., & Kingsley, D. M. (2005) · Science · doi:10.1126/science.1107239 · Cited by 1,448
Blount, Z. D., Borland, C. Z., & Lenski, R. E. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803151105 · Cited by 840
The protein trinity—linking function and disorder
Dunker, A. K., & Obradovic, Z. (2001) · Nature Biotechnology · doi:10.1038/nbt0901-805 · Cited by 581
Robustness–epistasis link shapes the fitness landscape of a randomly drifting protein
Bershtein, S., Segal, M., Bekerman, R., Tokuriki, N., & Tawfik, D. S. (2006) · Nature · doi:10.1038/nature05385 · Cited by 414
Complete mutagenesis of the HIV-1 protease
Loeb, D. D., Swanstrom, R., Everitt, L., Manchester, M., Stamper, S. E., & Hutchison, C. A. (1989) · Nature · doi:10.1038/340397a0 · Cited by 327
Cited by
Starr, T. N., Greaney, A. J., Hilton, S. K., Ellis, D., Crawford, K. H. D., Dingens, A. S., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.012 · Cited by 1,956
Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction
Koblan, L. W., Doman, J. L., Wilson, C., Levy, J. M., Tay, T., Newby, G. A., Maianti, J. P., Raguram, A., & Liu, D. R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4172 · Cited by 944
Mutation effects predicted from sequence co-variation
Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C., & Marks, D. S. (2017) · Nature Biotechnology · doi:10.1038/nbt.3769 · Cited by 775
Empirical fitness landscapes and the predictability of evolution
de Visser, J. A. G. M., & Krug, J. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3744 · Cited by 715
A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
Olson, C. A., Wu, N. C., & Sun, R. (2014) · Current Biology · doi:10.1016/j.cub.2014.09.072 · Cited by 408
Genetic diversity loss in the Anthropocene
Exposito-Alonso, M., Booker, T. R., Czech, L., Gillespie, L., Hateley, S., Kyriazis, C. C., Lang, P. L. M., Leventhal, L., Nogues-Bravo, D., Pagowski, V., et al. (2022) · Science · doi:10.1126/science.abn5642 · Cited by 288
Rossier, B. C., Baker, M. E., & Studer, R. A. (2015) · Physiological Reviews · doi:10.1152/physrev.00011.2014 · Cited by 269
Zou, Z., & Zhang, J. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv091 · Cited by 153
Diversity as opportunity: Insights from 600 million years of AHR evolution
Hahn, M. E., Karchner, S. I., & Merson, R. R. (2017) · Current Opinion in Toxicology · doi:10.1016/j.cotox.2017.02.003 · Cited by 134
Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module
McKeown, A. N., Bridgham, J. T., Anderson, D. W., Murphy, M. N., Ortlund, E. A., & Thornton, J. W. (2014) · Cell · doi:10.1016/j.cell.2014.09.003 · Cited by 107
Self-citationIntersecting transcription networks constrain gene regulatory evolution
Sorrells, T. R., Booth, L. N., Tuch, B. B., & Johnson, A. D. (2015) · Nature · doi:10.1038/nature14613 · Cited by 69
Kiefl, E., Esen, O. C., Miller, S. E., Kroll, K. L., Willis, A. D., Rappé, M. S., Pan, T., & Eren, A. M. (2023) · Science Advances · doi:10.1126/sciadv.abq4632 · Cited by 26
Mihalič, F., Åberg, E., Farkhondehkish, P., Theys, N., Andersson, E., & Jemth, P. (2023) · Protein Science · doi:10.1002/pro.4684 · Cited by 6
Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation
Nisler, C. R., Narui, Y., Scheib, E., Choudhary, D., Bowman, J. D., Mandayam Bharathi, H., Lynch, V. J., & Sotomayor, M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad057 · Cited by 4
Metadata
- Authors
- Harms, M. J., & Thornton, J. W.
- Venue
- Nature Reviews Genetics
- Published
- 2013-07-18
- Volume
- 14
- Issue
- 8
- Pages
- 559-571
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W1993646374
- Cited by
- 330
- References
- 6
- FWCI
- 3.84
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
