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Vlasov, PetrAuthorSoylemez OAuthor

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May 19, 2016
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Local fitness landscape of the green fluorescent protein

Publicated to: NATURE. 533 (7603): 397-+ - 2016-05-19, DOI: 10.1038/nature17995

Authors:

Sarkisyan, KS; Bolotin, DA; Meer, MV; Usmanova, DR; Mishin, AS; Sharonov, GV; Ivankov, DN; Bozhanova, NG; Baranov, MS; Soylemez, O; Bogatyreva, NS; Vlasov, PK; Egorov, ES; Logacheva, MD; Kondrashov, AS; Chudakov, DM; Putintseva, EV; Mamedov, IZ; Tawfik, DS; Lukyanov, KA; Kondrashov, FA
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Affiliations

Barcelona Inst Sci & Technol, CRG, Bioinformat & Genom Programme, 88 Dr Aiguader, Barcelona 08003, Spain - Author
ICREA, 23 Pg Lluis Companys, Barcelona 08010, Spain - Author
Masaryk Univ, Cent European Inst Technol, Brno 62500, Czech Republic - Author
Moscow Inst Phys & Technol, Inst Pereulok 9, G Dolgoprudny 141700, Russia - Author
Moscow MV Lomonosov State Univ, Dept Bioinformat & Bioengn, Moscow 119234, Russia - Author
Moscow MV Lomonosov State Univ, Fac Med, Lomonosov Ave 31-5, Moscow 119192, Russia - Author
Nizhny Novgorod State Med Acad, Minin Sq 10-1, Nizhnii Novgorod 603005, Russia - Author
Pirogov Russian Natl Res Med Univ, Ostrovitianov 1, Moscow 117997, Russia - Author
Russian Acad Sci, AA Kharkevich Inst Informat Transmiss Problems, Moscow 127051, Russia - Author
Russian Acad Sci, Inst Prot Res, Lab Prot Phys, 4 Inst Skaya Str, Pushchino 142290, Moscow Region, Russia - Author
Shemyakin Ovchinnikov Inst Bioorgan Chem, Miklukho Maklaya 16-10, Moscow 117997, Russia - Author
Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA - Author
UPF, Barcelona 08003, Spain - Author
Weizmann Inst Sci, Dept Biol Chem, IL-76100 Rehovot, Israel - Author
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Abstract

Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design.
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Keywords

DomainEpistasisEvolutionMutationsSelectionSequence space

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal NATURE due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2016, it was in position 1/63, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 7.9. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 13, 2025)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 3.25 (source consulted: FECYT Mar 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2026-11-12, the following number of citations:

  • WoS: 377
  • Scopus: 176
  • Europe PMC: 217
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-11-12:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 677.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 676 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 158.
  • The number of mentions on the social network Facebook: 1 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 43 (Altmetric).
  • The number of mentions in news outlets: 15 (Altmetric).
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Czech Republic; Israel; Russia; United States of America.

the author responsible for correspondence tasks has been Kondrashov FA.

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Awards linked to the item

We thank Y. Kulikova and G. Filion for discussion on statistical analysis and I. Osterman, R. Moretti and J. Meiler for technical assistance and M. Friesen for a critical reading of the manuscript. We thank H. Himmelbauer, CRG Genomic Unit and the Russian Science Foundation project (14-50-00150) for sequencing. Experiments were partially carried out using the equipment provided by the IBCH core facility (CKP IBCH). The work was supported by HHMI International Early Career Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329), Spanish Ministry of Economy and Competitiveness Centro de Excelencia Severo Ochoa 2013-2017 grant (SEV-2012-0208), Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat's AGAUR program (2014 SGR 0974), Russian Science Foundation (14-25-00129) and the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013, ERC grant agreement, 335980_EinME).
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