ArticleHFSP journal2007
A structural model of latent evolutionary potentials underlying neutral networks in proteins.
Article in HFSP journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- A simple model captures key characteristics of biological non-deterministic genotype-phenotype maps.PLoS computational biology · 2026Article
- Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity.JACS Au · 2024Article
- Analysing a Group of Homologous BAHD Enzymes Provides Insights into the Evolutionary Transition of Rosmarinic Acid Synthases from Hydroxycinnamoyl-CoA:Shikimate/Quinate Hydroxycinnamoyl Transferases.Plants (Basel, Switzerland) · 2024Article
- The Boltzmann distributions of molecular structures predict likely changes through random mutations.Biophysical journal · 2023Article
- Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations.RNA (New York, N.Y.) · 2022Article
- Droplet-based screening of phosphate transfer catalysis reveals how epistasis shapes MAP kinase interactions with substrates.Nature communications · 2022Article
- Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation.Journal of the Royal Society, Interface · 2021Article
- Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution.Chemical reviews · 2020Review
- Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding.Genome biology and evolution · 2019Article
- Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.Current opinion in structural biology · 2017Review
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- The Evolutionary Potential of Phenotypic Mutations.PLoS genetics · 2015Article
- The amino acid alphabet and the architecture of the protein sequence-structure map. I. Binary alphabets.PLoS computational biology · 2014Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- Smooth functional transition along a mutational pathway with an abrupt protein fold switch.Biophysical journal · 2014Article
- Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts.PLoS computational biology · 2012Article
- Article
- Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A central question in molecular evolution concerns the nature of phenotypic transitions, in particular, if neutral mutations hamper or somehow facilitate adaptability of proteins to new requirements. Proteins have been found to fluctuate between different structures, with frequencies of structures being proportional to their stability. Therefore, functional promiscuity may correspond to different structures with energies close to the ground state which then represent multiple selectable traits. We here postulate that these near-ground-state structures facilitate smooth transitions between phenotypes. Using a biophysical heteropolymer model with exhaustive mappings of sequences onto structures, we demonstrate that this is indeed possible because of a smooth gradient of stability along which any structural phenotype can be optimized and also because of mutational proximity of similar phenotypes in genotype space. Our model provides a biophysical rationalization of the intriguing, and otherwise puzzling experimental observation that adaptation to new requirements, e.g., latent function of a promiscuous enzyme, can proceed while the "old," phenotypically dominant function is maintained along a series of seemingly neutral mutations (see accompanying article). Thus pleiotropy may facilitate adaptation of latent traits before gene duplications and increase the effective adaptability of proteins.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.