ArticleProteins2010
Computational exploration of the network of sequence flow between protein structures.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Fluid protein fold space and its implications.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- A review of visualisations of protein fold networks and their relationship with sequence and function.Biological reviews of the Cambridge Philosophical Society · 2023Review
- Reversible switching between two common protein folds in a designed system using only temperature.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Multistep mutational transformation of a protein fold through structural intermediates.Protein science : a publication of the Protein Society · 2018Article
- Structural metamorphism and polymorphism in proteins on the brink of thermodynamic stability.Protein science : a publication of the Protein Society · 2018Review
- How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis.Biophysical journal · 2017Article
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- The role of negative selection in protein evolution revealed through the energetics of the native state ensemble.Proteins · 2016Article
- Comprehensive analysis of sequences of a protein switch.Protein science : a publication of the Protein Society · 2016Article
- Studying protein fold evolution with hybrids of differently folded homologs.Protein engineering, design & selection : PEDS · 2015Article
- Two is a pair, three is a network.Biophysical journal · 2015Article
- Smooth functional transition along a mutational pathway with an abrupt protein fold switch.Biophysical journal · 2014Article
- A polymetamorphic protein.Protein science : a publication of the Protein Society · 2013Article
- Mutational tipping points for switching protein folds and functions.Structure (London, England : 1993) · 2012Article
- Super folds, networks, and barriers.Proteins · 2012Article
- Proteins that switch folds.Current opinion in structural biology · 2010Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We investigate small sequence adjustments (of one or a few amino acids) that induce large conformational transitions between distinct and stable folds of proteins. Such transitions are intriguing from evolutionary and protein-design perspectives. They make it possible to search for ancient protein structures or to design protein switches that flip between folds and functions. A network of sequence flow between protein folds is computed for representative structures of the Protein Data Bank. The computed network is dense, on an average each structure is connected to tens of other folds. Proteins that attract sequences from a higher than expected number of neighboring folds are more likely to be enzymes and alpha/beta fold. The large number of connections between folds may reflect the need of enzymes to adjust their structures for alternative substrates. The network of the Cro family is discussed, and we speculate that capacity is an important factor (but not the only one) that determines protein evolution. The experimentally observed flip from all alpha to alpha + beta fold is examined by the network tools. A kinetic model for the transition of sequences between the folds (with only protein stability in mind) is proposed. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
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Registered trials
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