ArticleACS chemical biology2010
Why does binding of proteins to DNA or proteins to proteins not necessarily spell function?
Article in ACS chemical biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.Scientific reports · 2017Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Multiple conformational selection and induced fit events take place in allosteric propagation.Biophysical chemistry · 2014Review
- Dipeptide analysis of p53 mutations and evolution of p53 family proteins.Biochimica et biophysica acta · 2014Article
- A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL.Nucleic acids research · 2014Article
- Dynamic conformational switching in the chemokine ligand is essential for G-protein-coupled receptor activation.The Biochemical journal · 2013Article
- The spatial structure of cell signaling systems.Physical biology · 2013Article
- Structured crowding and its effects on enzyme catalysis.Topics in current chemistry · 2013Review
- The underappreciated role of allostery in the cellular network.Annual review of biophysics · 2013Review
- Selective molecular recognition in amyloid growth and transmission and cross-species barriers.Journal of molecular biology · 2012Review
- Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.Cell reports · 2012Article
- Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles.European biophysics journal : EBJ · 2011Review
- Gene-specific transcription activation via long-range allosteric shape-shifting.The Biochemical journal · 2011Review
- The role of response elements organization in transcription factor selectivity: the IFN-β enhanceosome example.PLoS computational biology · 2011Article
- Allostery and population shift in drug discovery.Current opinion in pharmacology · 2010Review
- Enzyme dynamics point to stepwise conformational selection in catalysis.Current opinion in chemical biology · 2010Review
- Lysine120 interactions with p53 response elements can allosterically direct p53 organization.PLoS computational biology · 2010Article
- Dynamic multiprotein assemblies shape the spatial structure of cell signaling.Progress in biophysics and molecular biologyReview
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Studies of binding are often question: first, is the observed binding functional, and second, if it is, which function? Is it activation or repression? The first question relates to binding at different sites; the second relates to binding at similar sites. These questions apply to transcription factors binding to genomic DNA and to protein interaction domains binding to their partners. Here, we explain that both can be understood in terms of allostery and the cellular (or in vitro) environment. The idea is simple yet powerful; it emphasizes the role of allostery in defining whether binding between transcription factors and (cognate or noncognate) DNA sequences will lead to function and to the type of function. Allosteric effects are the outcome of dynamically shifting populations; thus binding to even slightly different DNA sequences will lead to different transcription factor conformations that can be reflected in the binding sites to their co-regulators. Currently, allostery is not considered when trying to understand how binding phenomena determine the functional outcome. Allosteric effects can enhance the binding specificity in a function-oriented manner. Here we provide a biological rationale that considers cellular crowding effects.
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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.