ArticleProceedings of the National Academy of Sciences of the United States of America2013
The allosteric communication pathways in KIX domain of CBP.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Identification of the first peptide inhibitor of UBE2C enzymatic activity: insights from metadynamics-guided folding and binding studies.Journal of enzyme inhibition and medicinal chemistry · 2026Article
- Recognition of two hydrophobic pockets in the KIX domain of CBP by FOXO4 transactivation domain.Communications biology · 2025Article
- Synthesis, biological evaluation and metadynamics simulations of novelRSC medicinal chemistry · 2024Article
- Molecular View on theJournal of chemical information and modeling · 2023Article
- Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states.PLoS computational biology · 2022Article
- Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery.Journal of the American Chemical Society · 2022Article
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy.Journal of computer-aided molecular design · 2020Article
- Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- SAR by (Protein-Observed)Accounts of chemical research · 2019Review
- Collision-Induced Unfolding Reveals Unique Fingerprints for Remote Protein Interaction Sites in the KIX Regulation Domain.Journal of the American Society for Mass Spectrometry · 2019Article
- Structural basis for cooperative regulation of KIX-mediated transcription pathways by the HTLV-1 HBZ activation domain.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Expanding the Paradigm: Intrinsically Disordered Proteins and Allosteric Regulation.Journal of molecular biology · 2018Review
- Dual Labeling of the CBP/p300 KIX Domain forChembiochem : a European journal of chemical biology · 2018Article
- Prion proteinProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations.Journal of chemical information and modeling · 2017Article
- DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.Nucleic acids research · 2016Article
- Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH.Biophysical journal · 2016Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
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Authors and funding
4 authors.
Funding
Abstract
Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing all-atom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale.
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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.