The allosteric communication pathways in KIX domain of CBP
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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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Metadynamics methods have been successfully applied to study free energy landscapes of flexible proteins, protein oligomers, peptide folding, ligand and selective ion permeation through membrane channels.
“These methods alone, or in combination with high-resolution experimental techniques such as x-ray crystallography and NMR, have been successfully applied to the study of the free energy landscape of flexible proteins and protein oligomers,36,388–389 peptide folding,390–392 ligand and selective ion permeation through cell membrane protein channels.393”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [36]
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- Authors
- Palazzesi, F., Barducci, A., Tollinger, M., & Parrinello, M.
- Affiliations
- ETH Zurich (CH)
- Universität Innsbruck (AT)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-08-12
- Volume
- 110
- Issue
- 35
- Pages
- 14237-14242
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3761601
- OpenAlex
- W2031593809
- Cited by
- 62
- References
- 67
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 1 · 2023: 1 · 2022: 3 · 2021: 1 · 2020: 6 · 2019: 2 · 2018: 5 · 2017: 8 · 2016: 13 · 2015: 3 · 2014: 13 · 2013: 1
- FWCI
- 4.48
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- allosteric communication, KIX domain, CREB-binding protein, MLL, protein-protein interaction, protein dynamics, allosteric regulation, enhanced sampling
- MeSH terms
- Allosteric Regulation, Models, Molecular, Phosphorylation, CREB-Binding Protein, Myeloid-Lymphoid Leukemia Protein, Molecular Dynamics Simulation
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