Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
By Wenjun Zheng, Bernard R. Brooks, D. Thirumalai. 2006
249 citations recorded by the source corpus.
Subfields: Molecular Biology
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In Molecular Biology
- Eran Eyal
- Lee-Wei Yang
- Matthieu Wyart
- Carolina Brito
- Riccardo Ravasio
- Barbara Bravi
- Holger Flechsig
- Zhenxing Liu
Citations in the corpus
- Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein (2013, background): “The robustness of the low frequency cooperative modes should depend on their nearly invariant nature, placing their foundations on the core network of residues responsible for transmitting signals as suggested by [52].”
- Terahertz Dielectric Sensitivity to Biomolecular Structure and Function (2008, background): “913424 the first few normal vibrational modes of the structure [14].”
- Direct coupling analysis of epistasis in allosteric materials (2018, background): “On a larger length scale, these regions must assemble to create an extended soft elastic mode [27,38,39], fraction of these pairs - averaged over 100 configurations randomly chosen - belongs to the 400 largest couplings, as a function of the number of pairs with maximal epistasis considered.”
- On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model (2009, methodology): “5,12,27 To implement the SPM for the PDZ domain, we represent the native state using the C a -side chain elastic network model (ENM) in which each amino acid (except Gly) is represented using the coordinates of C a atoms and the center of mass of the side chain atoms.”
- Global dynamics of proteins: bridging between structure and function. (2010, background): “(82) demonstrated that not only are ligand-induced conformational changes dominated by few”
- Design of Elastic Networks with Evolutionary Optimized Long-Range Communication as Mechanical Models of Allosteric Proteins (2017, background): “[21] Zheng W, Brooks BR, Thirumalai D (2006) Lowfrequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.”