ArticleMethods in molecular biology (Clifton, N.J.)2012
Combining NMR and molecular dynamics studies for insights into the allostery of small GTPase-protein interactions.
Article in Methods in molecular biology (Clifton, N.J.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 34 citations in OpenAlex.
- Systematic QM/MM Study for PredictingJournal of chemical theory and computation · 2024Article
- The "violin model": Looking at community networks for dynamic allostery.The Journal of chemical physics · 2023Review
- Protective effects of a small molecule inhibitor ligand against hyperphosphorylated tau-induced mitochondrial and synaptic toxicities in Alzheimer disease.Human molecular genetics · 2021Article
- Protein Dynamics Influence the Enzymatic Activity of Phospholipase A/Acyltransferases 3 and 4.Biochemistry · 2021Article
- Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS).Biomolecules · 2021Review
- Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.PLoS computational biology · 2020Article
- NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes.Biophysical reviews · 2020Review
- Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.Journal of chemical theory and computation · 2017Article
- Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1.The journal of physical chemistry. B · 2017Article
- Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions.Scientific reports · 2016Article
- Solution NMR Spectroscopy for the Study of Enzyme Allostery.Chemical reviews · 2016Review
- What Mutagenesis Can and Cannot Reveal About Allostery.Biophysical journal · 2016Review
- Structure and dynamics analysis on plexin-B1 Rho GTPase binding domain as a monomer and dimer.The journal of physical chemistry. B · 2014Article
- Identification of regions of rabbit muscle pyruvate kinase important for allosteric regulation by phenylalanine, detected by H/D exchange mass spectrometry.Biochemistry · 2013Article
- Analysis of 15N-1H NMR relaxation in proteins by a combined experimental and molecular dynamics simulation approach: picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the dimeric state indicates allosteric pathways.The journal of physical chemistry. B · 2013Article
- Plexin structures are coming: opportunities for multilevel investigations of semaphorin guidance receptors, their cell signaling mechanisms, and functions.Cellular and molecular life sciences : CMLS · 2012Review
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
Combinations of experimentally derived data from nuclear magnetic resonance spectroscopy and analyses of molecular dynamics trajectories increasingly allow us to obtain a detailed description of the molecular mechanisms by which proteins function in signal transduction. This chapter provides an introduction into these two methodologies, illustrated by example of a small GTPase-effector interaction. It is increasingly becoming clear that new insights are provided by the combination of experimental and computational methods. Understanding the structural and protein dynamical contributions to allostery will be useful for the engineering of new binding interfaces and protein functions, as well as for the design/in silico screening of chemical agents that can manipulate the function of small GTPase-protein interactions in diseases such as cancer.
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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.