Measuring the signs of the methyl 1H chemical shift differences between major and ‘invisible’ minor protein conformational states using methyl 1H multi-quantum spectroscopy
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Biomolecular NMR"
DOI: 10.1007/s10858-018-0171-8
Abstract: Carr–Purcell–Meiboom–Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the μs to millisecond (ms) timescale between a visible major state and ‘invisible’ minor states. The exchange… read more here.
Keywords: state; quantum; protein conformational; invisible minor ... See more keywords
A methyl 1H double quantum CPMG experiment to study protein conformational exchange
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Biomolecular NMR"
DOI: 10.1007/s10858-018-0208-z
Abstract: Protein conformational changes play crucial roles in enabling function. The Carr–Purcell–Meiboom–Gill (CPMG) experiment forms the basis for studying such dynamics when they involve the interconversion between highly populated and sparsely formed states, the latter having… read more here.
Keywords: methyl; quantum; experiment; protein conformational ... See more keywords
Protein conformational dynamics and phenotypic switching.
Sign Up to like & getrecommendations! Published in 2021 at "Biophysical reviews"
DOI: 10.1007/s12551-021-00858-x
Abstract: Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure but exist as conformational ensembles. Because of their structural plasticity, they can interact with multiple partners. The protein interactions between IDPs and their partners… read more here.
Keywords: protein conformational; noise; conformational dynamics; phenotypic switching ... See more keywords
Computation of the Protein Conformational Transition Pathway on Ligand Binding by Linear Response-Driven Molecular Dynamics.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01243
Abstract: While extremely important for relating the protein structure to its biological function, determination of the protein conformational transition pathway upon ligand binding is made difficult due to the transient nature of intermediates, a large and… read more here.
Keywords: ligand binding; ligand; protein; protein conformational ... See more keywords
Resolving Protein Conformational Plasticity and Substrate Binding via Machine Learning.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00932
Abstract: A long-standing target in elucidating the biomolecular recognition process is the identification of binding-competent conformations of the receptor protein. However, protein conformational plasticity and the stochastic nature of the recognition processes often preclude the assignment… read more here.
Keywords: recognition; conformational plasticity; machine learning; protein conformational ... See more keywords
Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Medicinal Chemistry"
DOI: 10.1021/acs.jmedchem.2c00708
Abstract: Protein flexibility is important for ligand binding but often ignored in drug design. Considering proteins as ensembles rather than static snapshots creates opportunities to target dynamic proteins that lack FDA-approved drugs, such as the human… read more here.
Keywords: scale ligand; large scale; ligand; conformational landscape ... See more keywords
Engineering the hCRBPII domain-swapped dimer into a new class of protein switches.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.9b04664
Abstract: Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a… read more here.
Keywords: domain swapped; protein conformational; metal; hcrbpii ... See more keywords
Monitoring protein conformational changes using fluorescent nanoantennas.
Sign Up to like & getrecommendations! Published in 2021 at "Nature methods"
DOI: 10.1038/s41592-021-01355-5
Abstract: Understanding the relationship between protein structural dynamics and function is crucial for both basic research and biotechnology. However, methods for studying the fast dynamics of structural changes are limited. Here, we introduce fluorescent nanoantennas as… read more here.
Keywords: protein conformational; monitoring protein; conformational changes; using fluorescent ... See more keywords
Emerging role of metabolomics in protein conformational disorders
Sign Up to like & getrecommendations! Published in 2021 at "Expert Review of Proteomics"
DOI: 10.1080/14789450.2021.1948330
Abstract: ABSTRACT Introduction: Metabolomics focuses on interactions among different metabolites associated with various cellular functions in cells, tissues, and organs. In recent years, metabolomics has emerged as a powerful tool to identify perturbed metabolites, pathways influenced… read more here.
Keywords: conformational disorders; protein conformational; emerging role; disease ... See more keywords
Impact of protein conformational diversity on AlphaFold predictions
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac202
Abstract: MOTIVATION After the outstanding breakthrough of AlphaFold in predicting protein 3D models, new questions appeared and remain unanswered. The ensemble nature of proteins, for example, challenges the structural prediction methods because the models should represent… read more here.
Keywords: conformational diversity; impact protein; diversity; alphafold predictions ... See more keywords
Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints
Sign Up to like & getrecommendations! Published in 2021 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1009107
Abstract: We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a… read more here.
Keywords: deer; methodology; modeling protein; protein conformational ... See more keywords