Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ).
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7759-8_31
Abstract: Heterogeneous and dynamic biomolecular complexes play a central role in many cellular processes but are poorly understood due to experimental challenges in characterizing their structural ensembles. To address these difficulties, we developed a hybrid methodology… read more here.
Keywords: conformational ensembles; selecting conformational; anomalous density; electron anomalous ... See more keywords
Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala.
Sign Up to like & getrecommendations! Published in 2018 at "Biophysical journal"
DOI: 10.1016/j.bpj.2018.05.003
Abstract: Characterizing ensembles of intrinsically disordered proteins is experimentally challenging because of the ill-conditioned nature of ensemble determination with limited data and the intrinsic fast dynamics of the conformational ensemble. Amide I two-dimensional infrared (2D IR)… read more here.
Keywords: ala ala; ala; ensemble refinement; conformational ensembles ... See more keywords
Conformational Ensembles of Antibodies Determine Their Hydrophobicity.
Sign Up to like & getrecommendations! Published in 2020 at "Biophysical journal"
DOI: 10.1016/j.bpj.2020.11.010
Abstract: A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation is exposure of hydrophobic surface regions to the solvent. Many current techniques predict the relative aggregation… read more here.
Keywords: hydrophobicity conformational; antibodies determine; determine hydrophobicity; ensembles antibodies ... See more keywords
Resolution of Maximum Entropy Method-Derived Posterior Conformational Ensembles of a Flexible System Probed by FRET and Molecular Dynamics Simulations.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c01090
Abstract: Maximum entropy methods (MEMs) determine posterior distributions by combining experimental data with prior information. MEMs are frequently used to reconstruct conformational ensembles of molecular systems for experimental information and initial molecular ensembles. We performed time-resolved… read more here.
Keywords: dynamics simulations; flexible system; conformational ensembles; molecular dynamics ... See more keywords
Visualizing Conformational Ensembles of the Nucleosome by NMR.
Sign Up to like & getrecommendations! Published in 2022 at "ACS chemical biology"
DOI: 10.1021/acschembio.1c00954
Abstract: The formation of chromatin not only compacts the eukaryotic genome into the nucleus but also provides a mechanism for the regulation of all DNA templated processes. Spatial and temporal modulation of the chromatin structure is… read more here.
Keywords: conformational ensembles; spectroscopy; nucleosome nmr; ensembles nucleosome ... See more keywords
Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase
Sign Up to like & getrecommendations! Published in 2018 at "Scientific Reports"
DOI: 10.1038/s41598-018-20012-0
Abstract: Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational… read more here.
Keywords: characterization conformational; gas phase; ensembles protonated; conformational ensembles ... See more keywords
Predicting loop conformational ensembles
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx718
Abstract: Motivation: Protein function is often facilitated by the existence of multiple stable conformations. Structure prediction algorithms need to be able to model these different conformations accurately and produce an ensemble of structures that represent a… read more here.
Keywords: predicting loop; prediction; loop conformational; conformational ensembles ... See more keywords
How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case
Sign Up to like & getrecommendations! Published in 2021 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2021.694130
Abstract: The reliability and usefulness of molecular dynamics simulations of equilibrium processes rests on their statistical precision and their capability to generate conformational ensembles in agreement with available experimental knowledge. Metadynamics Metainference (M&M), coupling molecular dynamics… read more here.
Keywords: ensembles metadynamics; conformational ensembles; metadynamics metainference; determine accurate ... See more keywords
Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.910956
Abstract: Intrinsically disordered proteins play key roles in regulatory protein interactions, but their detailed structural characterization remains challenging. Here we calculate and compare conformational ensembles for the disordered protein Sic1 from yeast, starting from initial ensembles… read more here.
Keywords: integrative conformational; optimization methods; conformational ensembles; ensembles sic1 ... See more keywords