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9 results for “Conformational Heterogeneity”
Ligand binding remodels protein side chain conformational heterogeneity
<p>While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decrease and relative hydrophobicity increases. Across a series of 13 inhibitor bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from NMR studies suggesting that residual side chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.</p>
Statistical analyses of the impact of X-ray damage effects on conformational heterogeneity in room temperature (277 K) and cryo-cooled (100 K) protein crystals
<p>These data are published in support of the manuscript "Evaluating the impact of X-ray damage on conformational heterogeneity in room temperature and cryo-cooled protein crystals" submitted to Acta Crystallographica section D, authors:</p> <p>Filip Yabukarski<sup>1,</sup><sup>#,</sup>*, Tzanko Doukov<sup>5</sup>, Daniel A Mokhtari<sup>1</sup>, Siyuan Du<sup>1</sup>, Daniel Herschlag<sup>1,2,3,4</sup><sup>,</sup>*</p> <p><sup>1</sup>Department of Biochemistry, <sup>2</sup>Department of Chemistry, <sup>3</sup>Department of Chemical Engineering, <sup>4</sup>Stanford ChEM-H, Stanford University, Stanford, California 94305, United States, <sup>5</sup>Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States.</p> <p># Current address: Bristol Myers Squibb, San Diego, California 92121, United States.</p> <p>* Correspondence: fyabukar@stanford.edu, herschla@stanford.edu</p>
qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps
<p>Benchmark dataset and prospective cases tested for the development of <em>qFit-ligand</em>. Files included: refined single conformer models, un-refined qFit-ligand multiconformer models, and refined qFit-ligand multiconformer models. </p>
Ligand binding remodels protein side chain conformational heterogeneity
<p>While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decrease and relative hydrophobicity increases. Across a series of 13 inhibitor bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from NMR studies suggesting that residual side chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.</p>
Data From: Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
<p>This dataset contains MD simulation results for CCR5 receptor in different states. There are three states this GPCR could be in: 1.apo state, i.e. not bound to any other protein or ligand 2.holo state, i.e. bound by maraviroc (MRV) 3.GP120 bound state, i.e. bounded to HIV envelope protein GP120 and human receptor CD4. </p> <p>For apo state simulations, three different starting structure were used and the simulation results for them are given in three different folders named after the PDB ID of initial structures. </p> <p>One critical residue of CCR5 receptor, GLU283, was considered in two different protonation state, hence there are two folders for each studied system, GLU283 and GLH283 for differently protonated systems. </p> <p>The MD trajectories of studied systems are in dcd format and due to size issues waters, ions and membrane atoms were removed. </p> <p>For each system, three replica MD simulations were performed, hence, there are three folders with names REPLICA1, REPLICA2, REPLICA3.</p> <p> </p>
Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes
GEO Series GSE208602. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing; Other.
Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes [Hi-C]
GEO Series GSE208600. Mus musculus. 16 samples. Type: Other.
Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes [RNA-seq]
GEO Series GSE208601. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion
GEO Series GSE243328. Homo sapiens. 36 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.