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53 results for “protein folding”
Fig. 6 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 6. (A) Three-dimensional (3D) structural model of the ICChI- NAG complex illustrating by Docking. (B) DIMPLOT result revels the interacting amino acid residue during formation of complex.
Fig. 2 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 2. The three dimensional crystal structure of ICChI where outer ball and stick (green-red) are glycan ligands, Alpha helices (red coil); parallel beta sheets (yellow arrow); random coils or loop (green); (A) topview of ICChI structure, (B) side view of ICChI structure.
Fig. 1 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 1. (A) Silver stained 12.5% SDS-PAGE gel of purified ICChI. Lane 1 contains molecular weight markers (Pageruler prestained protein ladder, Fermentas SM0671) and lane 2 represents pure and homogeneous ICChI protein shown by arrow. (B) Crystals of ICChI grown in 4–5 days in a hanging drop at 291 K equilibrated against 750 μl reservoir solution containing 0.005 M Cobalt chloride, 0.005 M Cadmium chloride, 0.005 M Magnesium chloride, 0.005 M Nickel chloride and 11% (w/v) PEG 3350 in 0.1 M HEPES buffer, pH 7.0. The tetragonal bipyramide-shaped crystals had a typical size of 300 × 200 × 200 μm. (C) X-ray diffraction from the crystal of ICChI protein produced interference pattern.
Fig. 5. The electron density and N in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 5. The electron density and N-linked glycosylation sites. (A) Asparagine residue 45. (B) Asparagine residue 172. (C) Asparagine residue 194.
Fig. 4 in TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity
Fig. 4. The catalytic residues of the ICChI structure are: aspartate 125; glutamate 127 and tyrosine 184. The grey mesh is electron density whereas the amino acid residues are green.
Data from: Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours
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ProtASR2: Ancestral Reconstruction of Protein Sequences accounting for Folding Stability
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Energy-dependent protein folding: modeling how a protein folding machine may work
<p>MD trajectories of all-atom MD simulations for peptides P1-P5. </p>
Data from: The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold
Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187–385) determined to 2.0 Å resolution. BR187–385 adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.
A Folding–Docking–Affinity framework for protein–ligand binding affinity prediction
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The ribosome lowers the entropic penalty of protein folding
<p>This dataset contains concatenated MD trajectories for unfolded, isolated FLN5 A3A3 (iso.pdb and iso_traj.xtc) and the unfolded FLN5+31 A3A3 ribosome-nascent chain complex (RNC, nc.pdb and nc_traj.xtc). A representative structure of the ribosome model used in the simulations is also provided (ribosome_sim.pdb). Numpy array files (ending in .npy) contain the weights obtained for every frame in the ensembles after reweighting with PRE-NMR data. Text files including the trajectory frames (1-indexed, frames_nc.ndx and frames_iso.ndx) corresponding to the weights are also included (a few frames were removed because MTSL/spinlabel rotamers could not be accomdated sterically to allow for PRE calculations at protein labelling sites of interest). Both ensembles consist of ~100,000 frames. The FLN5 A3A3 ensemble was generated from ten independent MD trajectories of 2 microseconds, and FLN5+31 A3A3 consists of ten independent simulations lasting 1.5 microseconds (20 and 15 microseconds total, respectively). Independent simulations were initiated from different starting structures. The *.tar files contain initial coordinate files, MD input files and topologies. </p>
294-fold mini all-α protein library encoded by 7,350 amino-acid sequences (project "flood of fold" )
<p>This repository includes 3 compressed archive files for the “flood-of-fold” mini-protein library project. </p> <ol> <li>FloodOfFolds_294_backbone_models.tar.gz includes 294 mini all-α backbone models showing distinct topologies (folds). They are poly-VAL models. </li> <li>FloodOfFolds_7350_designs_MODEL.tar.gz includes 7,350 design protein models in the pdb format for the 294 mini-protein library. 25 amino-acid sequences were designed for each backbone model (25 x 294 = 7,350). </li> <li>FloodOfFolds_7350_designs_FASTA.tar.gz includes 7,350 fasta files derived from the pdb files in FloodOfFolds_7350_designs_MODEL.tar.gz.<br> </li> </ol> <p>See also here for results of folding simulations: https://zenodo.org/record/5526849#.YWRhFBBBw1I</p> <p>Acknowledgement: K.S. and S.M. would like to deeply thank Koga laboratory at Institute for Molecular Science providing computational resources. Most of the computations for model building and folding simulations were performed using the facilities at the Research Center for Computational Science, Okazaki, Japan.</p>
Data from: The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold
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Data from: ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability
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Data from: Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments
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Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris
GEO Series GSE116415. Komagataella pastoris. 60 samples. Type: Expression profiling by high throughput sequencing.
Codon usage influences the local rate of translation elongation to regulate co-translational protein folding
GEO Series GSE71032. Neurospora crassa. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis
GEO Series GSE291748. Escherichia coli. 4 samples. Type: Other.
Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors
GEO Series GSE56840. Mus musculus. 19 samples. Type: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing.
Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [ChIP-seq]
GEO Series GSE56839. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.