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219 results for “protein dynamics”
Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations
<p># *"Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"*</p> <p>The input files and data used for the paper *"Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"* are separated in the different folders depending stage they belong to.</p> <p>## Folders</p> <p> 1. **01_inputs:** The MD trajectory of DhaA used (only protein atoms present)<br> 2. **02_sliced_trajectory:** The CAVER3 results for the sliced trajectory (eight parts)<br> 3. **03_sliced_filtered:** Filtered CAVER3 results and results from the divide-and-conquer approach<br> 4. **04_full_trajectory:** The CAVER3 results for the full trajectory analysis<br> 5. **05_guided_example:** Guided example for the divide-and-conquer approach<br> </p>
Reinforcing Tunnel Network Exploration in Proteins using Gaussian Accelerated Molecular Dynamics (inputs, outputs, analysis)
<ul> <li>00_LinB-Wt.tar.gz - LinB-Wt: contains raw data that are used for analysis, also conatin folder for GaMD testing.</li> </ul> <p> 1. cMD(Classical MD simulation) analysis files :<br> <br> 1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.<br> 2. Inputs and output files of caver calculations. <br> 3. H-bond raw distance files from all simulations named run1-run5. <br> 4. Distance files used to calculate PCA and cluster analysis.<br> 5. Input files and input structure used to run simulations along with output restart files from each stage of production.<br> <br> 2. GaMD(Gaussian Accelerated MD simulation) analysis files : <br> <br> 1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.<br> 2. Inputs and output files of caver calculations. <br> 3. H-bond raw distance files from all simulations named run1-run5. <br> 4. Distance files used to calculate PCA and cluster analysis.<br> 5. Input files and input structure used to run simulations along with output restart files from each stage of production.</p> <p> 3. GaMD-testing :</p> <p> 1. Input file of GaMD used to run testing and output gamd.log files for multiple run of σOP 1.2 - 1.4 and σOD 2.5.</p> <p> 4. Initial 200ns cMD simulation files used for cluster analysis :</p> <p> 1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format<br> 2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.<br> 3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder.</p> <ul> <li>01_LinB-Open.tar.gz - LinB Open mutant: contains raw data that are used for analysis.</li> </ul> <p> 1. cMD(Classical MD simulation) analysis files :<br> <br> 1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.<br> 2. Inputs and output files of caver calculations. <br> 3. H-bond raw distance files from all simulations named run1-run5. <br> 4. Distance files used to calculate PCA and cluster analysis.<br> 5. Input files and input structure used to run simulations along with output restart files from each stage of production.<br> <br> 2. GaMD(Gaussian Accelerated MD simulation) analysis files : <br> <br> 1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.<br> 2. Inputs and output files of caver calculations. <br> 3. H-bond raw distance files from all simulations named run1-run5. <br> 4. Distance files used to calculate PCA and cluster analysis.<br> 5. Input files and input structure used to run simulations along with output restart files from each stage of production.</p> <p> 3. Initial 200ns cMD simulation files used for cluster analysis :</p> <p> 1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format<br> 2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.<br> 3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder.</p> <ul> <li>02_LinB-Closed.tar.gz - LinB Closed mutant: contains raw data that are used for analysis.</li> </ul> <p><br> 1. cMD(Classical MD simulation) analysis files :<br> <br> 1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.<br> 2. Inputs and output files of caver calculations. <br> 3. H-bond raw distance files from all simulations named run1-run5. <br> 4. Distance files used to calculate PCA and cluster analysis.<br> 5. Input files and input structure used to run simulations along with output restart files from each stage of production.<br> <br> 2. GaMD(Gaussian Accelerated MD simulation) analysis files : <br> <br> 1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.<br> 2. Inputs and output files of caver calculations. <br> 3. H-bond raw distance files from all simulations named run1-run5. <br> 4. Distance files used to calculate PCA and cluster analysis.<br> 5. Input files and input structure used to run simulations along with output restart files from each stage of production.</p> <p> 3. Initial 200ns cMD simulation files used for cluster analysis :</p> <p> 1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format<br> 2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.<br> 3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder.</p> <ul> <li>03_TT_analysis.tar.gz - TransportTools: contains config file and all the raw data from all set and subset of reclustered (using in-house python script) caver calculations used for running TT.</li> </ul> <p> 1. Caver input data for comparison between 500ns, 1 us, 2.5 us and 5us between LinB-Wt and it’s mutants.<br> 2. TransportTools log file.<br> 3. Main statistics result of comparative analysis.</p> <ul> <li>04_reweighting.tar.gz: directory contains reweighted .csv files after running in-house reweighting protocol.<br> <br> 1. GaMD log files from each simulation of LinB-Wt and it’s mutants.<br> 2. CSV files from TT result folder.<br> 3. Result *.csv file contained reweighted tunnel properties in folder reweighted_filtered_new.</li> <li>05_caverdock.tar.gz: contains raw data for caverdock calculations uisng 100 best tunnels with four ligands 2-bromoethanol (be), 1,2-dibromoethane (dbe), Bromide ion (br-) and water (h2o).</li> </ul> <p> 1. Top 100 tunnels present in tunnel folder for all three tunnels ST, p1b and p3 with subdirectory containing three variants and four ligand, whichare used for running caverdock.<br> 2. Ligand *.pdbqt file and receptor *.pdbqt are present in each 100 tunnel folder of respective caverdock calculation.<br> 3. Inside each variant and each ligand, there is respective result of migration analysis with energy barrier calculation of respective tunnels *energy_barriers-new.log* and further simplied *.csv files that was used for preparing figure in manuscript.</p> <p> </p>
Initial Structures of PKM1/M2 proteins for AMOEBA Molecular Dynamics studies (xyz Tinker format)
<p>Here are presented our initial structures of PKM1/M2 (solvated and neutralized) for the different states to initiate molecular dynamics in AMOEBA force field.</p> <p>Those are represented in xyz Tinker format and come from their respectives PDB crystal structure after extraction of the unwanted ligands :</p> <p>3SRF for PKM1,</p> <p>1ZJH for monomer PKM2,</p> <p>6B6U for dimer PKM2,</p> <p>3SRH for free-tetramer PKM2,</p> <p>3SRD for tetramer PKM2 bound to FBP,</p> <p>3U2Z for tetramer PKM2 bound to TEPP-46.</p>
AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes
<p>Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2 that combines<span> randomized</span> <span><span> </span>alanine<span> </span>sequence masking<span> </span>with shallow multiple sequence alignment<span> </span>subsampling to expand the conformational diversity of the predicted structural<span> </span>ensembles and<span> </span>capture conformational changes between apo and holo protein forms. Using several well-established datasets of<span> </span>structurally diverse apo-holo protein pairs, the proposed approach </span><span>enables<span> </span>robust predictions of apo and holo structures and conformational ensembles, while also displaying notably similar dynamics distributions. These observations are consistent with<span> </span>the view </span><span> </span>that the intrinsic dynamics of allosteric proteins is defined by the structural topology of the fold and favors conserved conformational motions driven by soft modes among orthologs. We also found<span> </span>a significant <span>correlation </span>between conformational flexibility and <span> </span>AlphaFold2 metric of statistical significance pLDDT for the apo-holo pairs in which ligand binding induced local moderate conformational changes. For apo-holo pairs exhibiting larger structural changes, this relationship<span> </span>becomes nonlinear, reflecting inability of AlphaFold2 confidence metrics to identify high energy functional conformations. Our findings support the notion that AlphaFold2 approaches can yield reasonable accuracy in predicting minor conformational adjustments between apo and holo states, especially for proteins with <span> </span>moderate localized changes upon ligand binding. However, for large, hinge-like domain movements, AF2 tends to predict the most stable domain orientation which is typically the apo form rather than the full range of functional conformations characteristic of the holo ensemble. These results indicate that modeling of multiple functional states of proteins may require more accurate detection of flexible region conformations and cannot solely rely on the pLDDT metric as the major determinant of the prediction accuracy in reproducing functional conformational ensembles.<span> </span></p>
Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Coronavirus Helicases
<p>The files included here are a set of Galaxy workflows, starting structure files (PDB, mol2, and frcmod), and specialized force field files (ZAFF) for the simulation of coronavirus helicases in the apo and drug-bound state. The inhibitor molecules include those from virtual screening (FCID1 and thioguanine), as well as experimentally validated candidates (Lumacaftor and SSYA10-001).</p>
Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases
<p>The files included here are a set of Galaxy workflows and starting structure files (PDB, mol2, and frcmod) for the simulation of flavivirus helicases in the apo and drug-bound state. The inhibitors include the 4th highest ranking compound from a virtual screening of more than 12.7 million drug-like molecules.</p>
Silica in Silico: a Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
<p>The .zip archive contains the trajectories of all the simulations performed and analysed within the manuscript. The water molecules were removed for control systems.</p>
Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Coronavirus Helicases -- Output Files
<p>These are the output files generated using the input files and Galaxy workflows for coronavirus helicase simulations, from: </p> <pre>https://doi.org/10.5281/zenodo.7492987</pre>
Data underlying the article: 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
<p>This repository contains the datasets and results supporting the conclusions of the manuscript "<strong>3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors</strong>". </p> <p>Publicly available data is not included in this repository. The source code to generate the results gathered here can be found on GitHub (https://github.com/CDDLeiden/3ddpd). </p>
Fig. 8. A-D in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 8. A-D − Nomarski (leftmost lane), FITC-immunofluorescence images labeled with anti-α-tubulin monoclonal antibody and their magnified images (middle two lanes), and red fluorescence images (rightmost lane) stained with Acti-stain 555 phalloidin (detection for F-actin) of encysting cells of C. cucullus Nag-1. Each set of photomicrographs arranged in a horizontal row shows an identical cell except for Fig. 8C (FITC image, inset). A − Vegetative cell. B-D − Encysting cells of C. cucullus Nag-1 at 1.5 h (B), 3 h (C) and 3 days (D) after encystment induction. E − Nomarski image (left), red fluorescence images (middle) stained with Acti-stain 555 phalloidin, and a Nomarski image superimposed with a red fluorescence image obtained by Acti-stain 555 phalloidin staining (right) in encysting cells of C. cucullus Nag-1 at 3 h after encystment induction. F − Silver impregnation of a 3-day-aged cyst showing the basal structure of cilia. This photograph was reproduced from our previous work (Watoh et al. 2005, Fig. 9b). ant: anterior end, le: lepidosome, mu: mucus layer, ec/en: ectocyst layer lined with endocyst layer, m: plasma membrane. B − arrowheads: swollen tip of cilia. C − arrowhead: oral apparatus.
Fig. 6 in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 6. Ca2+/overpopulation-stimulated in vivo phosphorylation of p43 (actin, identified by MS) during resting cyst formation of C. cucullus Nag-1, detected by biotinylated Phos-tag/ECL assays (A), and blots stained with CBB after the biotinylated Phos-tag/ECL detection (B). Figures above the photographs indicate time lapse after onset of encystment induction.
Fig. 5 in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 5. Photomicrographs (Nomarski images) (A) and transmission electron micrographs (B) of C. cucullus Nag-1 after onset of encystment induction, showing resorption of cilia. (A) Vegetative cell at 0 h (A-1) and 2.5 h (A-2) after onset of encystment induction. (B) Encysting 3-h-aged cell (B-1) and 4-h-aged cell (B-2). ci: cilia, m: plasma membrane, ec: ectocyst layer, le: lepidosome. (B-2) a different electron micrograph of the same ultrathin section used in a previous paper (Funatani et al. 2010; Fig. 3).
Fig. 3 in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 3. Immunoblotting assay using anti α-tubulin antibody showing total α-tubulin content during resting cyst formation of C. cucullus Nag-1. Figures above the photographs indicate time lapse after on- set of encystment induction.
Fig. 2 in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 2. Changes of the amount of β-tubulin (p56) and its fragments (p37 and p19) contained in water-soluble fraction during resting cyst formation of C. cucullus Nag-1. Figures above the photographs indicate time lapse after onset of encystment induction.
Fig. 1. 2-D in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 1. 2-D PAGE showing an alteration of the water-soluble protein composition at 0 h–4 weeks after the onset of encystment induction of C. cucullus Nag-1. Arrowheads indicate the proteins (p56, p37, p19) whose amount uniquely and markedly changed during resting cyst formation. These proteins were identified as β-tubulin and its fragments by MS analysis (see Table 1).
Fig. 7 in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 7. Effects of 10 µM taxol (A) and 10 µM cytochalasin B (B) on Ca2+/overpopulation-mediated globulation of C. cucullus Nag-1 (A-1, B-1) and ciliary resorption (A-2, B-2). A-1, B-1 − The rate of encysting (rounded) cells was expressed as a percentage of the total number of tested cells (100 randomly selected cells). Open squares (negative control). The cells were suspended in 1 mM Tris-HCl (pH 7.2) solu- tion without inhibitors at low cell density (<2,000 cells/ml). Under this condition, encystment was hardly induced. Closed circles (positive control). The cells were suspended in an encystment-inducing medium [1 mM Tris-HCl (pH 7.2) and 0.1 mM CaCl2] without inhibitors at high cell density (> 30,000 cells/ml) (Ca2+/overpopulation stimulation). In this condition, the encystment was markedly induced. Open circles (experiment). The cells were suspended in an encystment-inducing medium containing taxol (Ta) or cytochalasin B (CB) at high cell density (> 30,000 cells/ml). Points and attached bars correspond to the means of 5 measurements (100 cells per measurement) obtained from different batches and standard errors, respectively. A-2, B-2 − Length of cilia at 2 h after onset of encystment induction in the presence or absence of taxol (Ta) or cytochalasin B (CB). In the negative control [Induced without 'Ta' (0 h) or Induced without 'CB' (0 h)], the cultured cells were collected, then suspended in encystment-inducing medium, and quickly fixed with 3.7% paraformaldehyde. In the positive control [Induced without 'Ta' (2 h) or Induced without 'CB' (2 h)], the cells were suspended for 2 h in an encystment-inducing medium without inhibitors at high cell density (> 30,000 cells/ml), and then fixed with 3.7% paraformaldehyde. In the experimental groups [Induced with 'Ta' (2 h) or Induced with 'CB' (2 h)], the cells were suspended for 2 h in an encystment-inducing medium containing inhibitors at high cell density (> 30,000 cells/ml), and then fixed with 3.7% paraformaldehyde. Columns and attached bars correspond to the means in 26 cells and standard errors, respectively.
Supporting Data for "Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics"
<p>Molecular dynamics topologies (.prmtop), initial coordinates (.inpcrd), and trajectories (.nc) associated with the preprint: https://doi.org/10.1101/2023.07.23.550226. Tarballs are included for each of the six systems, named by the PDB ID for the starting structure and state (ligand/apo). The four replicates of 155ns are included in each tarball in AMBER's netcdf format (.nc). All trajectories have been stripped of solvent and ions and are autoimaged. Input files and an example script for running simulations in AMBER20 are provided (infiles.tar.gz) as well as the topologies and coordinates for the solvated systems (solvated_topologies.tar.gz).</p>
Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly - Molecular Dynamics Simulation Dataset
<p>The molecular dynamics (MD) simulation dataset. The contents:</p> <ul> <li><strong>5ire_BIOMT_expanded.pdb</strong>: The complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE) </li> <li><strong>5ire_Mprotein_BIOMT_expanded.pdb</strong>: The M proteins extracted from the complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE). The biological assembly shows the dimeric organization of M proteins.</li> <li><strong>0chol.zip, 10chol.zip, 20chol.zip, and 30chol.zip</strong> contain simulation input and output files for the simulated membrane compositions: 0:100, 10:90, 20:80, 30:70 (mol%:mol%) Cholesterol:POPC, respectively. <ul> <li>In each zip file, there are 5 directories: <strong>wt, R253L+F257A, R253L+F257S, K275L+Y278A, K275L+Y278S</strong> corresponding to each simulated M protein dimer variant: wild type, CARC 2-A, CARC 2-S, CARC 3-A, and CARC 3-S. In each directory, there are the following files: <ul> <li><strong>toppar</strong>: This directory contains all force field topologies and parameters</li> <li><strong>topol.top</strong>: GROMACS topology (top) file</li> <li><strong>index.ndx</strong>: GROMACS index (ndx) file</li> <li><strong>prod.mdp</strong>: GROMACS MD parameters (mdp) file</li> <li><strong>0, 1, 2, 3, 4, 5, 6, 7, 8, 9</strong>: These directories contain the simulation inputs and outputs for each simulation repeat. In each of these directories, there are the following files: <ul> <li><strong>t0.pdb</strong>: The pdb file of the starting coordinates</li> <li><strong>prod0.tpr</strong>: GROMACS binary run input (tpr) file </li> <li><strong>prod0.edr</strong>: GROMACS energy (edr) file</li> <li><strong>prod0.gro</strong>: GROMACS output coordinates and velocities after 1 microsecond of simulation</li> <li><strong>prod0.cpt</strong>: GROMACS checkpoint file after 1 microsecond of simulation</li> <li><strong>noW.pdb</strong>: The pdb file of the starting coordinates with all water molecules removed</li> <li><strong>noW.xtc</strong>: GROMACS compressed trajectory (xtc) file with all water molecules removed</li> </ul> </li> </ul> </li> </ul> </li> </ul>
Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data (Simulation input files)
<p>Simulation input files for gromacs to reproduce the data from the manuscript "Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data" (submitted to Comm. Chem.)</p>
Data and code for: Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist and stimulatory G protein
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