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opencc-by-4.0May 2016View details →

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in water. Number of DMPC: 32. Number of DMTAP: 96. Number of Cl--ions: 96. Number of waters: 5496. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 109 ns. Previously equilibrated for: 31 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0Feb 2017View details →

Simulation snapshots of complex I molecular dynamics simulation

These are snapshots from the molecular dynamics simulations of complex I (setups I and II). These can be loaded in the VMD software for visualization, and 'segname' keyword can be used to distinguish the different parts of the protein.

opencc-by-4.0Apr 2017View details →

Data Release: A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

The archive contains the supporting data for the results described in the paper titled "A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms". For more information see either the individual README files or consult the project git repository: https://bitbucket.org/wrs20/ppmd Copyright W.R.Saunders 2017

opencc-zeroOct 2023View details →

Molecular Dynamics Simulations and associated data for: Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases

Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The Doublecortin Like Kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory 'tail' segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to 'supercharge' the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other Calcium Calmodulin Kinases (CAMKs), and a 'Swiss-army' assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for auto-regulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor-binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome–wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically-divergent DCLK1 modulators, stabilizers or degraders.

opencc-by-4.0Nov 2023View details →

Rate-enhancing PETase mutations determined through DFT/MM molecular dynamics simulations†

Raw data for classical MD simulations ran with Gromacs 2018.3 for the two mutants Asp83Asn and Asp89Asn.Raw data for quantum mechanics/molecular mechanics simulations ran with CP2K 6.1 for the two mutants Asp83Asn and Asp89Asn.Distance and free energy analysis from the QM/MM MD simulations  for the wild-type and the two mutants Asp83Asn and Asp89Asn.

opencc-by-4.0Aug 2023View details →

Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023

Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology,  2023

opencc-by-4.0Jul 2023View details →

The steered discrete molecular dynamics simulation data of amyloids with EC1 and EC12 cadherin dimer

The steered discrete molecular dynamics (sDMD) simulation parameters are provided. Binding frequency of amyloids with EC1 and EC1-2 cadherin dimer. Trajectories of sDMD simulations of EC1 cadherin dimer with Abeta species.

opencc-by-4.0Nov 2023View details →

Simulations for "Molecular Dynamics-Based Identification of Binding Pathways and Two Distinct High-Affinity Sites for Succinate in the Succinate Receptor 1 SUCNR1/GPR91"

Open the record for dataset details and reuse information.

opencc-zeroNov 2023View details →

Data from: programming co-assembled peptide nanofiber morphology via anionic amino acid type: insights from molecular dynamics simulations

Co-assembling peptides can be crafted into supramolecular biomaterials for use in biotechnological applications, such as cell culture scaffolds, drug delivery, biosensors, and tissue engineering. Peptide co-assembly refers to the spontaneous organization of two different peptides into a supramolecular architecture. Here we use molecular dynamics simulations to quantify the effect of anionic amino acid type on co-assembly dynamics and nanofiber structure in binary CATCH(+/-) peptide systems. CATCH peptide sequences follow a general pattern: CQCFCFCFCQC, where all C's are either a positively charged or a negatively charged amino acid. Specifically, we investigate the effect of substituting aspartic acid residues for the glutamic acid residues in the established CATCH(6E-) molecule, while keeping CATCH(6K+) unchanged. Our results show that structures consisting of CATCH(6K+) and CATCH(6D-) form flatter β-sheets, have stronger interactions between charged residues on opposing β-sheet faces, and have slower co-assembly kinetics than structures consisting of CATCH(6K+) and CATCH(6E-). Knowledge of the effect of sidechain type on assembly dynamics and fibrillar structure can help guide the development of advanced biomaterials and grant insight into sequence-to-structure relationships.

Molecular dynamics results of the complex 3CLpro allosteric groove with compound 5

Molecular dynamics results of the complex 3CLpro allosteric groove with compound 5. The protein structure is shown in gray and the compound 5 is shown in magenta.

Photoactivation of the Orange Carotenoid Protein Requires Two Light-Driven Reactions Mediated by a Metastable Monomeric Intermediate – Absorption Spectra and Global Analysis Results, Molecular Dynamics Simulations

Time-resolved absorption and molecular dynamics trajectory datasets associated with: Rose, J. B.; Gascón, J. A.; Sutter, M.; Sheppard, D. I.; Kerfeld, C. A.; Beck, W. F. Photoactivation of the Orange Carotenoid Protein Requires Two Light-Driven Reactions Mediated by a Metastable Monomeric Intermediate. Phys. Chem. Chem. Phys. 2023, DOI: 10.1039/d3cp04484j.

Molecular dynamics simulation of CFTR with inhibitor CFTRinh-172

Molecular dynamics simulation trajectory, parameter files for the systems of human CFTR protein with inhibitor CFTRinh-172. CFTRinh-172 was tested with two different poses.

opencc-zeroJan 2024View details →

Molecular dynamics dataset for pharmacological repositioning in the treatment of non-small-cell lung cancer

Non-small cell lung cancer (NSCLC) is a type of lung cancer associated with translocation of the EML4 and ALK genes on the short arm of chromosome 2. This leads to the development of an aberrant protein kinase with a deregulated catalytic domain, the cdALK+. Currently, different ALK inhibitors (iALKs) have been proposed to treat ALK+ NSCLC patients. However, the recent resistance to iALKs stimulates the exploration of new iALKs for NSCLC. Here, we describe an in silico approach to finding FDA-approved drugs that can be used by pharmacological repositioning as iALK. We used homology modelling to obtain a structural model of cdALK+ protein and then performed molecular docking and molecular dynamics of the complex cdALK+-iALKs to generate the pharmacophore model. The pharmacophore was used to identify potential iALKs from FDA-approved drugs library by ligand-based virtual screening. Four pharmacophores with different atomistic characteristics were generated, resulting in six drugs that satisfied the proposed atomistic positions and coupled at the ATP-binding site. Mitoxantrone, riboflavin and abacavir exhibit the best interaction energies with 228.29, 165.40 and 133.48 kjoul/mol respectively. In addition, the special literature proposed these drugs for other types of diseases due to pharmacological repositioning. This study proposes FDA-approved drugs with ALK inhibitory characteristics. Moreover, we identified pharmacophores sites that can be tested with other pharmacological libraries.

opencc-zeroFeb 2024View details →

Synthetic eco-evolutionary dynamics in simple molecular environment

The understanding of eco-evolutionary dynamics, and in particular the mechanism of emergence of species, is still fragmentary and in need of test bench model systems. To this aim, we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 10^15 single-strand DNA oligonucleotide 'individuals'. We begin with a seed of random sequences which we select via affinity capture from ∼ 10^12 DNA oligomers of fixed sequence ('resources') over which they compete. At each cycle ('generation'), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences ('species') drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource binding dominates the selection in the first generations, while inter and intra-individual interactions becomes important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.

opencc-by-4.0Feb 2024View details →

All-atom molecular dynamics simulations of incomplete ATP synthase rotor rings with unusually high stoichiometry predicted by the AlphaFold2-based method

The trajectories of all-atom MD simulations of AlphaFold2 4, 11, 16 or 18-mer structures of the subunit c from Candidatus Kryptonium thompsoni (CKt_Nmer_lipid_mix_CHM36m_303K_500ns) and Thalassoglobus polymorphus (Tp_Nmer_lipid_mix_CHM36m_303K_500ns), and AlphaFold2 11-mer structure of the subunit c from Spinacia oleracea (So_11mer-c20_POPC_CHM36m_303K_300ns) in a lipid bilayer. Simulations have been performed using the CHARMM36m force field, running with the GROMACS 2022 package.

opencc-by-4.0Mar 2024View details →

Molecular dynamic simulations of histamine-bound H4R

MD simulations data for Histamine-bound H4R

opencc-by-4.0Mar 2024View details →

Molecular Dynamics Trajectories for the D3 receptor (D3R) complexes bound with a GαOβγ heterotrimer and 1) FOB02-04A bitopic agonist; 2) pramipexole.

Molecular Dynamics Data for publication "Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket". Sandra Arroyo-Urea, Antonina L. Nazarova, Ángela Carrión-Antolí et al., Nat. Comm., revision (2024). https://doi.org/10.21203/rs.3.rs-3433207/v1 This directory includes the PDB (Protein Data Bank) format file detailing the topology and the XTC (eXtended Trajectory) format file outlining the trajectories for two distinct complexes: 1) the FOB02-04A-bound structure of D3 receptor (D3R) complexes in association with a GαOβγ heterotrimer, and 2) the pramipexole-bound structures of D3R complexes also coupled to a GαOβγ heterotrimer. The data is organized in a strided trajectory with a timestep of 0.5 nanoseconds per frame. To reapply periodic boundary conditions, users can employ the standard periodic boundary condition commands available in Visual Molecular Dynamics (VMD) package.   The MD trajectory data for this study was acquired as well as uploaded by Antonina L. Nazarova.

Molecular dynamics simulation of MFSD1 in apo, His-Ala, Lys-Ala and Leu-Ala bound

The MFSD1 structures were placed in a heterogenous bilayer composed of POPE (20%), 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC, 30%), Cholesterol (30%), and N-Palmitoyl-sphingomyelin (SPM, 20%) using CHARMM-GUI scripts and all simulations were performed using GROMACS 2021.3.  Substrates were fitted into the binding site based on non-protein density observed in the outward-open Cryo-EM structure of GLMP-MFSD1+HisAla.  Here, inital structures and 500 ns simulations for each replicate (Rep1-3) with the respective ligands and its starting conformation (Conf1 or Conf2) are given in PDB-format.  The following ligands were used for the molecular dynamics simulations: <ul> <li>LA - Leucyl-alanine dipeptide: both termini are charged</li> <li>KA - Lysyl-alanine dipeptide: both termini are charged, side chain of lysine is positively charged</li> <li>H0A - Histidyl-alanine dipeptide: both termini are charged, side chain of histidine is neutral</li> <li>HA - Histidyl-alanine dipeptide: both termini are charged, side chain of histidine is positively charged</li> </ul>

opencc-zeroApr 2024View details →

03_HTMD_Bulk: Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites

# Contains input, output and restart files used for HTMD (High-throughput molecular dynamics) adaptive sampling simulations at 310K for Bulk schemes.  # The forders are organized as: Input_files/ # Contains .parm7 and .rst files of 30 seed conformations obtained from equilibrations and used for adaptive sampling inputs, **run_adaptiveMD.py** : Script file executing the adaptive sampling using distance matrix considering protein C-alpha atoms and heavy atoms of DBE. rep1/ └── adaptive_data/     ├── generators/ # Contains the initial generator files provided by the user     │   ├── ../structure.parm7     │   ├── ../input.ncrst     │   └── ...     ├── input/ # Contains the files needed to start all simulations of all epochs (automatically generated)     │   ├── ../equil1.log     │   ├── ../input.ncrst     │   └── ... └──rep2/ ... ...