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Watergate: Visual Exploration of Water Trajectories in Protein Dynamics
[article]
2017
Eurographics Workshop on Visual Computing for Biomedicine
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To ease the exploration of such rich spatio-temporal data, we propose a novel workflow for the analysis and visualization of large sets of water-molecule trajectories. ...
Our solution consists of a set of visualization techniques, which help biochemists to classify, cluster, and filter the trajectories and to explore the properties and behavior of selected subsets in detail ...
Case Study In the second case study we analyzed a molecular dynamics simulation containing the DhaA haloalkane dehalogenase protein interacting with water molecules in the presence of 2,3-dichloropropan ...
doi:10.2312/vcbm.20171235
dblp:conf/vcbm/VadBJVGHMDK17
fatcat:mysp4ckiincqfmm7s643jba7lu
Investigating the Dynamic Aspects of Drug-Protein Recognition through a Combination of MD and NMR Analyses: Implications for the Development of Protein-Protein Interaction Inhibitors
2014
PLoS ONE
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In this paper, we investigate the dynamic aspects of the molecular recognition between a small molecule ligand and a flat, exposed protein surface, representing a typical target in the development of protein-protein ...
We propose this kind of representation and approach as a useful tool in particular for the characterization of systems where the mutual dynamic influence between the interacting partners is expected to ...
In this kind of spectra peak intensities depend on distance between water and protein protons, on protein dynamics, and on the residence time of water on the protein [32] . ...
doi:10.1371/journal.pone.0097153
pmid:24865844
pmcid:PMC4035249
fatcat:mzugrdk6bjbg5pwrjscaqa4en4
Conformational Study on Pheromonotropin neuropeptide using NMR and Molecular Dynamics
2015
Pharmaceutica Analytica Acta
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A combined NMR and Molecular Dynamics (MD) methods were used to fathom the conformational behaviour in water which was used as a solvent. ...
The peptide predominately adopts a β-sheet structure in water. ...
Post processing analysis tools were applied to visualize the trajectories and to quantify the configurations of the system using the Visual Molecular Dynamics (VMD) software and GROMACS package tools. ...
doi:10.4172/2153-2435.1000359
fatcat:worhcauzsrfflkve3tfwpx6lxa
Applications of water molecules for analysis of macromolecule properties
2020
Computational and Structural Biotechnology Journal
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The analysis of water molecules' distribution and trajectories sheds a light on proteins' interactions with small molecules, on the dynamics of tunnels and cavities, on protein composition and also on ...
Finally, the correct placement of water molecules in protein crystal structures can significantly improve the reliability of molecular dynamics simulations. ...
At the same time, Watergate, a software application for statistical overview of the overall solvent flow, water trajectory clustering, and visualisation was developed [113] . ...
doi:10.1016/j.csbj.2020.02.001
pmid:32123557
pmcid:PMC7036622
fatcat:hpqagubnm5czha7gtxiaela5py
Sulfamate proton solvent exchange in heparin oligosaccharides: Evidence for a persistent hydrogen bond in the antithrombin-binding pentasaccharide Arixtra
2012
Glycobiology
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In this work, proton nuclear magnetic resonance (NMR) line-shape analysis is used to explore the solvent exchange properties of the sulfamate NH groups within heparin-related mono-, di-, tetra-and pentasaccharides ...
structure in a way that facilitates binding to antithrombin-III. ...
Acknowledgements The authors are grateful for the assistance of C Roberts with the molecular dynamics simulations. R.P.Y. gratefully acknowledges support through NSF GRFP Award No. DGE-0813967. ...
doi:10.1093/glycob/cws085
pmid:22593556
fatcat:ykenygaqovctbcon53lwrkeikm
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I
2014
Proceedings of the National Academy of Sciences of the United States of America
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In molecular dynamics simulations, we find the resulting structural changes to be metastable and reversible at the protein backbone level. ...
In hybrid quantum mechanics/classical mechanics simulations, we find that the observed water wires support rapid proton transfer from the protein surface to the center of the membrane domain. ...
We thank the high-performance Biowulf cluster (http://biowulf.nih.gov) at the National Institutes of Health for computer time. ...
doi:10.1073/pnas.1319156111
pmid:24778264
pmcid:PMC4024853
fatcat:6364dnxkizfclkyzklvpwklyqe
Probing the pH-dependent structural features of α-KTx12.1, a potassium channel blocker from the scorpionTityus serrulatus
2005
Protein Science
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Moreover, essential dynamics analysis reveals variations in the toxin's coherent motions. ...
To better understand its molecular mechanism of action, we studied ␣-KTx 12.1 using pH as a tool to explore its plasticity and NMR in combination with MD calculations to detect it. ...
The Interfaculty Center for Measurements (CIM) of the University of Parma, Italy; the CeBiME-LNLS, Campinas, Brazil; the Slovenian NMR Center in Ljubljana; and the European Large Scale Facility for Biomolecular ...
doi:10.1110/ps.041131205
pmid:15772309
pmcid:PMC2253457
fatcat:arflqf4iz5bm3potr4v74w4bku
Quercetin Directly Interacts with Vitamin D Receptor (VDR): Structural Implication of VDR Activation by Quercetin
2016
Biomolecules & Therapeutics
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The binding mode of quercetin was investigated by a docking study combined with molecular dynamics (MD) simulation. ...
Quercetin is a widely distributed flavonoid in nature that is known to enhance transactivation of VDR target genes. ...
A 3-9-19 pulse scheme of gradient tailored excitation (WATERGATE) was employed to suppress the residual water. ...
doi:10.4062/biomolther.2015.122
pmid:26902087
pmcid:PMC4774501
fatcat:cx3kmgtw55fojgqxnr4fsvwqza
Tracking the ATP-binding response in adenylate kinase in real time
2021
Science Advances
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We acknowledge the ESRF for provision of synchrotron radiation facilities and access to the ID09 beamline where the TR-XSS measurements were performed. ...
(86)HSQC pulse sequence with a water-suppressing "Watergate" sequence, recording 2048 × 256 points with a sweep width of 11,111 × 2585 Hz in the 1 H and15N dimensions, respectively.Each line was an ...
X-ray free-electron laser (XFEL) technology has enabled visualization of protein quakes in, e.g., photosynthetic reaction center (69) and myoglobin (70, 71) proteins as release of strain along propagation ...
doi:10.1126/sciadv.abi5514
pmid:34788091
pmcid:PMC8597995
fatcat:yklqv6kbhfbvtpo4gu65vuamsa
Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA
2014
Nucleic Acids Research
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Given the ubiquitous participation of the histidine-based imidazole group in protein recognition and catalysis events, single histidine-like modified duplexes were investigated. ...
We here explore the use of a 14mer DNA duplex as a scaffold for the precise and predictable positioning of catalytic functionalities. ...
ACKNOWLEDGEMENT The 700MHz is part of the INMRF jointly operated by UGent, UA and VUB and funded by the Flemish Government via the FFEU-ZWAP initiative. ...
doi:10.1093/nar/gku1306
pmid:25520197
pmcid:PMC4288195
fatcat:ws4mppz7k5drxgux4zw6sbstsa
Structural dynamics of double-stranded DNA with epigenome modification
2020
Nucleic Acids Research
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The structural flexibility of DNA is known to affect the binding of proteins to methylated DNA. ...
Collectively, our findings imply that the epigenetic modulation of cytosine dynamics in dsDNA mediates destabilization of the GC Watson-Crick base pair to allow base-flipping in living cells. ...
Processing of the trajectories was carried out by tools integrated in GROMACS and 3DNA. Distributions were analysed by numpy and scipy using matplotlib for visualization (39) (40) (41) . ...
doi:10.1093/nar/gkaa1210
pmid:33337470
pmcid:PMC7826269
fatcat:qfycpxed3zfw5oxvjb626sxam4
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function
2021
PLoS Computational Biology
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methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding. ...
Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). ...
Fabio of the IRB Barcelona, for her help in the programming and correlation calculations. ...
doi:10.1371/journal.pcbi.1009547
pmid:34748533
pmcid:PMC8601608
fatcat:eq52omdz3nblrm2u6oqldc4wbe
Structure of the His44 → Ala Single Point Mutant of the Distal Finger Motif of HIV-1 Nucleocapsid Protein: A Combined NMR, Molecular Dynamics Simulation, and Fluorescence Study†
2004
Biochemistry
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Modeling of the DNA:NCp7 complex using structures of the variant peptide suggests that the residues forming a hydrophobic cleft in the native protein are improperly oriented for efficient DNA binding by ...
The nucleocapsid protein (NCp7) of human immunodeficiency virus type 1 (HIV-1) contains two highly conserved CCHC zinc fingers that strongly bind Zn 2+ through coordination of one His and three Cys residues ...
ACKNOWLEDGMENT Claude Ling is acknowledged for his technical support and Patrice Petitjean for the synthesis of the mutant protein. ...
doi:10.1021/bi036137u
pmid:15196011
fatcat:3cxwve5i4rfpxeobvvf3cfjpbm
NMR and molecular modeling reveal key structural features of synthetic nodulation factors
2011
Glycobiology
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Conformational studies of natural compounds and synthetic analogs have been performed combining molecular dynamics simulations in explicit water and NMR. ...
Data revealed that the glycosidic head group can adopt only restricted conformations, whereas chemical modifications of the lipid chains, highly flexible in a water environment, influence the global shape ...
Accesses to supercomputing time at CESGA and to the CAI NMR of Universidad Complutense are gratefully acknowledged. ...
doi:10.1093/glycob/cwr014
pmid:21415035
fatcat:qherkwlxcnbirn6byvoacv3bgq
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data
2013
Molecules
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We simulated the association of PW2 with a pre-built DPC micelle and with free-DPC molecules that spontaneously forms micelles in the presence of the peptide along the simulation. ...
Fast micelle dynamics without dissociation of surfactants leads to only superficial binding. ...
[21] simulated the properties of the bacterial outer membrane protein OmpA in the presence of DPC. ...
doi:10.3390/molecules180810056
pmid:23966088
fatcat:c447s4pwybg5vappxxodfeamue
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