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Watergate: Visual Exploration of Water Trajectories in Protein Dynamics [article]

Viktor Vad, Jan Byška, Adam Jurcík, Ivan Viola, Eduard Gröller, Helwig Hauser, Sérgio M. Marques, Jiří Damborský, Barbora Kozlíková
2017 Eurographics Workshop on Visual Computing for Biomedicine  
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

Massimiliano Meli, Katiuscia Pagano, Laura Ragona, Giorgio Colombo, Danilo Roccatano
2014 PLoS ONE  
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

Deep Bhattacharya Nitin Mishra
2015 Pharmaceutica Analytica Acta  
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

Karolina Mitusińska, Agata Raczyńska, Maria Bzówka, Weronika Bagrowska, Artur Góra
2020 Computational and Structural Biotechnology Journal  
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

Derek J Langeslay, Robert P Young, Szabolcs Beni, Consuelo N Beecher, Leonard J Mueller, Cynthia K Larive
2012 Glycobiology  
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

V. R. I. Kaila, M. Wikstrom, G. Hummer
2014 Proceedings of the National Academy of Sciences of the United States of America  
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

Sérgio Oyama, Primož Pristovšek, Lorella Franzoni, Thelma A. Pertinhez, Eugenia Schininá, Christian Lücke, Heinz Rüterjans, Eliane Candiani Arantes, Alberto Spisni
2005 Protein Science  
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

Ki-Young Lee, Hye-Seung Choi, Ho-Sung Choi, Ka Young Chung, Bong-Jin Lee, Han-Joo Maeng, Min-Duk Seo
2016 Biomolecules & Therapeutics  
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

Fredrik Orädd, Harsha Ravishankar, Jack Goodman, Per Rogne, Lars Backman, Annette Duelli, Martin Nors Pedersen, Matteo Levantino, Michael Wulff, Magnus Wolf-Watz, Magnus Andersson
2021 Science Advances  
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

Dieter Buyst, Vicky Gheerardijn, Krisztina Fehér, Bjorn Van Gasse, Jos Van Den Begin, José C. Martins, Annemieke Madder
2014 Nucleic Acids Research  
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

Ayako Furukawa, Erik Walinda, Kyohei Arita, Kenji Sugase
2020 Nucleic Acids Research  
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

Federica Battistini, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, Modesto Orozco, Shi-Jie Chen
2021 PLoS Computational Biology  
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†

Roland H. Stote, Esther Kellenberger, Hervé Muller, Elisa Bombarda, Bernard P. Roques, Bruno Kieffer, Yves Mély
2004 Biochemistry  
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

Maria A Morando, Alessandra Nurisso, Nathalie Grenouillat, Boris Vauzeilles, Jean-Marie Beau, F Javier Cañada, Jesus Jiménez-Barbero, Anne Imberty
2011 Glycobiology  
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

Francisco Gomes-Neto, Ana Valente, Fabio Almeida
2013 Molecules  
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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