Search Results - "Bucher, Denis"

Orientational relaxation of water trapped inside C60 fullerenes by Bucher, Denis

“…Computer simulations are conducted to study the rotational motion of a single water molecule encapsulated inside a C60 fullerene at temperatures below the…”
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Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation by Miao, Yinglong, Sinko, William, Pierce, Levi, Bucher, Denis, Walker, Ross C, McCammon, J. Andrew

“…Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for sampling biomolecular…”
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Dissociation of NaCl in water from ab initio molecular dynamics simulations by Timko, Jeff, Bucher, Denis, Kuyucak, Serdar

“…We perform ab initio molecular dynamics simulations to study the dissociation of NaCl in water. The potential of mean force (PMF) between the two ions is…”
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Membranes serve as allosteric activators of phospholipase A₂, enabling it to extract, bind, and hydrolyze phospholipid substrates by Mouchlis, Varnavas D., Bucher, Denis, McCammon, J. Andrew, Dennis, Edward A.

“…Significance The catalytic mechanisms of interfacial enzymes acting directly on the interfacial surface of the membrane are notoriously difficult to study…”
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Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein by Bucher, Denis, Grant, Barry J, McCammon, J. Andrew

“…A full characterization of the thermodynamic forces underlying ligand-associated conformational changes in proteins is essential for understanding and…”
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Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation by Botte, Mathieu, Ni, Dongchun, Schenck, Stephan, Zimmermann, Iwan, Chami, Mohamed, Bocquet, Nicolas, Egloff, Pascal, Bucher, Denis, Trabuco, Matilde, Cheng, Robert K. Y., Brunner, Janine D., Seeger, Markus A., Stahlberg, Henning, Hennig, Michael

“…Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for…”
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On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations by Bucher, Denis, Pierce, Levi C. T, McCammon, J. Andrew, Markwick, Phineus R. L

“…We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the…”
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Discovery and Optimization of Orally Bioavailable Phthalazone and Cinnolone Carboxylic Acid Derivatives as S1P2 Antagonists against Fibrotic Diseases by Mammoliti, Oscar, Jansen, Koen, El Bkassiny, Sandy, Palisse, Adeline, Triballeau, Nicolas, Bucher, Denis, Allart, Brigitte, Jaunet, Alex, Tricarico, Giovanni, De Wachter, Maxim, Menet, Christel, Blanc, Javier, Letfus, Vatroslav, Rupčić, Renata, Šmehil, Mario, Poljak, Tanja, Coornaert, Beatrice, Sonck, Kathleen, Duys, Inge, Waeckel, Ludovic, Lecru, Lola, Marsais, Florence, Jagerschmidt, Catherine, Auberval, Marielle, Pujuguet, Philippe, Oste, Line, Borgonovi, Monica, Wakselman, Emanuelle, Christophe, Thierry, Houvenaghel, Nicolas, Jans, Mia, Heckmann, Bertrand, Sanière, Laurent, Brys, Reginald

“…Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease. Current treatments only slow down disease progression, making new therapeutic…”
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Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics by Bucher, Denis, Grant, Barry J, Markwick, Phineus R, McCammon, J Andrew

“…Periplasmic binding proteins (PBPs) are a large family of molecular transporters that play a key role in nutrient uptake and chemotaxis in Gram-negative…”
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Importance of water polarization for ion permeation in narrow pores by Bucher, Denis, Kuyucak, Serdar

“…Carbon nano tube and gramicidin A channel used in the simulations. Molecular dynamics (MD) simulations are mostly performed using non-polarizable force fields…”
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Crystal structure of adenosine A2A receptor in complex with clinical candidate Etrumadenant reveals unprecedented antagonist interaction by Claff, Tobias, Schlegel, Jonathan G., Voss, Jan H., Vaaßen, Victoria J., Weiße, Renato H., Cheng, Robert K. Y., Markovic-Mueller, Sandra, Bucher, Denis, Sträter, Norbert, Müller, Christa E.

“…The G s  protein-coupled adenosine A 2A receptor (A 2A AR) represents an emerging drug target for cancer immunotherapy. The clinical candidate Etrumadenant was…”
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Ab Initio Study of Water Polarization in the Hydration Shell of Aqueous Hydroxide: Comparison between Polarizable and Nonpolarizable Water Models by Bucher, Denis, Gray-Weale, Angus, Kuyucak, Serdar

“…Ab initio simulations of aqueous hydroxide are performed to study the structure and polarization of water molecules in the first solvation shell. Polarization…”
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Fluoroketone Inhibition of Ca2+-Independent Phospholipase A2 through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics by Hsu, Yuan-Hao, Bucher, Denis, Cao, Jian, Li, Sheng, Yang, Sheng-Wei, Kokotos, George, Woods, Virgil L, McCammon, J. Andrew, Dennis, Edward A

“…The mechanism of inhibition of group VIA Ca2+-independent phospholipase A2 (iPLA2) by fluoroketone (FK) ligands is examined by a combination of deuterium…”
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Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations by Bucher, Denis, Hsu, Yuan-Hao, Mouchlis, Varnavas D, Dennis, Edward A, McCammon, J Andrew

“…Group VI Ca²⁺-independent phospholipase A₂ (iPLA₂) is a water-soluble enzyme that is active when associated with phospholipid membranes. Despite its clear…”
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Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods by Bucher, Denis, Stouten, Pieter, Triballeau, Nicolas

“…Water molecules play an important role in the association of drugs with their pharmaceutical targets. For this reason, calculating the energetic contribution…”
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Polarization of Water in the First Hydration Shell of K+ and Ca2+ Ions by Bucher, Denis, Kuyucak, Serdar

“…Accurate representation of the interactions of water molecules with charges is essential for correct description of biomolecules and their interactions and,…”
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Mechanistic Implications of Reductive Co–C Bond Cleavage in B12-Dependent Methylmalonyl CoA Mutase by Kumar, Neeraj, Bucher, Denis, Kozlowski, Pawel M

“…Vitamin B12-dependent enzymes catalyze several difficult radical reactions. There are fundamental open questions that need to be addressed to fully understand…”
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Mechanistic Implications of Reductive Co-C Bond Cleavage in B 12 -Dependent Methylmalonyl CoA Mutase by Kumar, Neeraj, Bucher, Denis, Kozlowski, Pawel M

“…Vitamin B -dependent enzymes catalyze several difficult radical reactions. There are fundamental open questions that need to be addressed to fully understand…”
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Molecular simulations of ion channels: a quantum chemist's perspective by Bucher, Denis, Rothlisberger, Ursula

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Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics by Bucher, Denis, Guidoni, Leonardo, Carloni, Paolo, Rothlisberger, Ursula

“…Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K+ and Na+ ions in the…”
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