Search Results - "Henchman, Richard H"

How Do Electrostatic Perturbations of the Protein Affect the Bifurcation Pathways of Substrate Hydroxylation versus Desaturation in the Nonheme Iron-Dependent Viomycin Biosynthesis Enzyme? by Ali, Hafiz Saqib, Henchman, Richard H, Warwicker, Jim, de Visser, Sam P

“…The viomycin biosynthesis enzyme VioC is a nonheme iron and α-ketoglutarate-dependent dioxygenase involved in the selective hydroxylation of l-arginine at the…”
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Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity by Huggins, David J., Biggin, Philip C., Dämgen, Marc A., Essex, Jonathan W., Harris, Sarah A., Henchman, Richard H., Khalid, Syma, Kuzmanic, Antonija, Laughton, Charles A., Michel, Julien, Mulholland, Adrian J., Rosta, Edina, Sansom, Mark S. P., van der Kamp, Marc W.

“…Biomolecular simulation is increasingly central to understanding and designing biological molecules and their interactions. Detailed, physics‐based simulation…”
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Mechanism of Oxidative Ring‐Closure as Part of the Hygromycin Biosynthesis Step by a Nonheme Iron Dioxygenase by Ali, Hafiz Saqib, Henchman, Richard H., Visser, Sam P.

“…Nonheme iron dioxygenases catalyze vital reactions for biosystems including the biosynthesis of antibiotics. One such enzyme, namely the hygromycin…”
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Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution by Irudayam, Sheeba Jem, Henchman, Richard H

“…Two theoretical formulations are proposed and compared for the loss of translational and rotational entropy upon protein−ligand binding in water. The two…”
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Entropy of Simulated Liquids Using Multiscale Cell Correlation by Ali, Hafiz Saqib, Higham, Jonathan, Henchman, Richard H

“…Accurately calculating the entropy of liquids is an important goal, given that many processes take place in the liquid phase. Of almost equal importance is…”
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Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy by Swanson, Jessica M.J., Henchman, Richard H., McCammon, J. Andrew

“…The prediction of absolute ligand-receptor binding affinities is essential in a wide range of biophysical queries, from the study of protein-protein…”
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Thermodynamic Origin of Differential Excipient-Lysozyme Interactions by Kalayan, Jas, Curtis, Robin A., Warwicker, Jim, Henchman, Richard H.

“…Understanding the intricate interplay of interactions between proteins, excipients, ions and water is important to achieve the effective purification and…”
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Entropy of Proteins Using Multiscale Cell Correlation by Chakravorty, Arghya, Higham, Jonathan, Henchman, Richard H

“…A new multiscale method is presented to calculate the entropy of proteins from molecular dynamics simulations. Termed Multiscale Cell Correlation (MCC), the…”
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Protons and Hydroxide Ions in Aqueous Systems by Agmon, Noam, Bakker, Huib J, Campen, R. Kramer, Henchman, Richard H, Pohl, Peter, Roke, Sylvie, Thämer, Martin, Hassanali, Ali

“…Understanding the structure and dynamics of water’s constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies…”
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Agonist-mediated Conformational Changes in Acetylcholine-binding Protein Revealed by Simulation and Intrinsic Tryptophan Fluorescence by Gao, Fan, Bren, Nina, Burghardt, Thomas P, Hansen, Scott, Henchman, Richard H, Taylor, Palmer, McCammon, J Andrew, Sine, Steven M

“…We delineated acetylcholine (ACh)-dependent conformational changes in a prototype of the nicotinic receptor ligand binding domain by molecular dynamics…”
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Total free energy analysis of fully hydrated proteins by Kalayan, Jas, Chakravorty, Arghya, Warwicker, Jim, Henchman, Richard H.

“…The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of…”
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Model for Counterion Binding and Charge Reversal on Protein Surfaces by Kalayan, Jas, Henchman, Richard H, Warwicker, Jim

“…The structural stability and solubility of proteins in liquid therapeutic formulations is important, especially since new generations of therapeutics are…”
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Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA by Ali, Hafiz Saqib, Henchman, Richard H., Visser, Sam P.

“…A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O‐demethylation or alternatively an acetal formation…”
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Overcoming the limitations of cutoffs for defining atomic coordination in multicomponent systems by Higham, Jonathan, Henchman, Richard H.

“…A common way to understand structure in multimolecular systems is the coordination shell which comprises all the neighbors of an atom. Coordination, however,…”
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Inhibitors of PIM-1 Kinase: A Computational Analysis of the Binding Free Energies of a Range of Imidazo [1,2-b] Pyridazines by Doudou, Slimane, Sharma, Raman, Henchman, Richard H, Sheppard, David W, Burton, Neil A

“…The binding of a selection of competitive imidazo [1,2-b] pyridazine inhibitors of PIM-1 kinase with nanomolar activity has been analyzed using computational…”
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What Determines the Selectivity of Arginine Dihydroxylation by the Nonheme Iron Enzyme OrfP? by Ali, Hafiz Saqib, Henchman, Richard H., Visser, Sam P.

“…The nonheme iron enzyme OrfP reacts with l‐Arg selectively to form the 3R,4R‐dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase…”
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Topological Hydrogen-Bond Definition to Characterize the Structure and Dynamics of Liquid Water by Henchman, Richard H, Irudayam, Sheeba Jem

“…A definition that equates a hydrogen bond topologically with a local energy well in the potential energy surface is used to study the structure and dynamics of…”
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Structural and dynamic properties of water around acetylcholinesterase by Henchman, Richard H., McCammon, J. Andrew

“…Structural and dynamic properties of water molecules around acetylcholinesterase are examined from a 10‐nsec molecular dynamics simulation to help understand…”
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Molecular interpretation of Trouton’s and Hildebrand’s rules for the entropy of vaporization of a liquid by Green, James A., Irudayam, Sheeba Jem, Henchman, Richard H.

“…► A method to calculate a liquid’s entropy of vaporization is proposed. ► The entropy of vaporisation depends on force magnitudes from computer simulation. ►…”
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Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force by Doudou, Slimane, Burton, Neil A, Henchman, Richard H

“…A practical approach that enables one to calculate the standard free energy of binding from a one-dimensional potential of mean force (PMF) is proposed…”
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