Browsing by Subject "molecular dynamics"
Now showing items 21-40 of 41
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Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs
(2012)We report the computational and rational design of new generations of potential peptide-based inhibitors of the complement protein C3 from the compstatin family. The binding efficacy of the peptides is tested by extensive ...
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Near critical behavior in the two-dimensional spin-gap system SrCu2(BO3)2
(2002)The temperature dependence of the powdered X-band ESR spectra has been measured in a two-dimensional spin-gap system SrCu2(BO3)2 in the temperature range between 5 and 300 K. The spectra are composed of two overlapping ...
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New compstatin peptides containing n-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics
(2015)Compstatin peptides are complement inhibitors that bind and inhibit cleavage of complement C3. Peptide binding is enhanced by hydrophobic interactions
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NMR and theoretical investigations on the structures and dynamics of octahedral bis(chelate)dichloro VIII compounds isolated by an unusual reduction of non-oxo VIV species
(2003)Reaction of the non-oxo VIV species [VIVCl2(LOO)2] [LOO = acetylacetonate (acac-) or benzoylacetonate (bzac-)] with a chelate nitrogen-donor ligand LNN in acetonitrile leads to the reduction of VIV to VIII and the formation ...
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The origin of the Fe IV = O intermediates in cytochrome aa 3 oxidase
(2012)The dioxygen reduction mechanism in cytochrome oxidases relies on proton control of the electron transfer events that drive the process. Proton delivery and proton channels in the protein that are relevant to substrate ...
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Article
Photoselected electron transfer pathways in DNA photolyase
(2007)Cyclobutane dimer photolyases are proteins that bind to UV-damaged DNA containing cyclobutane pyrimidine dimer lesions. They repair these lesions by photo-induced electron transfer. The electron donor cofactor of a photolyase ...
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Protein dynamics and electron transfer: Electronic decoherence and non-Condon effects
(2005)We compute the autocorrelation function of the donor-acceptor tunneling matrix element 〈TDA(t)TDA(0)〉 for six Ru-azurin derivatives. Comparison of this decay time to the decay time of the time-dependent Franck-Condon factor ...
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Proton binding to proteins: A free-energy component analysis using a dielectric continuum model
(2005)Proton binding plays a critical role in protein structure and function. We report pKa calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. ...
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Recognition of ribonuclease A by 3′-5′-pyrophosphate-linked dinucleotide inhibitors: A molecular dynamics/continuum electrostatics analysis
(2007)The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic ...
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A reductive-aggregation route to [Mn12O12(OMe) 2(O2CPh)16(H2O)2] 2- single-molecule magnets related to the [Mn12] family
(2004)Axes of power: Jahn-Teller isomerism (that is, Jahn-Teller distortion along different axes) accounts for the presence of both faster and slower relaxing magnetization dynamics of the title compound (see core structure
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Relative stabilities and hydride affinities of silatropylium and silabenzyl cations and their isomers. Comparison with the carbon analogues tropylium and benzyl cations
(1996)High-level ab initio calculations on silatropylium (1-Si) and silabenzyl (2-Si) cations and seven of their low-lying isomers (3-8), as well as on their carbon analogues, tropylium (1-C) and benzyl (2-C) cations, are reported. ...
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Resonance Raman detection of the myoglobin nitrito heme Fe-O-N=O/2-nitrovinyl species: Implications for helix E-helix F interactions
(2015)The description of biological activity in heme proteins responsible for activating small molecules requires identification of ligand movement into the metal and non-metal binding sites. Mechanisms of nitrite reductase ...
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Ring opening of the cyclopropylcarbinyl radical and its N- and O- substituted analogues: A theoretical examination of very fast unimolecular reactions
(1998)High level ab initio molecular orbital calculations have been used to examine the ring opening of the cyclopropylcarbinyl radical and its heterosubstituted analogues. The applicability of various theoretical techniques to ...
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Self-assembly of phenylalanine oligopeptides: Insights from experiments and simulations
(2009)Studies of peptide-based nanostructures provide general insights into biomolecular self-assembly and can lead material engineering toward technological applications. The diphenylalanine peptide (FF) self-assembles into ...
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Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations
(2010)The development of compounds to regulate the activation of the complement system in non-primate species is of profound interest because it can provide models for human diseases. The peptide compstatin inhibits protein C3 ...
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Synthesis, characterization and evaluation of amphiphilic diblock copolymer emulsifiers based on methoxy hexa(ethylene glycol) methacrylate and benzyl methacrylate
(2004)Linear, amphiphilic diblock copolymers based on the nonionic, hydrophilic monomer methoxy hexa(ethylene glycol) methacrylate (HEGMA) and the hydrophobic monomer benzyl methacrylate (BzMA) of different molecular weights and ...
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Synthetic analogues for oxovanadium(IV) - Glutathione interaction: An EPR, synthetic and structural study of oxovanadium(IV) compounds with sulfhydryl-containing pseudopeptides and dipeptides
(1999)Valuable analogues of the VIVO2+ - glutathione complex have been synthesized and characterized. The reaction of [VIVO(CH3COO)2(phen)] (phen = 1,10-phenanthroline) with the sulfhydryl-containing pseudopeptides (scp) ...
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A theoretical study of chlorine atom and methyl radical addition to nitrogen bases: Why do Cl atoms form two-center - Three electron bonds whereas CH3 radicals form two-center - Two-electron bonds?
(1996)Ab initio molecular orbital calculations have been carried out on a series of adducts between chlorine atom and NH3, NMe3, NCl3, HN=CH2, and pyridine, and between methyl radical and HN=CH2 and pyridine. A two-center-three-electron ...
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Time-Resolved Resonance Raman and Time-Resolved Step-Scan FTIR Studies of Nitric Oxide Reductase from Paracoccus denitrificans: Comparison of the Heme b3-FeB Site to That of the Heme-CuB in Oxidases
(2003)Time-resolved resonance Raman (TR3) and time-resolved step-scan (TRS2) FTIR spectroscopies have been used to probe the structural dynamics at the heme b3 proximal and distal sites after carbon monoxide photolysis from fully ...
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Time-resolved resonance Raman studies of halooxide photoisomerization kinetics
(2003)The condensed-phase photoisomerization dynamics of chlorine dioxide and dichlorine monoxide are investigated using femtosecond pump-probe and time-resolved resonance Raman. These studies demonstrate that photoisomerization ...