A5069970299- Protein Structure and Dynamics
- Enzyme Structure and Function
- Spectroscopy and Quantum Chemical Studies
- DNA and Nucleic Acid Chemistry
- Biochemical and Molecular Research
- RNA and protein synthesis mechanisms
- Mass Spectrometry Techniques and Applications
- Chemical Synthesis and Analysis
- Advanced Chemical Physics Studies
- Hemoglobin structure and function
- Folate and B Vitamins Research
- Lipid Membrane Structure and Behavior
- Photosynthetic Processes and Mechanisms
- Porphyrin Metabolism and Disorders
- Photoreceptor and optogenetics research
- Mitochondrial Function and Pathology
- Crystallography and molecular interactions
- HIV/AIDS drug development and treatment
- Phase Equilibria and Thermodynamics
- RNA Interference and Gene Delivery
- Electron Spin Resonance Studies
- Neuropeptides and Animal Physiology
- Wnt/β-catenin signaling in development and cancer
- Crystallization and Solubility Studies
- Endoplasmic Reticulum Stress and Disease
University of Kansas
2016-2025
University of Maryland, College Park
2011
Baylor University
2009-2010
National Heart Lung and Blood Institute
2009
National Institutes of Health
2009
The University of Texas at Austin
2009
Hinckley and Bosworth Community Hospital
2006
Florida International University
2005
University of Toronto
2003
Hospital for Sick Children
2003
New protein parameters are reported for the all-atom empirical energy function in CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve balance between internal (bonding) and interaction (nonbonding) terms of force field among solvent-solvent, solvent-solute, solute-solute interactions. Optimization used experimental gas-phase geometries, vibrational spectra, torsional surfaces supplemented with ab initio results. peptide backbone bonding were...
Iron species with terminal oxo ligands are implicated as key intermediates in several synthetic and biochemical catalytic cycles. However, there is a dearth of structural information regarding these types complexes because their instability has precluded isolation under ambient conditions. The characterization an iron(III) complex ligand, derived directly from dioxygen (O 2 ), reported. A stable structure resulted placing the oxoiron unit within cavity lined hydrogen-bonding groups. creates...
A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules free energy changes in proteins. Its application hemoglobin interface mutant Asp G1(99) β→Ala shows that some difference cooperativity are as large 60 kilocalories (kcal) per mole. Since overall change only -5.5 kcal/mole (versus experimental value -3.4 kcal/mole), essential elements thermodynamics hidden measured results. By exposing contributions, provides...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLigand binding and protein relaxation in heme proteins: a room temperature analysis of nitric oxide geminate recombinationJ. W. Petrich, J. C. Lambry, K. Kuczera, Martin Karplus, Poyart, L. MartinCite this: Biochemistry 1991, 30, 16, 3975–3987Publication Date (Print):April 23, 1991Publication History Published online1 May 2002Published inissue 23 April...
Abstract In molecular dynamics simulations, the fastest components of potential field impose severe restrictions on stability and hence speed computational methods. One possibility for treating this problem is to replace with algebraic length constraints. article resulting systems mixed differential equations are studied. Commonly used discretization schemes constrained Hamiltonian discussed. The form nonlinear examined in detail give convergence results traditional solution technique SHAKE...
Molecular dynamics simulations are used to calculate the incoherent neutron scattering spectra of myoglobin between 80 K and 325 compared with experimental data. There is good agreement over entire temperature range for elastic, quasi-elastic, inelastic components scattering. This provides support accuracy internal motions that make dominant contributions atomic displacements on a time scale 0.3-100 ps (100-0.3 cm-1). Analysis shows at low temperatures harmonic description molecule...
ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTUnusual Encapsulation of Two Nitrates in a Single Bicyclic CageSusan Mason, Thomas Clifford, Larry Seib, Krzysztof Kuczera, and Kristin Bowman-JamesView Author Information Department Chemistry, University Kansas Lawrence, 66045 Cite this: J. Am. Chem. Soc. 1998, 120, 34, 8899–8900Publication Date (Web):August 15, 1998Publication History Received7 April 1998Published online15 August inissue 1 September...
In order to investigate the possibility that calmodulin (CaM) may be a principal target of reactive oxygen species (ROS) produced under conditions oxidative stress, we have examined wheat germ CaM for presence highly sites correlate with loss function. Using reversed-phase HPLC and FAB mass spectrometry after proteolytic digestion, identified modification by hydrogen peroxide. We find one vicinal methionines (i.e., Met146 or Met147) near C-terminus is selectively oxidized. The ability bind...
The unfolding process of a helical heteropeptide is studied by computer simulation in explicit solvent. A combination functional optimization to determine the reaction coordinate and short time trajectories between "milestones" used study kinetics unfolding. One hundred along three different pathways are computed all nearby milestones, providing adequate statistics compute overall first passage time. radius gyration smaller for intermediate configurations compared initial final states,...
Cellular transport machinery, such as channels and pumps, is working against the background of unassisted material through membranes. The permeation a blocked tryptophan 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane investigated to probe or physical transport. rate measured experimentally modeled computationally. time scale by parallel artificial assay (PAMPA) experiments ~8 h. Simulations with milestoning algorithm suggest mean first passage (MFPT) ~4 h presence large barrier at...
Polysorbate 80 (PS80) is widely used in pharmaceutical formulations, and its commercial grades exhibit certain levels of structural heterogeneity. The objective this study was to apply coarse-grained molecular dynamics simulations better understand the effect PS80 heterogeneity on micelle self-assembly, loading hydrophobic small molecules into core, interactions between a protein, bovine serum albumin (BSA). Four representative variants with different head tail structures were studied. Our...
The oxidative modification of methionines within the primary sequence calmodulin (CaM) results in an inability to activate PM-Ca-ATPase fully, and may contribute alterations calcium homeostasis under conditions stress. To identify differences sensitivities CaM isoforms modification, we have compared function patterns resulting from exposure isolated bovine testes wheat germ H2O2. In comparison germ, vertebrate is functionally resistant oxidant-induced loss function. decreased functional...
S-Adenosylhomocysteine hydrolase (AdoHcy hydrolase) crystallizes from solutions containing the intermediate analogue neplanocin A with bound in its 3'-keto form at active sites of all four subunits and tightly cofactors their reduced (NADH) state. The enzyme is closed conformation, which corresponds to structure catalytic chemistry occurs. Examination light available, very detailed kinetic studies [Porter, D. J., Boyd, F. L. (1991) J. Biol. Chem. 266, 21616−21625. Porter, (1992) 267,...
We present complementary molecular simulations and experimental results of phase equilibria for carbon dioxide expanded acetonitrile, methanol, ethanol, acetone, acetic acid, toluene, 1-octene. The volume expansion measurements were done using a high-pressure Jerguson view cell. Molecular performed the Gibbs ensemble Monte Carlo method. Calculations in canonical (NVT) to determine coexistence curve pure solvent systems. Binary mixtures simulated isobaric-isothermal distribution (NPT)....
We used a combined approach of experiment and simulation to determine the helical population folding pathway small helix forming blocked pentapeptide, Ac-(Ala)5-NH2. Experimental structural characterization this peptide was carried out with far UV circular dichroism spectroscopy, FTIR, NMR measurements. These measurements confirm presence α-helical state in buffer solution. Direct molecular dynamics replica-exchange simulations pentapeptide were performed using several popular force fields...
We have characterized and quantified pathways by which sulfide radical cation complexes of N-methionyl peptides (Met-Met, Met-Met-Ala, Met-Leu) transform into various products through the reaction with superoxide or oxygen. Sulfide cations were generated photolytically either triplet carboxybenzophenone (3CB) hydroxyl radicals (HO•). Met-Met 3CB, formed intramolecularly sulfur−sulfur three-electron-bonded complexes, [R2S∴SR2]+, efficiently reacted to yield respective disulfoxides...
Hexamers of β-amino acids with different substituent patterns at the Cα- and Cβ-backbone atoms (none, β2, β3, β2,2, β3,3, (R,S)β2,3, (S,S)β2,3) were subject molecular dynamics simulations on basis CHARMm23.1 force field to generate conformational free energy surfaces for concerted changes in (φ,ψ) dihedrals employing a multidimensional integration approach. Application this technique provides insight into intrinsic folding propensities these homooligomers including cooperativity effects. The...
Molecular dynamics simulations of myoglobin after ligand photodissociation show that the out-of-plane motion heme iron has a rapid subpicosecond phase followed by slower nonexponential process involving more global protein relaxation. Individual trajectories rather different behavior, suggesting there is an inhomogeneous component to The calculated time dependence over 100 ps in excellent agreement with frequency shift band III group [see Lim, M., Jackson, T. A. & Anfinrud, P. (1993)...
Nitrate complexes of two different polyammonium macrocycles, the tetrahydrogen nitrate salts 1,4,7,16,19,21-hexaaza-10,13-dioxacyclotetracosane [24]N6O2·4HNO3, 1, and 1,4,10,13-tetraaza-7,16-dioxacyclooctadecane, [18]N4O2·4HNO3, 2, have been isolated their structures determined by X-ray crystallographic methods. Compound 1 crystallizes in orthorhombic space group Imma with unit cell dimensions a = 22.692(3) Å, b 19.563(3) c 7.005(1) V 3110(1) Å3, Z 4. 2 Pbca 13.877(1) 15.553(1) 10.742(1)...
Molecular dynamics simulations and fluorescence anisotropy decay measurements are used to investigate the rotational diffusion of anthracene in two organic solvents—cyclohexane 2-propanol—at several temperatures. 1 ns length were performed for cyclohexane (at 280, 296, 310 K) 2-propanol 296 K). The calculated time constants reorientation short in-plane axis 7–9 11–16 ps at K 2-propanol, respectively, excellent agreement with corresponding depolarization 8 14 ps. measured times average...