Subject Areas on Research
- 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.
- 3D patterned stem cell differentiation using thermo-responsive methylcellulose hydrogel molds.
- A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.
- A THERMODYNAMIC STUDY OF THE HYDROLYSIS OF CYTIDINE 2',3'-CYCLIC PHOSPHATE.
- A calorimetric and monolayer investigation of the influence of ions on the thermodynamic properties of phosphatidylcholine.
- A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution.
- A gradient-directed Monte Carlo approach for protein design.
- A mass spectrometry-based probe of equilibrium intermediates in protein-folding reactions.
- A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.
- A multidisciplinary approach to probing enthalpy-entropy compensation and the interfacial mobility model.
- A nanoscale force probe for gauging intermolecular interactions.
- A new H/D exchange- and mass spectrometry-based method for thermodynamic analysis of protein-DNA interactions.
- A new monofluorinated phosphatidylcholine forms interdigitated bilayers.
- A new role for phytochromes in temperature-dependent germination.
- A potentially abundant junctional RNA motif stabilized by m6A and Mg2.
- A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy.
- A statistical thermodynamic model of the protein ensemble.
- A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.
- A thermodynamic ligand binding study of the third PDZ domain (PDZ3) from the mammalian neuronal protein PSD-95.
- A thermodynamic study of the partition of n-hexane into phosphatidylcholine and phosphatidylcholine-cholesterol bilayers.
- AFLOW-CHULL: Cloud-Oriented Platform for Autonomous Phase Stability Analysis.
- Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase.
- Ab initio based calculations of electron-transfer rates in metalloproteins.
- Accuracy and precision of a new H/D exchange- and mass spectrometry-based technique for measuring the thermodynamic properties of protein-peptide complexes.
- Accuracy of SUPREX (stability of unpurified proteins from rates of H/D exchange) and MALDI mass spectrometry-derived protein unfolding free energies determined under non-EX2 exchange conditions.
- Acid phosphatase activity in subcellular fractions of fish liver exposed to methyl mercuric chloride.
- Acid-base and electrochemical properties of manganese meso(ortho- and meta-N-ethylpyridyl)porphyrins: potentiometric, spectrophotometric and spectroelectrochemical study of protolytic and redox equilibria.
- Acid-base and electrochemical properties of manganese meso(ortho- and meta-N-ethylpyridyl)porphyrins: voltammetric and chronocoulometric study of protolytic and redox equilibria.
- Activated human plasma carboxypeptidase B is retained in the blood by binding to alpha2-macroglobulin and pregnancy zone protein.
- Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes.
- Additivity and the physical basis of multivalency effects: a thermodynamic investigation of the calcium EDTA interaction.
- Adhesion and motility of gliding bacteria on substrata with different surface free energies.
- Adsorption of clofibric acid and ketoprofen onto powdered activated carbon: effect of natural organic matter.
- Affinity of (alpha-P-borano)-NTP analogs to rabbit muscle pyruvate kinase.
- Alternate states of proteins revealed by detailed energy landscape mapping.
- An automated decision-tree approach to predicting protein interaction hot spots.
- An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants.
- An enthalpic basis of additivity in biphenyl hydroxamic acid ligands for stromelysin-1.
- An enthalpic model of anesthesia.
- An investigation of the equilibria between aqueous ribose, ribulose, and arabinose.
- Analysis of ligand binding specificity of receptor chimeras.
- Analysis of protein binding to receptor-doped lipid monolayers by Monte Carlo simulation.
- Analysis of the effect of three different allosteric ligands on oxygen binding by hemocyanin of the shrimp, Penaeus setiferus.
- Analytic gradients, geometry optimization and excited state potential energy surfaces from the particle-particle random phase approximation.
- Apolipoprotein C-III/sphingomyelin recombinants: formation, isolation, and characterization.
- Apparent cooperative assembly of the bacterial cell division protein FtsZ demonstrated by isothermal titration calorimetry.
- Application of Edwards' statistical mechanics to high-dimensional jammed sphere packings.
- Assessing Possible Mechanisms of Micrometer-Scale Electron Transfer in Heme-Free Geobacter sulfurreducens Pili.
- Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements.
- B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics.
- Basic principles of thermal dosimetry and thermal thresholds for tissue damage from hyperthermia.
- Beryllium(II) binding to ATP and ADP: potentiometric determination of the thermodynamic constants and implications for in vivo toxicity.
- Beyond static structures of RNA by NMR: folding, refolding, and dynamics at atomic resolution.
- Biochemistry. Friction in motor proteins.
- Biochemistry. Photosynthesis from the protein's perspective.
- Bivalent peptides as PDZ domain ligands.
- Boranophosphates support the RNase H cleavage of polyribonucleotides.
- Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies.
- Bridged peptide macrocycles as ligands for PDZ domain proteins.
- Broken detailed balance at mesoscopic scales in active biological systems.
- C-nitroso compounds: synthesis, physicochemical properties and biological activities.
- Calcium binding by synaptotagmin's C2A domain is an essential element of the electrostatic switch that triggers synchronous synaptic transmission.
- Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.
- Calorimetric analysis of the binding of lectins with overlapping carbohydrate-binding ligand specificities.
- Calorimetric determination of the standard transformed enthalpy of a biochemical reaction at specified pH and pMg.
- Calorimetric evaluation of protein-carbohydrate affinities.
- Can regular solution theory be applied to lipid bilayer membranes?
- Carbon monoxide binding by simple heme proteins under photodissociating conditions.
- Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices.
- Chain stiffness and attachment-dependent attraction between polyelectrolyte-grafted colloids.
- Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM.
- Chaperones rescue luciferase folding by separating its domains.
- Characterization of Fe(III) sequestration by an analog of the cytotoxic siderophore brasilibactin A: implications for the iron transport mechanism in mycobacteria.
- Characterization of non-equilibrium nanoparticle adsorption on a model biological substrate.
- Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique.
- Characterization of the interaction between alpha2-macroglobulin and fibroblast growth factor-2: the role of hydrophobic interactions.
- Characterizing RNA Excited States Using NMR Relaxation Dispersion.
- Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.
- Chemical Denaturation and Protein Precipitation Approach for Discovery and Quantitation of Protein-Drug Interactions.
- Chiral action at a distance: remote substituent effects on the optical activity of calyculins A and B.
- Chloride and pH dependence of cooperative interactions in Limulus polyphemus hemocyanin.
- Clustered charged amino acids of human adenosine deaminase comprise a functional epitope for binding the adenosine deaminase complexing protein CD26/dipeptidyl peptidase IV.
- Co-operativity in protein-protein association. The structure and stability of the actin filament.
- Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.
- Communication: An exact short-time solver for the time-dependent Schrödinger equation.
- Complexes between serpins and inactive proteinases are not thermodynamically stable but are recognized by serpin receptors.
- Computational design of receptor and sensor proteins with novel functions.
- Computational design of receptors for an organophosphate surrogate of the nerve agent soman.
- Computational study on the relative acidity of acetic acid by the qm/mm method combined with the theory of energy representation
- Computing van der Waals energies in the context of the rotamer approximation.
- Conformational kinetics reveals affinities of protein conformational states.
- Conformationally averaged score functions for electronic propagation in proteins.
- Conjugate of Doxorubicin to Albumin-Binding Peptide Outperforms Aldoxorubicin.
- Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins.
- Consensus and variant cAMP-regulated enhancers have distinct CREB-binding properties.
- Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold.
- Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics.
- Contributions of hydration and steric (entropic) pressures to the interactions between phosphatidylcholine bilayers: experiments with the subgel phase.
- Conversion of a maltose receptor into a zinc biosensor by computational design.
- Coordination chemistry of siderophores: thermodynamics and kinetics of iron chelation and release.
- Cytosine deamination in mismatched base pairs.
- Cytotoxicity and thermomechanical behavior of biomedical shape-memory polymer networks post-sterilization.
- DNA base modification: ionized base pairs and mutagenesis.
- DNA mismatches reveal conformational penalties in protein-DNA recognition.
- De novo design of a single-chain diphenylporphyrin metalloprotein.
- Deposition of aggregated nanoparticles--a theoretical and experimental study on the effect of aggregation state on the affinity between nanoparticles and a collector surface.
- Describing Complex Structure-Function Relationships in Biomolecules at Equilibrium.
- Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins.
- Designing safer chemicals: predicting the rates of metabolism of halogenated alkanes.
- Determining absolute configuration in flexible molecules: a case study.
- Differences between the effect of anisotropic and isotropic laminin and nerve growth factor presenting scaffolds on nerve regeneration across long peripheral nerve gaps.
- Direct analysis of backbone-backbone hydrogen bond formation in protein folding transition states.
- Direct evaluation of electronic coupling mediated by hydrogen bonds: implications for biological electron transfer.
- Direct force measurements of the streptavidin-biotin interaction.
- Disruption of Acetyl-Lysine Turnover in Muscle Mitochondria Promotes Insulin Resistance and Redox Stress without Overt Respiratory Dysfunction.
- Dissecting the differences between the alpha and beta anomers of the oxidative DNA lesion FaPydG.
- Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies.
- Distinct properties of cell-type-specific and shared transcription factor binding sites.
- Divergent regulation of protein synthesis in the cytosol and endoplasmic reticulum compartments of mammalian cells.
- Divergent transducer-specific molecular efficacies generate biased agonism at a G protein-coupled receptor (GPCR).
- Dominant kinetic paths on biomolecular binding-folding energy landscape.
- Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA.
- Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes.
- Effect of protein fusion on the transition temperature of an environmentally responsive elastin-like polypeptide: a role for surface hydrophobicity?
- Efficiency, selectivity, and robustness of nucleocytoplasmic transport.
- Elastic deformation and failure of lipid bilayer membranes containing cholesterol.
- Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry.
- Electron transfer in the photosynthetic reaction center: mechanistic implications of mutagenesis studies.
- Elucidating solvent contributions to solution reactions with ab initio QM/MM methods.
- Emergence of limit-periodic order in tiling models.
- Energetic contribution of non-essential 5' sequence to catalysis in a hepatitis delta virus ribozyme.
- Energetics-based methods for protein folding and stability measurements.
- Energy Transduction in Nitrogenase.
- Engineering protein stability and specificity using fluorous amino acids: the importance of packing effects.
- Enthalpic signature of methonium desolvation revealed in a synthetic host-guest system based on cucurbituril.
- Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.
- Evaluation of an elastin-like polypeptide-doxorubicin conjugate for cancer therapy.
- Exchange of monooleoylphosphatidylcholine as monomer and micelle with membranes containing poly(ethylene glycol)-lipid.
- Experimental tests for protrusion and undulation pressures in phospholipid bilayers.
- Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate.
- Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys + H(+)vs. Ac-Lys-Ala19 + H(+) and the current reach of DFT.
- Extent of equilibrium perturbation of the DNA helix upon enzymatic methylation of adenine residues.
- Extreme electronic modulation of the cofacial porphyrin structural motif.
- Facile chemical synthesis and equilibrium unfolding properties of CopG.
- False-positive rate determination of protein target discovery using a covalent modification- and mass spectrometry-based proteomics platform.
- Fast and forceful refolding of stretched alpha-helical solenoid proteins.
- Fe(III) coordination properties of a new saccharide-based exocyclic trihydroxamate analogue of ferrichrome.
- First observation of the P-wave spin-singlet bottomonium states hb(1P) and hb(2P).
- First-Principles Molecular Structure Search with a Genetic Algorithm.
- Flory theorem for structurally asymmetric mixtures
- Folding dynamics of phenylalanine hydroxylase depends on the enzyme's metallation state: the native metal, iron, protects against aggregate intermediates.
- Folding mechanism of a multiple independently-folding domain protein: double B domain of protein A.
- Free energy landscape of salt-actuated reconfigurable DNA nanodevices.
- Free sphingosine formation from endogenous substrates by a liver plasma membrane system with a divalent cation dependence and a neutral pH optimum.
- Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes
- Functional complexity and regulation through RNA dynamics.
- Ga3+ as a mechanistic probe in Fe3+ transport: characterization of Ga3+ interaction with FbpA.
- Giant vesicle bilayers composed of mixtures of lipids, cholesterol and polypeptides. Thermomechanical and (mutual) adherence properties.
- Global analysis of protein folding thermodynamics for disease state characterization.
- Grb7 binds to Hax-1 and undergoes an intramolecular domain association that offers a model for Grb7 regulation.
- Guanidine-induced equilibrium unfolding of a homo-hexameric enzyme 4-oxalocrotonate tautomerase (4-OT).
- H/D exchange and mass spectrometry-based method for biophysical analysis of multidomain proteins at the domain level.
- H/D exchange- and mass spectrometry-based strategy for the thermodynamic analysis of protein-ligand binding.
- Harnessing Environmental Ca2+ for Extracellular Protein Thermostabilization.
- Heat and cold denatured states of monomeric lambda repressor are thermodynamically and conformationally equivalent.
- Hierarchical Self-Assembly of Noncovalent Amphiphiles
- Hierarchy of RNA functional dynamics.
- High-throughput combinatorial database of electronic band structures for inorganic scintillator materials.
- How do halogen substituents contribute to protein-binding interactions? A thermodynamic study of peptide ligands with diverse aryl halides.
- Hydrogen/deuterium exchange- and protease digestion-based screening assay for protein-ligand binding detection.
- Hydrolysis of N3-methyl-2'-deoxycytidine: model compound for reactivity of protonated cytosine residues in DNA.
- Hyperthermia classic commentary: 'Arrhenius relationships from the molecule and cell to the clinic' by William Dewey, Int. J. Hyperthermia, 10:457-483, 1994.
- Hyperthermic treatment of malignant diseases: current status and a view toward the future.
- Impact of holmium laser settings and fiber diameter on stone fragmentation and endoscope deflection.
- Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.
- Insights into the nature of DNA binding of AbrB-like transcription factors.
- Interaction of aspartate transcarbamylase with 5-bromocytidine 5'-tri-, di-, and monophosphates.
- Interaction of benzene with bilayers. Thermal and structural studies.
- Interaction of dihydrofolate reductase with methotrexate: ensemble and single-molecule kinetics.
- Interaction of halothane with lipid bilayers.
- Interaction of synthetic HA2 influenza fusion peptide analog with model membranes.
- Interaction of the Shiga-like toxin type 1 B-subunit with its carbohydrate receptor.
- Interactions between charged, uncharged, and zwitterionic bilayers containing phosphatidylglycerol.
- Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR relaxation studies.
- Interdigitated hydrocarbon chain packing causes the biphasic transition behavior in lipid/alcohol suspensions.
- Inverse techniques in hyperthermia: a sensitivity study.
- Investigation of quercetin binding sites on chloroplast coupling factor 1.
- Invisible RNA state dynamically couples distant motifs.
- Ionic influences on the phase transition of dipalmitoylphosphatidylserine.
- Isolation of novel EGFR-specific VHH domains.
- Kinetic role of helix caps in protein folding is context-dependent.
- Kinetics and mechanism of iron(III) complexation by ferric binding protein: the role of phosphate.
- Kinetics of iron release from ferric binding protein (FbpA): mechanistic implications in bacterial periplasm-to-cytosol Fe3+ transport.
- Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using SILAC-SPROX.
- Learning about Biomolecular Solvation from Water in Protein Crystals.
- Learning protein-DNA interaction landscapes by integrating experimental data through computational models.
- Ligation-state hydrogen exchange: coupled binding and folding equilibria in ribonuclease P protein.
- Linking ligand-induced alterations in androgen receptor structure to differential gene expression: a first step in the rational design of selective androgen receptor modulators.
- Lipid monolayer states and their relationships to bilayers.
- Lipopolysaccharides in bacterial membranes act like cholesterol in eukaryotic plasma membranes in providing protection against melittin-induced bilayer lysis.
- Long range dynamic effects of point-mutations trap a response regulator in an active conformation.
- Long-range electron transfer in myoglobin.
- Manipulation of ligand binding affinity by exploitation of conformational coupling.
- Mass spectrometry- and lysine amidination-based protocol for thermodynamic analysis of protein folding and ligand binding interactions.
- Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data.
- Maxwell's demons everywhere: evolving design as the arrow of time.
- Measurement of interbilayer adhesion energies.
- Measurements of protein stability by H/D exchange and matrix-assisted laser desorption/ionization mass spectrometry using picomoles of material.
- Measurements of the top-quark mass and the tt cross section in the hadronic τ+jets decay channel at sqrt[s] = 1.96 TeV.
- Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.
- Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase.
- Mechanism of specific site location and DNA cleavage by EcoR I endonuclease.
- Mechanism of time-dependent inhibition of 5 alpha-reductases by delta 1-4-azasteroids: toward perfection of rates of time-dependent inhibition by using ligand-binding energies.
- Microdomain evolution on giant unilamellar vesicles.
- Microtubule treadmilling in vitro investigated by fluorescence speckle and confocal microscopy.
- Mitochondrial metabolism sets the maximal limit of fuel-stimulated insulin secretion in a model pancreatic beta cell: a survey of four fuel secretagogues.
- Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements
- Model of creation and evolution of stable electropores for DNA delivery.
- Modulation of Hoogsteen dynamics on DNA recognition.
- Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.
- Molprobity's ultimate rotamer-library distributions for model validation.
- Monomeric yeast frataxin is an iron-binding protein.
- Multilayer adsorption of lysozyme on a hydrophobic substrate.
- Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics.
- Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae).
- Multivalency effects in protein--carbohydrate interaction: the binding of the Shiga-like toxin 1 binding subunit to multivalent C-linked glycopeptides.
- Mutational analysis of active site residues in the Staphylococcus aureus transpeptidase SrtA.
- Mutations that destabilize the gp41 core are determinants for stabilizing the simian immunodeficiency virus-CPmac envelope glycoprotein complex.
- NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.
- New sensitive micro-measurements of dynamic surface tension and diffusion coefficients: Validated and tested for the adsorption of 1-Octanol at a microscopic air-water interface and its dissolution into water.
- Nitroxyl disulfides, novel intermediates in transnitrosation reactions.
- Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
- Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase.
- Optical rotation of noncovalent aggregates.
- Optimal sequence selection in proteins of known structure by simulated evolution.
- Orbital-dependent correlation energy in density-functional theory based on a second-order perturbation approach: success and failure.
- Ordering in granular-rod monolayers driven far from thermodynamic equilibrium.
- Origins of the helical wrapping of phenyleneethynylene polymers about single-walled carbon nanotubes.
- Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand.
- Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies.
- Painting proteins with covalent labels: what's in the picture?
- Persistence of structure over fluctuations in biological electron-transfer reactions.
- Phase changes induced by cyclopropane of phosphatidylserine bilayers in the presence and absence of calcium.
- Phase separation in biological membranes: integration of theory and experiment.
- Phonon self-energy and origin of anomalous neutron scattering spectra in SnTe and PbTe thermoelectrics.
- Phospholipid membrane stabilization by dimethylsulfoxide and other inducers of Friend leukemic cell differentiation.
- Photoinduced electron transfer between the Rieske iron-sulfur protein and cytochrome c(1) in the Rhodobacter sphaeroides cytochrome bc(1) complex. Effects of pH, temperature, and driving force.
- Physical constraints on charge transport through bacterial nanowires.
- Physical parameters of the anesthetic site.
- Physical properties of cholesteryl esters having 20 carbons or more.
- Physical properties of cholesteryl esters.
- Point mutations alter the mechanical stability of immunoglobulin modules.
- Polyphosphazenes: effect of molecular motions on thrombogenesis.
- Potentiometric, electronic structural, and ground- and excited-state optical properties of conjugated bis[(porphinato)zinc(II)] compounds featuring proquinoidal spacer units.
- Predicting transition temperatures of elastin-like polypeptide fusion proteins.
- Preorganized secondary structure as an important determinant of fast protein folding.
- Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.
- Primer3--new capabilities and interfaces.
- Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition.
- Probing structure-function relationships in missense variants in the carboxy-terminal region of BRCA1.
- Probing the ethanol-induced chain interdigitations in gel-state bilayers of mixed-chain phosphatidylcholines.
- Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein.
- Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units.
- Protein imperfections: separating intrinsic from extrinsic variation of torsion angles.
- Protein phosphorylation and intermolecular electron transfer: a joint experimental and computational study of a hormone biosynthesis pathway.
- Protein-DNA binding in the absence of specific base-pair recognition.
- Proteome-Wide Characterization of Phosphorylation-Induced Conformational Changes in Breast Cancer.
- Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale.
- Protocol for the thermodynamic analysis of some proteins using an H/D exchange- and mass spectrometry-based technique.
- Proton NMR of Escherichia coli sulfite reductase: the unligated hemeprotein subunit.
- Pseudomonas aeruginosa elastase degrades surfactant proteins A and D.
- Pushing the boundaries of intrinsically stable radicals: inverse design using the thiadiazinyl radical as a template.
- Quantifying intrinsic specificity: a potential complement to affinity in drug screening.
- Quantifying kinetic paths of protein folding.
- Quantifying the kinetic paths of flexible biomolecular recognition.
- Quantitation of protein-protein interactions by thermal stability shift analysis.
- Quantitative protein stability measurement in vivo.
- Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements.
- Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.
- Quantum mechanics simulation of protein dynamics on long timescale.
- Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
- Radium and barium removal through blending hydraulic fracturing fluids with acid mine drainage.
- Rates of fixation by lightning of carbon and nitrogen in possible primitive atmospheres.
- Rational protein design: combining theory and experiment.
- Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
- Reactions of manganese porphyrins with peroxynitrite and carbonate radical anion.
- Redox properties of human transferrin bound to its receptor.
- Refined solution structure of the LpxC-TU-514 complex and pKa analysis of an active site histidine: insights into the mechanism and inhibitor design.
- Reinterpretation of GCN4-p1 folding kinetics: partial helix formation precedes dimerization in coiled coil folding.
- Relaxation spectra of adenosine triphosphate-creatine phosphotransferase.
- Relaxation spectra of aspartate transcarbamylase. I. Interaction of 5-bromocytidine triphosphate with native enzyme and regulatory subunit.
- Remodeling Tissue Interfaces and the Thermodynamics of Zipping during Dorsal Closure in Drosophila.
- Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.
- Resonance Raman characterization of biotin sulfoxide reductase. Comparing oxomolybdenum enzymes in the ME(2)SO reductase family.
- Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.
- Ring current effects in adriamycin-flavin mononucleotide complexation as observed by 1H FT NMR spectroscopy.
- Role of membrane curvature in mechanoelectrical transduction: ion carriers nonactin and valinomycin sense changes in integral bending energy.
- SILAC-pulse proteolysis: A mass spectrometry-based method for discovery and cross-validation in proteome-wide studies of ligand binding.
- SUPREX (Stability of Unpurified Proteins from Rates of H/D Exchange) analysis of the thermodynamics of synergistic anion binding by ferric-binding protein (FbpA), a bacterial transferrin.
- Self-interaction-free exchange-correlation functional for thermochemistry and kinetics.
- Sequential quadratic programming method for determining the minimum energy path.
- Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.
- Simulation of electron transfer between cytochrome C2 and the bacterial photosynthetic reaction center: Brownian dynamics analysis of the native proteins and double mutants.
- Six-helix bundle assembly and characterization of heptad repeat regions from the F protein of Newcastle disease virus.
- Slow histidine H/D exchange protocol for thermodynamic analysis of protein folding and stability using mass spectrometry.
- Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis.
- Solution structure of a sweet protein single-chain monellin determined by nuclear magnetic resonance and dynamical simulated annealing calculations.
- Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.
- Sorption of 243Am(III) to multiwall carbon nanotubes.
- Sorting of lipids and transmembrane peptides between detergent-soluble bilayers and detergent-resistant rafts.
- Spectroscopic studies of the molybdenum-containing dimethyl sulfoxide reductase from Rhodobacter sphaeroides f. sp. denitrificans.
- Spontaneous Unfolding-Refolding of Fibronectin Type III Domains Assayed by Thiol Exchange: THERMODYNAMIC STABILITY CORRELATES WITH RATES OF UNFOLDING RATHER THAN FOLDING.
- Stability of Metal-Glutathione Complexes During Oxidation by Hydrogen Peroxide and Cu(II)-Catalysis
- Stability of oxidized Escherichia coli thioredoxin and its dependence on protonation of the aspartic acid residue in the 26 position.
- Stable isotope labeling strategy for protein-ligand binding analysis in multi-component protein mixtures.
- StableIsotope Labeling with Amino Acids in Cell Culture (SILAC)-based strategy for proteome-wide thermodynamic analysis of protein-ligand binding interactions.
- Streptavidin-biotin binding energetics.
- Strong means slow: dynamic contributions to the bulk mechanical properties of supramolecular networks.
- Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex.
- Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters.
- Structural determinants of insert retention of poliovirus expression vectors with recombinant IRES elements.
- Structural origin of the high affinity of a chemically evolved lanthanide-binding peptide.
- Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation.
- Structure and cohesive properties of sphingomyelin/cholesterol bilayers.
- Structure and mechanical properties of giant lipid (DMPC) vesicle bilayers from 20 degrees C below to 10 degrees C above the liquid crystal-crystalline phase transition at 24 degrees C.
- Structure and organization of hexadecanol isomers adsorbed to the air/water interface.
- Structure and phase behavior of lipid suspensions containing phospholipids with covalently attached poly(ethylene glycol).
- Structure and stability of monomeric lambda repressor: NMR evidence for two-state folding.
- Structure-activity relationships of noreperidine congeners on cholinesterase systems in vitro and analgesia in vivo.
- Substrate-dependent activation energy of the reaction catalyzed by monoamine oxidase.
- Sulfate as a synergistic anion facilitating iron binding by the bacterial transferrin FbpA: the origins and effects of anion promiscuity.
- Surface-bound iron: a metal ion buffer in the marine brown alga Ectocarpus siliculosus?
- Swelling and mechanical behaviors of chemically cross-linked hydrogels of elastin-like polypeptides.
- Synthesis and characterization of carbohydrate-based phospholipids.
- Synthesis, structure, and thermal properties of 1,2-dipalmitoylgalloylglycerol (DPGG), a novel self-adhering lipid.
- Temperature dependence of the repulsive pressure between phosphatidylcholine bilayers.
- Tension-stabilized pores in giant vesicles: determination of pore size and pore line tension.
- Tensions and free energies of formation of "solventless" lipid bilayers. Measurement of high contact angles.
- Ternary complex formation facilitates a redox mechanism for iron release from a siderophore.
- The 1.2 A structure of the human sulfite oxidase cytochrome b(5) domain.
- The cluster glycoside effect.
- The constructal law of design and evolution in nature.
- The constructal law of organization in nature: tree-shaped flows and body size.
- The crystal structure of the collagen-like polypeptide (glycyl-4(R)-hydroxyprolyl-4(R)-hydroxyprolyl)9 at 1.55 A resolution shows up-puckering of the proline ring in the Xaa position.
- The effects of lipid composition on the binding of lasalocid A to small unilamellar vesicles.
- The energetic contribution of backbone--backbone hydrogen bonds to the thermodynamic stability of a hyperstable P22 Arc repressor mutant.
- The energetics of binding of a signal peptide to lipid bilayers: the role of bilayer properties.
- The energy landscape of a fast-folding protein mapped by Ala-->Gly substitutions.
- The evolution of control and distribution of adaptive mutations in a metabolic pathway
- The extra fragment of the iron-sulfur protein (residues 96-107) of Rhodobacter sphaeroides cytochrome bc1 complex is required for protein stability.
- The failing heart utilizes 3-hydroxybutyrate as a metabolic stress defense.
- The hydrophobic core of Escherichia coli thioredoxin shows a high tolerance to nonconservative single amino acid substitutions.
- The materials engineering of temperature-sensitive liposomes.
- The nature of aqueous tunneling pathways between electron-transfer proteins.
- The organization of n-alkanes in lipid bilayers.
- The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment.
- The relationship between ligand-binding thermodynamics and protein-ligand interaction forces measured by atomic force microscopy.
- The role of subunit entropy in cooperative assembly. Nucleation of microtubules and other two-dimensional polymers.
- The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble.
- The temperature-dependent reaction between alpha 2-macroglobulin and streptokinase-plasmin(ogen) complex.
- Thermodynamic Analysis of the Geldanamycin-Hsp90 Interaction in a Whole Cell Lysate Using a Mass Spectrometry-Based Proteomics Approach.
- Thermodynamic Analysis of the Uptake of a Protein in a Spherical Polyelectrolyte Brush.
- Thermodynamic analysis of a hydrophobic binding site: probing the PDZ domain with nonproteinogenic peptide ligands.
- Thermodynamic analysis of a molecular chaperone binding to unfolded protein substrates.
- Thermodynamic analysis of cyclosporin a binding to cyclophilin a in a lung tumor tissue lysate.
- Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes.
- Thermodynamic analysis of protein folding and stability using a tryptophan modification protocol.
- Thermodynamic analysis of protein stability and ligand binding using a chemical modification- and mass spectrometry-based strategy.
- Thermodynamic analysis of protein-ligand binding interactions in complex biological mixtures using the stability of proteins from rates of oxidation.
- Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach.
- Thermodynamic analysis of subunit interactions in Escherichia coli molybdopterin synthase.
- Thermodynamic and kinetic aspects of assembly.
- Thermodynamic characterization of the binding interaction between the histone demethylase LSD1/KDM1 and CoREST.
- Thermodynamic characterization of the osmolyte- and ligand-folded states of Bacillus subtilis ribonuclease P protein.
- Thermodynamic constraints on the regulation of metabolic fluxes.
- Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns.
- Thermodynamic effects of reduction of the active-site disulfide of Escherichia coli thioredoxin explored by differential scanning calorimetry.
- Thermodynamic evaluation of binding interactions in the methionine repressor system of Escherichia coli using isothermal titration calorimetry.
- Thermodynamic limits to the ATP/site stoichiometries of oxidative phosphorylation by rat liver mitochondria.
- Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences.
- Thermodynamic parameters of the alpha-methyl aspartate-aspartate aminotransferase interaction.
- Thermodynamic profiling of conformationally constrained cyclic ligands for the PDZ domain.
- Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based method.
- Thermodynamics of DNA hybridization on gold nanoparticles.
- Thermodynamics of RNA melting, one base pair at a time.
- Thermodynamics of metal ion binding. 1. Metal ion binding by wild-type carbonic anhydrase.
- Thermodynamics of metal ion binding. 2. Metal ion binding by carbonic anhydrase variants.
- Thermodynamics of oxidation-reduction reactions in mammalian nitric-oxide synthase isoforms.
- Thermodynamics of pyridine coordination in 1,4-phenylene bridged bimetallic (Pd, Pt) complexes containing two N,C,N' motifs, 1,4-M2-[C6(CH2NR2)4-2,3,5,6].
- Thermodynamics of reactions catalyzed by PABA synthase.
- Thermodynamics, kinetics, and mechanism of the stepwise dissociation and formation of Tris(L-lysinehydroxamato)iron(III) in aqueous acid.
- Thermomechanical and transition properties of dimyristoylphosphatidylcholine/cholesterol bilayers.
- Thermopower of molecular junctions: an ab initio study.
- Thiol regulation by Mn porphyrins, commonly known as SOD mimics.
- Three Pyrimidine Decarboxylations in the Absence of a Catalyst.
- Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.
- Total chemical synthesis of the B1 domain of protein L from Peptostreptococcus magnus.
- Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network.
- Transient Hoogsteen base pairs in canonical duplex DNA.
- Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method.
- Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead.
- Twist propagation in dinucleosome arrays.
- Two-Electron Transfer Pathways.
- Type III protein secretion in plant pathogenic bacteria.
- Ultrafast excited-state dynamics of nanoscale near-infrared emissive polymersomes.
- Ultrasonic dispersion of nanoparticles for environmental, health and safety assessment--issues and recommendations.
- Ultrasound-heated photoacoustic flowmetry.
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.
- Use of phosphorus ligand NMR probes to investigate electronic and second-sphere solvent effects in ligand substitution reactions at manganese(II) and manganese(III).
- Using DNA duplex stability information for transcription factor binding site discovery.
- Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays.
- Using secondary structure to identify ribosomal numts: cautionary examples from the human genome.
- Valency-dependent affinity of bioactive hydroxyapatite-binding dendrons.
- Very long transients, irregular firing, and chaotic dynamics in networks of randomly connected inhibitory integrate-and-fire neurons.
- Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.
- Water adsorption at two unsolvated peptides with a protonated lysine residue: from self-solvation to solvation.
- Water exchange rates of water-soluble manganese(III) porphyrins of therapeutical potential.
- What is biased efficacy? Defining the relationship between intrinsic efficacy and free energy coupling.
- Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?
- Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.
- beta-Sheet topology and the relatedness of proteins.
- iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.
Keywords of People
- Bennett, Vann, George Barth Geller Distinguished Professor of Molecular Biology, Duke Cancer Institute
- Charles, Hal Cecil, Adjunct Associate Professor in the Department of Radiology, Radiology
- Erickson, Harold Paul, James B. Duke Distinguished Professor Emeritus, Cell Biology
- Gordan, Raluca Mihaela, Associate Professor in Biostatistics & Bioinformatics, Computer Science
- Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
- Hsu-Kim, Heileen, Professor in the Department of Civil and Environmental Engineering, Civil and Environmental Engineering
- Oas, Terrence Gilbert, Professor of Biochemistry, Biochemistry
- Patz Jr., Edward F., James and Alice Chen Distinguished Professor of Radiology, Pathology
- Sullivan, Daniel Carl, Professor Emeritus of Radiology, Radiology
- Twiss, Robert, Adjunct Associate Professor in the Thomas Lord Department of Mechanical Engineering and Materials Science, Thomas Lord Department of Mechanical Engineering and Materials Science
- Vengosh, Avner, Nicholas Distinguished Professor of Environmental Quality, Nicholas Institute-Energy Initiative