Thermodynamics

• 

  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 cucurbit[7]uril. 
  • 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