Molecular Conformation

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  Subject Areas on Research

  • 1,2,3-Triazole CH...Cl(-) contacts guide anion binding and concomitant folding in 1,4-diaryl triazole oligomers. 
  • A crystal structure of a dimer of the antibiotic ramoplanin illustrates membrane positioning and a potential Lipid II docking interface. 
  • A facile and efficient synthesis of 4-hydroxy-2,6-cis-tetrahydropyrans via tandem cross-metathesis/thermal S(N)2' reaction: protecting-group-free synthesis of (+/-)-diospongin A. 
  • A mutation in TNNC1-encoded cardiac troponin C, TNNC1-A31S, predisposes to hypertrophic cardiomyopathy and ventricular fibrillation. 
  • A new monofluorinated phosphatidylcholine forms interdigitated bilayers. 
  • A novel micropipet method for measuring the bending modulus of vesicle membranes. 
  • A prochelator activated by hydrogen peroxide prevents metal-induced amyloid Beta aggregation. 
  • A solid-liquid composite model of the red cell membrane. 
  • A subtransition in a phospholipid with a net charge, dipalmitoylphosphatidylglycerol. 
  • A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. 
  • Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants. 
  • Additivity and the physical basis of multivalency effects: a thermodynamic investigation of the calcium EDTA interaction. 
  • Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. 
  • Alamethicin-induced changes in lipid bilayer morphology. 
  • Analytic gradients, geometry optimization and excited state potential energy surfaces from the particle-particle random phase approximation. 
  • Anion binding of short, flexible aryl triazole oligomers. 
  • Apolipoprotein C-III/sphingomyelin recombinants: formation, isolation, and characterization. 
  • Application of chemoproteomics to drug discovery: identification of a clinical candidate targeting hsp90. 
  • Aqueous solution speciation of Fe(III) complexes with dihydroxamate siderophores alcaligin and rhodotorulic acid and synthetic analogues using electrospray ionization mass spectrometry. 
  • Area per molecule and distribution of water in fully hydrated dilauroylphosphatidylethanolamine bilayers. 
  • Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. 
  • Assessment of the CFTR and ENaC association. 
  • Association of TP53 mutational status and gender with survival after adjuvant treatment for stage III colon cancer: results of CALGB 89803. 
  • Asymmetric total synthesis of ent-(-)-roseophilin: assignment of absolute configuration. 
  • Atomic contributions to the optical rotation angle as a quantitative probe of molecular chirality. 
  • Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin. 
  • Boranophosphates as mimics of natural phosphodiesters in DNA. 
  • Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes. 
  • Cardiotonic agents. 8. Selective inhibitors of adenosine 3',5'-cyclic phosphate phosphodiesterase III. Elaboration of a five-point model for positive inotropic activity. 
  • Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM. 
  • Characterization and solubilization of pyrrole-imidazole polyamide aggregates. 
  • Chemistry and biology of the molybdenum cofactors. 
  • Chiral action at a distance: remote substituent effects on the optical activity of calyculins A and B. 
  • Classification and 3D averaging with missing wedge correction in biological electron tomography. 
  • Computational design of a biologically active enzyme. 
  • Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging. 
  • Computational studies of small carbon and iron-carbon systems relevant to carbon nanotube growth. 
  • Conformation-assisted inhibition of protein-tyrosine phosphatase-1B elicits inhibitor selectivity over T-cell protein-tyrosine phosphatase. 
  • Conformational mechanics, adsorption, and normal force interactions of lubricin and hyaluronic acid on model surfaces. 
  • Conformational selection or induced fit: a flux description of reaction mechanism. 
  • Constitutive activation of the N-methyl-D-aspartate receptor via cleft-spanning disulfide bonds. 
  • Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs. 
  • Correlated x-ray diffraction and freeze-fracture studies on membrane model systems. Perturbations induced by freeze-fracture preparative procedures. 
  • Cycloisomerization of functionalized 1,5- and 1,6-dienes catalyzed by cationic palladium phenanthroline complexes. 
  • Cytotoxicity and thermomechanical behavior of biomedical shape-memory polymer networks post-sterilization. 
  • Deep UV nano-microstructuring of substrates for surface plasmon resonance imaging. 
  • Design and synthesis of human immunodeficiency virus entry inhibitors: sulfonamide as an isostere for the alpha-ketoamide group. 
  • Design of an Escherichia coli expressed HIV-1 gp120 fragment immunogen that binds to b12 and induces broad and potent neutralizing antibodies. 
  • Design of potent thiophene inhibitors of polo-like kinase 1 with improved solubility and reduced protein binding. 
  • Detecting solvent-driven transitions of poly(A) to double-stranded conformations by atomic force microscopy. 
  • Determination of the depth of bromine atoms in bilayers formed from bromolipid probes. 
  • Determining absolute configuration in flexible molecules: a case study. 
  • Development of a Unified Enantioselective, Convergent Synthetic Approach Toward the Furanobutenolide-Derived Polycyclic Norcembranoid Diterpenes: Asymmetric Formation of the Polycyclic Norditerpenoid Carbocyclic Core by Tandem Annulation Cascade. 
  • Differential coordination demands in Fe versus Mn water-soluble cationic metalloporphyrins translate into remarkably different aqueous redox chemistry and biology. 
  • Direct allosteric regulation between the GAF domain and catalytic domain of photoreceptor phosphodiesterase PDE6. 
  • Direct detection of inter-residue hydrogen bonds in polysaccharides by single-molecule force spectroscopy. 
  • Direct determination of the electron density profile of nerve myelin. 
  • Direct determination of the lamellar structure of peripheral nerve myelin at low resolution (17 A). 
  • Direct determination of the lamellar structure of peripheral nerve myelin at moderate resolution (7A). 
  • Discovery of structurally diverse natural product antagonists of chemokine receptor CXCR3. 
  • Discovery of thiophene inhibitors of polo-like kinase. 
  • Distinct conformations of GPCR-β-arrestin complexes mediate desensitization, signaling, and endocytosis. 
  • Effect of benzyl alcohol on lipid bilayers. A comparisons of bilayer systems. 
  • Effect of sulfur substitution for the noncarbonyl oxygen in hemicholinium-3 and acetyl-seco-hemicholinium-3. Synthesis, biological activity, and structure-toxicity relationships. 
  • Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains. 
  • Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo. 
  • Elasticity, strength, and water permeability of bilayers that contain raft microdomain-forming lipids. 
  • Emergence of limit-periodic order in tiling models. 
  • Enantioselective diene Cyclization/Hydrosilylation catalyzed by optically active palladium bisoxazoline and pyridine-oxazoline complexes. 
  • Enthalpic signature of methonium desolvation revealed in a synthetic host-guest system based on cucurbit[7]uril. 
  • Evidence against formation of A23187 dimers and oligomers in solution: photo-induced degradation of Ionophore A23187. 
  • Extreme electronic modulation of the cofacial porphyrin structural motif. 
  • Fabrication of gold nanowires by electric-field-induced scanning probe lithography and in situ chemical development. 
  • Fabrication of high quality carbon nanotubes with a simple ethanol-assisted arc discharge process. 
  • Fabrication of small diameter few-walled carbon nanotubes with enhanced field emission property. 
  • Fibrin assembly: a comparison of electron microscopic and light scattering results. 
  • Ficoll is not a rigid sphere. 
  • First-Principles Molecular Structure Search with a Genetic Algorithm. 
  • First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. 
  • Flory theorem for structurally asymmetric mixtures. 
  • Fluorinated betulinic acid derivatives and evaluation of their anti-HIV activity. 
  • Force-induced prolyl cis-trans isomerization in elastin-like polypeptides. 
  • Formation of planar bilayer membranes from lipid monolayers. A critique. 
  • Functionalized few-walled carbon nanotubes for mechanical reinforcement of polymeric composites. 
  • Functionalized graphene sheets for polymer nanocomposites. 
  • Heme-copper oxidases use tunneling pathways. 
  • Hemoglobin providence. Functional consequences of two alterations of the 2,3-diphosphoglycerate binding site at position beta 82. 
  • High-affinity inhibitors of dihydrofolate reductase: antimicrobial and anticancer activities of 7,8-dialkyl-1,3-diaminopyrrolo[3,2-f]quinazolines with small molecular size. 
  • Hydration force and bilayer deformation: a reevaluation. 
  • IMDA/aldol strategy for transforming carbohydrates into functionalized trans-decalins. 
  • Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis. 
  • Images of divalent cations in unstained symmetric and asymmetric lipid bilayers. 
  • Improved computer program data for the resolution and fractionation of macromolecules by isokinetic sucrose density gradient sedimentation. 
  • Inhibition of prostate cancer cell growth by second-site androgen receptor antagonists. 
  • Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints. 
  • Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations. 
  • Interactions between charged, uncharged, and zwitterionic bilayers containing phosphatidylglycerol. 
  • Interdigitated hydrocarbon chain packing causes the biphasic transition behavior in lipid/alcohol suspensions. 
  • Interrogating conformationally dependent electron-transfer dynamics via ultrafast visible pump/IR probe spectroscopy. 
  • Iron chelation properties of an extracellular siderophore exochelin MS. 
  • Kinetic and nuclear magnetic resonance study of the interaction of NADP+ and NADPH with chicken liver fatty acid synthase. 
  • Kinetics and mechanism of iron(III) dissociation from the dihydroxamate siderophores alcaligin and rhodotorulic acid. 
  • Letter: Antitumor agents. XIII. Isolation and absolute configuration of carminomycin I from Streptosporangium sp. 
  • Light uncages a copper complex to induce nonapoptotic cell death. 
  • Lipid bilayer ultrastructure. Electron density profiles and chain tilt angles as determined by X-ray diffraction. 
  • Lipopolysaccharide 3-deoxy-D-manno-octulosonic acid (Kdo) core determines bacterial association of secreted toxins. 
  • Magnitude of the solvation pressure depends on dipole potential. 
  • Mechanical equilibrium of thick, hollow, liquid membrane cylinders. 
  • Mechanical unfolding of ubiquitin molecules. 
  • Mechanically induced scission and subsequent thermal remending of perfluorocyclobutane polymers. 
  • Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force. 
  • Mechanistic studies of the cycloisomerization of dimethyl diallylmalonate catalyzed by a cationic palladium phenanthroline complex. 
  • Microtubule surface lattice and subunit structure and observations on reassembly. 
  • Modulation of the interbilayer hydration pressure by the addition of dipoles at the hydrocarbon/water interface. 
  • Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein. 
  • Molecular mechanical properties of short-sequence peptide enzyme mimics. 
  • Monte Carlo simulation and molecular theory of tethered polyelectrolytes. 
  • Morphology of the intermediate stages in the lamellar to hexagonal lipid phase transition. 
  • Multiple ligand-specific conformations of the β2-adrenergic receptor. 
  • Mutagenesis of the phosphate-binding pocket of KDPG aldolase enhances selectivity for hydrophobic substrates. 
  • Mutation of the p53 tumor-suppressor gene is not a feature of endometrial hyperplasias. 
  • Nanopatterned polymer brushes: conformation, fabrication and applications. 
  • Negative-stain electron microscopy of inside-out FtsZ rings reconstituted on artificial membrane tubules show ribbons of protofilaments. 
  • New structural model for mixed-chain phosphatidylcholine bilayers. 
  • Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase. 
  • Nucleic acid binding drugs--XIV. The crystal structure of 1-methyl amsacrine hydrochloride; relationships to DNA-binding ability and anti-tumour activity. 
  • Nucleophilic addition of organozinc reagents to 2-sulfonyl cyclic ethers: stereoselective synthesis of manassantins A and B. 
  • One-pot synthesis of CdTe nanocrystals and shape control of luminescent CdTe-cystine nanocomposites. 
  • Optical rotation of noncovalent aggregates. 
  • Optimizing single-molecule conductivity of conjugated organic oligomers with carbodithioate linkers. 
  • PEGylated gold nanoparticles conjugated to monoclonal F19 antibodies as targeted labeling agents for human pancreatic carcinoma tissue. 
  • Plant antitumor agents. 31. The calycopterones, a new class of biflavonoids with novel cytotoxicity in a diverse panel of human tumor cell lines. 
  • Polymer reversal rate calculated via locally scaled diffusion map. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Purification and chemical characterization of melittin and acetylated derivatives. 
  • 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. 
  • Quantum-dot-decorated robust transductable bioluminescent nanocapsules. 
  • Range and magnitude of the steric pressure between bilayers containing phospholipids with covalently attached poly(ethylene glycol). 
  • Rapid self-healing hydrogels. 
  • Revealing noncovalent interactions. 
  • Right bipyramids of silver: a new shape derived from single twinned seeds. 
  • Roles of bilayer material properties in function and distribution of membrane proteins. 
  • Room temperature purification of few-walled carbon nanotubes with high yield. 
  • Scaffold-mediated symmetry breaking by Cdc42p. 
  • Scaling behavior of nanopatterned polymer brushes. 
  • Segrosome structure revealed by a complex of ParR with centromere DNA. 
  • Signal transduction. Unexpected mediators of protein phosphorylation. 
  • Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method. 
  • Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state. 
  • Single-handed helical wrapping of single-walled carbon nanotubes by chiral, ionic, semiconducting polymers. 
  • Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. 
  • Size-dependence of surface plasmon resonance and oxidation for Pd nanocubes synthesized via a seed etching process. 
  • Sphingolipid metabolism: roles in signal transduction and disruption by fumonisins. 
  • Spin labeled acetylcholine analogs: studies of cholinergic receptor. 
  • Stereoselective synthesis and osteogenic activity of subglutinols A and B. 
  • Stereospecific synthesis, assignment of absolute configuration, and biological activity of the enantiomers of 3-[[[3-[2-(7-chloroquinolin-2-yl)-(E)-ethenyl]phenyl] [[3-(dimethylamino)-3-oxopropyl]thio]methyl]thio]propionic acid, a potent and specific leukotriene D4 receptor antagonist. 
  • Steric repulsion between phosphatidylcholine bilayers. 
  • Stretching single polysaccharides and proteins using atomic force microscopy. 
  • Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport. 
  • Structural and dynamic analysis of residual dipolar coupling data for proteins. 
  • Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling. 
  • Structural and pH dependence of excited state PCET reactions involving reductive quenching of the MLCT excited state of [RuII(bpy)2(bpz)]2+ by hydroquinones. 
  • Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric polymerase (Pol) ζ, and Pol κ. 
  • Structure and dynamics of an extended conjugated NLO chromophore within an amphiphilic 4-helix bundle peptide by molecular dynamics simulation. 
  • Structure and interactive properties of highly fluorinated phospholipid 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 phase behavior of lipid suspensions containing phospholipids with covalently attached poly(ethylene glycol). 
  • Structure of the crystalline bilayer in the subgel phase of dipalmitoylphosphatidylglycerol. 
  • Surface-stress-induced phase transformation in metal nanowires. 
  • Synthesis and anti-HIV activity of bi-functional betulinic acid derivatives. 
  • Synthesis and evaluation of a novel series of 2-chloro-5-((1-methyl-2-(S)-pyrrolidinyl)methoxy)-3-(2-(4-pyridinyl)vinyl)pyridine analogues as potential positron emission tomography imaging agents for nicotinic acetylcholine receptors. 
  • Synthesis and optical properties of silver nanobars and nanorice. 
  • Synthesis and separation of diastereomers of uridine 2',3'-cyclic boranophosphate. 
  • Synthesis of high-density, large-diameter, and aligned single-walled carbon nanotubes by multiple-cycle growth methods. 
  • Synthesis of nucleoside boranophosphoramidate prodrugs conjugated with amino acids. 
  • Synthesis of oxidation-resistant cupronickel nanowires for transparent conducting nanowire networks. 
  • Synthesis of uniform double-walled carbon nanotubes using iron disilicide as catalyst. 
  • Synthetic efforts towards the stereoselective synthesis of NF00659B1. 
  • TSG-6 transfers proteins between glycosaminoglycans via a Ser28-mediated covalent catalytic mechanism. 
  • Temperature dependence of the repulsive pressure between phosphatidylcholine bilayers. 
  • Tensions and free energies of formation of "solventless" lipid bilayers. Measurement of high contact angles. 
  • The active conformation of beta-arrestin1: direct evidence for the phosphate sensor in the N-domain and conformational differences in the active states of beta-arrestins1 and -2. 
  • The effect of ethanol on the phase transition temperature and the phase structure of monounsaturated phosphatidylcholines. 
  • The effect of nanowire length and diameter on the properties of transparent, conducting nanowire films. 
  • The effects of bilayer thickness and tension on gramicidin single-channel lifetime. 
  • The force-driven conformations of heparin studied with single molecule force microscopy. 
  • The interaction of polyphenols with bilayers: conditions for increasing bilayer adhesion. 
  • The kinemage: a tool for scientific communication. 
  • The lamellar structure of nerve myelin after rehydration. 
  • The molecular basis for ligand specificity in a mouse olfactory receptor: a network of functionally important residues. 
  • The molecular mechanisms underlying the pharmacological actions of ER modulators: implications for new drug discovery in breast cancer. 
  • The molecular organization of asymmetric lipid bilayers and lipid-peptide complexes. 
  • The organization of n-alkanes in lipid bilayers. 
  • The penultimate rotamer library. 
  • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. 
  • The question of cholinergic antagonism. 
  • The size and curvature of anionic covesicle substrate affects the catalytic action of cytosolic phospholipase A2. 
  • Thermomechanical and transition properties of dimyristoylphosphatidylcholine/cholesterol bilayers. 
  • Thermopower of molecular junctions: an ab initio study. 
  • Time-resolved investigation of bright visible wavelength luminescence from sulfur-doped ZnO nanowires and micropowders. 
  • Total synthesis of (-)-hennoxazole A. 
  • Toward the development of prochelators as fluorescent probes of copper-mediated oxidative stress. 
  • Towards Raman optical activity calculations of large molecules. 
  • Tris buffer causes acyl chain interdigitation in phosphatidylglycerol. 
  • Tunable nanowire patterning using standing surface acoustic waves. 
  • Tuning the mechanical properties of graphene oxide paper and its associated polymer nanocomposites by controlling cooperative intersheet hydrogen bonding. 
  • Two crystal polymorphs of a flavonoid from Melicope ellyrana. 
  • Two extended structures constructed from sandwich-type polyoxometalates functionalized by organic amines. 
  • Unraveling the stability of polypeptide helices: critical role of van der Waals interactions. 
  • Unusual Synergism of Transferrin and Citrate in the Regulation of Ti(IV) Speciation, Transport, and Toxicity. 
  • Use of pentamethyldisiloxane in the palladium-catalyzed cyclization/hydrosilylation of functionalized dienes. 
  • Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. 
  • Vitamin A in liposomes. Inhibition of complement binding and alteration of membrane structure. 
  • XMAP215 is a long thin molecule that does not increase microtubule stiffness. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
  • Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases. 
  • alpha 1-Microglobulin destroys the proteinase inhibitory activity of alpha 1-inhibitor-3 by complex formation. 
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  Keywords of People

  • Berchuck, Andrew, James M. Ingram Professor of Gynecologic Oncology, Obstetrics and Gynecology, Gynecologic Oncology
  • Charles, Hal Cecil, Associate Professor of Radiology, Radiology
  • Erickson, Harold Paul, James B. Duke Professor of Cell Biology, Biomedical Engineering
  • McDonnell, Donald Patrick, Chair, Department of Pharmacology & Cancer Biology, Duke Innovation & Entrepreneurship
  • Muir, Kelly Walton, Associate Professor of Ophthalmology, Ophthalmology, Glaucoma
  • Oas, Terrence Gilbert, Professor of Biochemistry, Duke Cancer Institute
  • Sullivan, Daniel Carl, Professor Emeritus of Radiology, Radiology