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Subject Areas on Research
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(Aryloxy)aryl semicarbazones and related compounds: a novel class of anticonvulsant agents possessing high activity in the maximal electroshock screen.
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A historical account of Hoogsteen base-pairs in duplex DNA.
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A new generation of crystallographic validation tools for the protein data bank.
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A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA.
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A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions.
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A structural pathway for signaling in the E46Q mutant of photoactive yellow protein.
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Adhesion between cerebroside bilayers.
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Alignment of the HTLV-I Rex peptide bound to its target RNA aptamer from magnetic field-induced residual dipolar couplings and intermolecular hydrogen bonds.
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Alternate states of proteins revealed by detailed energy landscape mapping.
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Amino acid preferences for specific locations at the ends of alpha helices.
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An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity.
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An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants.
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An estimate to the first approximation of microtubule rupture force.
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Analysis of hydrogen-bond interaction potentials from the electron density: Integration of noncovalent interaction regions.
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Analysis of protein folding and function using backbone modified proteins.
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Area per molecule and distribution of water in fully hydrated dilauroylphosphatidylethanolamine bilayers.
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Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization.
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Assignment of aliphatic side-chain 1HN/15N resonances in perdeuterated proteins.
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Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.
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Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation.
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Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
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Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein.
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Biomimetic materials: marine inspiration.
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Calmodulin structure refined at 1.7 A resolution.
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Charged fullerenes as high-capacity hydrogen storage media.
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Choline Acetyltransferase Mutations Causing Congenital Myasthenic Syndrome: Molecular Findings and Genotype-Phenotype Correlations.
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Clustering gene expression time series data using an infinite Gaussian process mixture model.
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Comparative analysis of two different amide-to-ester bond mutations in the beta-sheet of 4-oxalocrotonate tautomerase.
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Computational Methods for RNA Structure Validation and Improvement.
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Computational design of a biologically active enzyme.
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Computational design of receptor and sensor proteins with novel functions.
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Consensus and variant cAMP-regulated enhancers have distinct CREB-binding properties.
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Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.
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Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold.
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Contribution of a buried hydrogen bond to lambda repressor folding kinetics.
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Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage.
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Coupling coherence distinguishes structure sensitivity in protein electron transfer.
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Crystal and molecular structures of ionophore-siderophore host-guest supramolecular assemblies relevant to molecular recognition.
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Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).
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Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices.
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Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
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Crystal structure of human type III collagen Gly991-Gly1032 cystine knot-containing peptide shows both 7/2 and 10/3 triple helical symmetries.
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Crystal structure of the human LRH-1 DBD-DNA complex reveals Ftz-F1 domain positioning is required for receptor activity.
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Crystal structure of the lactose operon repressor and its complexes with DNA and inducer.
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Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding.
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Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding.
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Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani.
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DNA base modification: ionized base pairs and mutagenesis.
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Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.
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Diarylaniline derivatives as a distinct class of HIV-1 non-nucleoside reverse transcriptase inhibitors.
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Different structural changes occur in blue- and green-proteorhodopsins during the primary photoreaction.
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Direct analysis of backbone-backbone hydrogen bond formation in protein folding transition states.
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Direct detection of inter-residue hydrogen bonds in polysaccharides by single-molecule force spectroscopy.
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Direct evaluation of electronic coupling mediated by hydrogen bonds: implications for biological electron transfer.
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Direct evidence for (G)O6···H2-N4(C)+ hydrogen bonding in transient G(syn)-C+ and G(syn)-m5C+ Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R1ρ relaxation dispersion measurements.
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Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9.
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Direct force measurements of the streptavidin-biotin interaction.
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Dissection of the protein G B1 domain binding site for human IgG Fc fragment.
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Emergent mechanical properties of self-assembled polymeric capsules.
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Evidence against formation of A23187 dimers and oligomers in solution: photo-induced degradation of Ionophore A23187.
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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.
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Extreme differences between hemoglobins I and II of the clam Lucina pectinalis in their reactions with nitrite.
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Fabrication of patterned polymer brushes on chemically active surfaces by in situ hydrogen-bond-mediated attachment of an initiator.
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Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation.
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Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.
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Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein.
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Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair.
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Guest exchange in an encapsulation complex: a supramolecular substitution reaction.
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How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?
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How cations change peptide structure.
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Hydration properties of lamellar and non-lamellar phases of phosphatidylcholine and phosphatidylethanolamine.
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Hydrogen bonding of beta-turn structure is stabilized in D(2)O.
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Identification of a high-affinity RNA-binding site for the human immunodeficiency virus type 1 Rev protein.
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Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.
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Inhibition of thermolysin by phosphonamidate transition-state analogues: measurement of 31P-15N bond lengths and chemical shifts in two enzyme-inhibitor complexes by solid-state nuclear magnetic resonance.
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Insights into the nature of DNA binding of AbrB-like transcription factors.
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Intrinsically disordered proteins access a range of hysteretic phase separation behaviors.
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Isomer-Selective Detection of Hydrogen-Bond Vibrations in the Protonated Water Hexamer
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MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.
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Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis.
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Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering.
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Mechanical unfolding intermediates in titin modules.
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Mechanism of corepressor-mediated specific DNA binding by the purine repressor.
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Methyl-directed DNA mismatch correction.
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Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs.
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Mismodeled purines: implicit alternates and hidden Hoogsteens.
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Modulating unimolecular charge transfer by exciting bridge vibrations.
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Modulation of Hoogsteen dynamics on DNA recognition.
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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
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Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.
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Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by (R)-muscone and diverse other musk-smelling compounds.
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NMR structure of activated CheY.
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Native like helices in a specially designed β peptide in the gas phase.
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Optical rotation of noncovalent aggregates.
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Origin of overstretching transitions in single-stranded nucleic acids.
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Pervasive conformational fluctuations on microsecond time scales in a fibronectin type III domain.
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Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion.
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Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein.
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Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution.
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Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex.
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Protonated base pairs explain the ambiguous pairing properties of O6-methylguanine.
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Rapid self-healing hydrogels.
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Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.
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Revealing noncovalent interactions.
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Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA.
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Secondary structure creates mismatched base pairs required for high-affinity binding of cAMP response element-binding protein to the human enkephalin enhancer.
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Self-assembly of ordered nanowires in biological suspensions of single-wall carbon nanotubes.
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Seven-base-pair inverted repeats in DNA form stable hairpins in vivo in Saccharomyces cerevisiae.
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Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3.
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Stereochemical recognition of doubly functional aminotransferase in 2-deoxystreptamine biosynthesis.
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Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold.
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Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.
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Structural basis of pilus subunit recognition by the PapD chaperone.
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Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry.
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Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
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Structural insights into the calcium-dependent interaction between calbindin-D28K and caspase-3.
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Structural mechanisms of QacR induction and multidrug recognition.
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Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
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Structure of gamma-chymotrypsin in the range pH 2.0 to pH 10.5 suggests that gamma-chymotrypsin is a covalent acyl-enzyme adduct at low pH.
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Structure, binding interface and hydrophobic transitions of Ca2+-loaded calbindin-D(28K).
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Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein.
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Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions.
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Synthesis, structure, and thermal properties of 1,2-dipalmitoylgalloylglycerol (DPGG), a novel self-adhering lipid.
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Template-based docking of a prolactin receptor proline-rich motif octapeptide to FKBP12: implications for cytokine receptor signaling.
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The SARS-CoV-2 Spike variant D614G favors an open conformational state.
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The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex.
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The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.
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The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog.
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The beta bulge: a common small unit of nonrepetitive protein structure.
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The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites.
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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.
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The effect of hydrogen bonding on the diffusion of water in n-alkanes and n-alcohols measured with a novel single microdroplet method.
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The effects of lipid composition on the binding of lasalocid A to small unilamellar vesicles.
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The energetic contribution of backbone--backbone hydrogen bonds to the thermodynamic stability of a hyperstable P22 Arc repressor mutant.
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The mechanical stability of ubiquitin is linkage dependent.
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The molecular basis for ligand specificity in a mouse olfactory receptor: a network of functionally important residues.
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The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.
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The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment.
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The structural basis for the selectivity of benzotriazole inhibitors of PTP1B.
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The structure of a CREB bZIP.somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding.
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The three-dimensional structure of H-2Db at 2.4 A resolution: implications for antigen-determinant selection.
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The tyrosine corner: a feature of most Greek key beta-barrel proteins.
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Thermodynamics of metal ion binding. 2. Metal ion binding by carbonic anhydrase variants.
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Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings.
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Transient Hoogsteen base pairs in canonical duplex DNA.
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Tuning the mechanical properties of graphene oxide paper and its associated polymer nanocomposites by controlling cooperative intersheet hydrogen bonding.
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Two crystal polymorphs of a flavonoid from Melicope ellyrana.
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Ultra-Tough Elastomers from Stereochemistry-Directed Hydrogen Bonding in Isosorbide-Based Polymers.
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Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays.
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Unraveling the stability of polypeptide helices: critical role of van der Waals interactions
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Validation challenge of density-functional theory for peptides-example of Ac-Phe-Ala5-LysH(+).
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Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.
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Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.
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Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.
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Water adsorption at two unsolvated peptides with a protonated lysine residue: from self-solvation to solvation.
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Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.
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Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?
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Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.
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X-ray crystallographic studies of streptavidin mutants binding to biotin.
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m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs.
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Keywords of People