Hydrogen Bonding

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  Subject Areas on Research

  • (Aryloxy)aryl semicarbazones and related compounds: a novel class of anticonvulsant agents possessing high activity in the maximal electroshock screen. 
  • A historical account of Hoogsteen base-pairs in duplex DNA. 
  • A new generation of crystallographic validation tools for the protein data bank. 
  • A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. 
  • A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. 
  • A structural pathway for signaling in the E46Q mutant of photoactive yellow protein. 
  • Adhesion between cerebroside bilayers. 
  • Alignment of the HTLV-I Rex peptide bound to its target RNA aptamer from magnetic field-induced residual dipolar couplings and intermolecular hydrogen bonds. 
  • Alternate states of proteins revealed by detailed energy landscape mapping. 
  • Amino acid preferences for specific locations at the ends of alpha helices. 
  • An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity. 
  • An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. 
  • An estimate to the first approximation of microtubule rupture force. 
  • Analysis of hydrogen-bond interaction potentials from the electron density: Integration of noncovalent interaction regions. 
  • Analysis of protein folding and function using backbone modified proteins. 
  • Area per molecule and distribution of water in fully hydrated dilauroylphosphatidylethanolamine bilayers. 
  • Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization. 
  • Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. 
  • Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation. 
  • Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. 
  • Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein. 
  • Biomimetic materials: marine inspiration. 
  • Calmodulin structure refined at 1.7 A resolution. 
  • Cell permeable fluorescent receptor for detection of H2PO4(-) in aqueous solvent. 
  • Charged fullerenes as high-capacity hydrogen storage media. 
  • Choline Acetyltransferase Mutations Causing Congenital Myasthenic Syndrome: Molecular Findings and Genotype-Phenotype Correlations. 
  • Clustering gene expression time series data using an infinite Gaussian process mixture model. 
  • Comparative analysis of two different amide-to-ester bond mutations in the beta-sheet of 4-oxalocrotonate tautomerase. 
  • Computational Methods for RNA Structure Validation and Improvement. 
  • Computational design of a biologically active enzyme. 
  • Computational design of receptor and sensor proteins with novel functions. 
  • Consensus and variant cAMP-regulated enhancers have distinct CREB-binding properties. 
  • Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. 
  • Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold. 
  • Contribution of a buried hydrogen bond to lambda repressor folding kinetics. 
  • Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage. 
  • Coupling coherence distinguishes structure sensitivity in protein electron transfer. 
  • Crystal and molecular structures of ionophore-siderophore host-guest supramolecular assemblies relevant to molecular recognition. 
  • Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG). 
  • Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. 
  • Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. 
  • Crystal structure of human type III collagen Gly991-Gly1032 cystine knot-containing peptide shows both 7/2 and 10/3 triple helical symmetries. 
  • Crystal structure of the human LRH-1 DBD-DNA complex reveals Ftz-F1 domain positioning is required for receptor activity. 
  • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. 
  • Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding. 
  • Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding. 
  • Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani. 
  • DNA base modification: ionized base pairs and mutagenesis. 
  • Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. 
  • Diarylaniline derivatives as a distinct class of HIV-1 non-nucleoside reverse transcriptase inhibitors. 
  • Different structural changes occur in blue- and green-proteorhodopsins during the primary photoreaction. 
  • Direct analysis of backbone-backbone hydrogen bond formation in protein folding transition states. 
  • Direct detection of inter-residue hydrogen bonds in polysaccharides by single-molecule force spectroscopy. 
  • Direct evaluation of electronic coupling mediated by hydrogen bonds: implications for biological electron transfer. 
  • 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. 
  • Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. 
  • Direct force measurements of the streptavidin-biotin interaction. 
  • Dissection of the protein G B1 domain binding site for human IgG Fc fragment. 
  • Emergent mechanical properties of self-assembled polymeric capsules. 
  • Evidence against formation of A23187 dimers and oligomers in solution: photo-induced degradation of Ionophore A23187. 
  • 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. 
  • Extreme differences between hemoglobins I and II of the clam Lucina pectinalis in their reactions with nitrite. 
  • Fabrication of patterned polymer brushes on chemically active surfaces by in situ hydrogen-bond-mediated attachment of an initiator. 
  • 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. 
  • Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. 
  • Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair. 
  • Guest exchange in an encapsulation complex: a supramolecular substitution reaction. 
  • How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts? 
  • How cations change peptide structure. 
  • Hydration properties of lamellar and non-lamellar phases of phosphatidylcholine and phosphatidylethanolamine. 
  • Hydrogen bonding of beta-turn structure is stabilized in D(2)O. 
  • Identification of a high-affinity RNA-binding site for the human immunodeficiency virus type 1 Rev protein. 
  • Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. 
  • 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. 
  • Intrinsically disordered proteins access a range of hysteretic phase separation behaviors. 
  • Isomer-Selective Detection of Hydrogen-Bond Vibrations in the Protonated Water Hexamer 
  • MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. 
  • Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis. 
  • Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. 
  • Mechanical unfolding intermediates in titin modules. 
  • Mechanism of corepressor-mediated specific DNA binding by the purine repressor. 
  • Methyl-directed DNA mismatch correction. 
  • Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs. 
  • Mismodeled purines: implicit alternates and hidden Hoogsteens. 
  • Modulating unimolecular charge transfer by exciting bridge vibrations. 
  • Modulation of Hoogsteen dynamics on DNA recognition. 
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. 
  • Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor. 
  • Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by (R)-muscone and diverse other musk-smelling compounds. 
  • NMR structure of activated CheY. 
  • Native like helices in a specially designed β peptide in the gas phase. 
  • Optical rotation of noncovalent aggregates. 
  • Origin of overstretching transitions in single-stranded nucleic acids. 
  • Pervasive conformational fluctuations on microsecond time scales in a fibronectin type III domain. 
  • Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion. 
  • Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein. 
  • Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution. 
  • Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex. 
  • Protonated base pairs explain the ambiguous pairing properties of O6-methylguanine. 
  • Rapid self-healing hydrogels. 
  • Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. 
  • Revealing noncovalent interactions. 
  • Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA. 
  • Secondary structure creates mismatched base pairs required for high-affinity binding of cAMP response element-binding protein to the human enkephalin enhancer. 
  • Self-assembly of ordered nanowires in biological suspensions of single-wall carbon nanotubes. 
  • Seven-base-pair inverted repeats in DNA form stable hairpins in vivo in Saccharomyces cerevisiae. 
  • Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3. 
  • Stereochemical recognition of doubly functional aminotransferase in 2-deoxystreptamine biosynthesis. 
  • 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. 
  • Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. 
  • Structural basis of pilus subunit recognition by the PapD chaperone. 
  • Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. 
  • Structural mechanisms of QacR induction and multidrug recognition. 
  • Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. 
  • 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. 
  • Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein. 
  • Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions. 
  • Synthesis, structure, and thermal properties of 1,2-dipalmitoylgalloylglycerol (DPGG), a novel self-adhering lipid. 
  • Template-based docking of a prolactin receptor proline-rich motif octapeptide to FKBP12: implications for cytokine receptor signaling. 
  • The SARS-CoV-2 Spike variant D614G favors an open conformational state. 
  • The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex. 
  • 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. 
  • The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog. 
  • The beta bulge: a common small unit of nonrepetitive protein structure. 
  • The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites. 
  • 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 effect of hydrogen bonding on the diffusion of water in n-alkanes and n-alcohols measured with a novel single microdroplet method. 
  • 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 mechanical stability of ubiquitin is linkage dependent. 
  • The molecular basis for ligand specificity in a mouse olfactory receptor: a network of functionally important residues. 
  • The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. 
  • The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment. 
  • The structural basis for the selectivity of benzotriazole inhibitors of PTP1B. 
  • The structure of a CREB bZIP.somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding. 
  • The tyrosine corner: a feature of most Greek key beta-barrel proteins. 
  • Thermodynamics of metal ion binding. 2. Metal ion binding by carbonic anhydrase variants. 
  • Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. 
  • Transient Hoogsteen base pairs in canonical duplex DNA. 
  • 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. 
  • Ultra-Tough Elastomers from Stereochemistry-Directed Hydrogen Bonding in Isosorbide-Based Polymers. 
  • Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. 
  • Unraveling the stability of polypeptide helices: critical role of van der Waals interactions 
  • Validation challenge of density-functional theory for peptides-example of Ac-Phe-Ala5-LysH(+). 
  • Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. 
  • Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. 
  • Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes. 
  • Water adsorption at two unsolvated peptides with a protonated lysine residue: from self-solvation to solvation. 
  • Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase. 
  • 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. 
  • X-ray crystallographic studies of streptavidin mutants binding to biotin. 
  • 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

  • Erickson, Harold Paul, James B. Duke Distinguished Professor of Cell Biology, Cell Biology