Multiple Hydrogen Bonds (multiple + hydrogen_bond)

Distribution by Scientific Domains


Selected Abstracts


WATGEN: An algorithm for modeling water networks at protein,protein interfaces

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2007
Huynh-Hoa Bui
Abstract Water molecules at protein,protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein,protein or protein,peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein,peptide interfaces (X-ray resolutions , 2.0 ), using different criteria for water placement. The energies of the predicted water networks were evaluated in AMBER8 and used in the choice of parameters for WATGEN. The 126 interfaces include 1264 experimentally determined bridging water sites, and the WATGEN algorithm predicts 72 and 88% of these sites within 1.5 and 2.0 , respectively. The predicted number of water molecules at each interface was much higher than the number of water molecules identified experimentally. Therefore, random placement of the same number of water molecules as that predicted at each interface was performed as a control, and resulted in only 22 and 40% of water sites placed within 1.5 and 2.0 of experimental sites, respectively. Based on these data, we conclude that WATGEN can accurately predict the location of water molecules at a protein,peptide interface, and this may be of value for understanding the energetics and specificity of biomolecular association. 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source]


2-Amino-4-(piperidin-1-yl)-11H -pyrimido[4,5- b][1,5]benzodiazepin-6-ium chloride monohydrate and 2-amino-4-[methyl(2-methylphenyl)amino]-11H -pyrimido[4,5- b][1,5]benzodiazepin-6-ium chloride,benzene-1,2-diamine (1/1): complex sheets generated by multiple hydrogen bonds

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010
Jairo Quiroga
In each of 2-amino-4-(piperidin-1-yl)-11H -pyrimido[4,5- b][1,5]benzodiazepin-6-ium chloride monohydrate, C16H19N6+Cl,H2O, (I), and 2-amino-4-[methyl(2-methylphenyl)amino]-11H -pyrimido[4,5- b][1,5]benzodiazepin-6-ium chloride,benzene-1,2-diamine (1/1), C19H19N6+Cl,C6H8N2, (II), the seven-membered ring in the cation adopts a boat conformation. The pyrimidine ring in (II) adopts a twist-boat conformation, but the corresponding ring in (I) is essentially planar. The amino groups of the benzene-1,2-diamine component of (II) are both pyramidal. The independent components of (I) are linked into complex sheets by a combination of N,H...O, N,H...N, N,H...Cl and O,H...Cl hydrogen bonds. In the crystal structure of (II), one N,H...N hydrogen bond and six independent N,H...Cl hydrogen bonds combine to link the components into complex sheets. [source]


Structures of the PKC-, kinase domain in its ATP-bound and apo forms reveal defined structures of residues 533,551 in the C-terminal tail and their roles in ATP binding

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010
Tetsuo Takimura
Protein kinase C (PKC) plays an essential role in a wide range of cellular functions. Although crystal structures of the PKC-,, PKC-, and PKC-,II kinase domains have previously been determined in complexes with small-molecule inhibitors, no structure of a PKC,substrate complex has been determined. In the previously determined PKC-, complex, residues 533,551 in the C-terminal tail were disordered. In the present study, crystal structures of the PKC-, kinase domain in its ATP-bound and apo forms were determined at 2.1 and 2.0, resolution, respectively. In the ATP complex, the electron density of all of the C-terminal tail residues was well defined. In the structure, the side chain of Phe543 protrudes into the ATP-binding pocket to make van der Waals interactions with the adenine moiety of ATP; this is also observed in other AGC kinase structures such as binary and ternary substrate complexes of PKA and AKT. In addition to this interaction, the newly defined residues around the turn motif make multiple hydrogen bonds to glycine-rich-loop residues. These interactions reduce the flexibility of the glycine-rich loop, which is organized for ATP binding, and the resulting structure promotes an ATP conformation that is suitable for the subsequent phosphoryl transfer. In the case of the apo form, the structure and interaction mode of the C-terminal tail of PKC-, are essentially identical to those of the ATP complex. These results indicate that the protein structure is pre-organized before substrate binding to PKC-,, which is different from the case of the prototypical AGC-branch kinase PKA. [source]


Conformational Stability of Bovine Serum Albumin in Aqueous Amides: A Further Insight into the Mechanism of Urea Acting on the Protein

CHINESE JOURNAL OF CHEMISTRY, Issue 6 2010
Lin Ma
Abstract The binding distances of fluorescein to bovine serum albumin (BSA) in formamide-water and N,N -dimethyl- formamide-water mixtures were determined by fluorescence quenching method and compared with the values in urea-water mixtures in our previous work. The results, together with the analysis of fluorescence spectra, were utilized to probe the conformational stability of protein in aqueous amides, providing a further insight into the mechanism of urea acting on protein. The spectral properties of BSA showed significant difference in the aqueous solutions of the three kinds of amide and indicated that both NH2 group and C=O group could form hydrogen bond with the protein, serving as donor and acceptor, respectively. However, the results revealed that the multiple hydrogen bonds of NH2 group with back bond and hydrophilic side chains of the protein played a key role in the nonspecific urea-mediated network of intramolecular interaction due to its higher hydrogen bonding capability compared to C=O group. [source]


Synthesis and Characterization of Three Diverse Coordination Frameworks under Co-ligand Intervention

CHINESE JOURNAL OF CHEMISTRY, Issue 2 2009
Ping LIU
Abstract The chelating organic ligands of 2,2,-bipyridine (2,2,-bipy), di(pyrid-2-yl)amine (dpa) and 2,6-di(pyrid-2-ylamino)pyridine (dpap) were respectively applied to react with H2fum (fumaric acid) and copper salts, affording three different complexes [Cu2(fum)(2,2,-bipy)4]2ClO4 (1), [Cu2(-OH)2(fum)(dpa)2]2H2O (2) and [Cu(SO4)(H2O)(dpap)]H2O (3). These complexes were determined by single-crystal X-ray diffraction. Each penta-coordinated Cu(II) ion exhibits a distorted trigonal bipyramidal geometry in 1. The fum ligand links copper ions to form a dinuclear copper unit. While in 2, the fum ligands connect [Cu2(-OH)2(dpa)2] unit to construct a 1D zigzag chain. Unexpectedly, when dpap instead of dpa was used under the same conditions, only one mononuclear complex 3 was formed. Crystal packings show that 1,3 form 3D supramolecular architectures through non-covalent interactions (multiple hydrogen bonds and C,H ,/,-, interactions). In addition, the study of the magnetic property reveals dominating ferromagnetic interactions between Cu(II) atoms in 1. [source]