Ab initio models for receptor–ligand interactions in proteins. Part 1. Models for asparagine, glutamine, serine, threonine and tyrosine

J, Lindroos; Peräkylä, Mikael; Björkroth, Jussi-Pekka; Pakkanen, Tapani A.

doi:10.1039/p29920002271

Cited by 6 publications

(4 citation statements)

References 43 publications

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“…Quantum mechanics calculations provide much more detailed information about the preferred geometries of hydrogen bonds. However, their use is restricted to small molecules owing to the large computational resources required; other types of model must be used to predict the hydrogen-bonding properties of large and even medium-sized drug molecules [12]. A statistical examination of the hydrogen bonds occurring in crystals provides an unambiguous method for deriving information about hydrogen-bond directionality and strength.…”

Section: Introductionmentioning

confidence: 99%

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Mills

Dean

1996

J Computer-Aided Mol Des

249

222

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An extensive crystal survey of the Cambridge Structural Database has been carried out to provide hydrogen-bond data for use in drug-design strategies. Previous crystal surveys have generated 1D frequency distributions of hydrogen-bond distances and angles, which are not sufficient to model the hydrogen bond as a ligand-receptor interaction. For each hydrogen-bonding group of interest to the drug designer, geometric hydrogen-bond criteria have been derived. The 3D distribution of complementary atoms about each hydrogen-bonding group has been ascertained by dividing the space about each group into bins of equal volume and counting the number of observed hydrogen-bonding contacts in each bin. Finally, the propensity of each group to form a hydrogen bond has been calculated. Together, these data can be used to predict the potential site points with which a ligand could interact and therefore could be used in molecular-similarity studies, pharmacophore query searching of databases, or de novo design algorithms.

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Section: Introductionmentioning

confidence: 99%

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Mills

Dean

1996

J Computer-Aided Mol Des

249

222

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“…The (Mulliken) partial charge on oxygen of phenol is -0.750 and that is almost equal to ethanol and higher than H2O. 58 The Mulliken partial charges on (-O-H) group of benzoic acid is -0.66 which is slightly higher than oxygen of water. 59 After the H-bond formation between (-O-H) group of GO functional group and with (-O-H) group of ethanol, core of ethanol will be outside ( Figure 1c groups on GO surface will get protonated by the solvent and the resultant pH of the colloid will increase.…”

Section: Resultsmentioning

confidence: 89%

“…Herein, the (Mulliken) partial charge on ethanol oxygen (-0.787) is larger than that of (Mulliken) partial charge on oxygen (-0.634) of water. [57][58] This charge difference will force the ethanol to get polymerize by H-bonding, preferentially among ethanol molecules rather than the H-bonding between water and ethanol. This way ethanol polymer (C2H5OH)n, creates a hydrophobic core, the outer surface of which will partialy experience H-bonded with water.…”

Section: Resultsmentioning

confidence: 99%

Solvent transfer of graphene oxide for synthesis of tin mono-sulfide graphene composite and application as anode of lithium-ion battery

Tripathi

Mitra

2016

Materials Science and Engineering: B

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Tin mono sulfide (SnS) graphene composite has been synthesized for anode of lithium-ion battery. For synthesis of composite, graphene oxide (GO)-water (H2O) colloid has been destabilized and ensured the complete transfer of graphene oxide into another organic solvent N, N-dimethyl formamide (DMF). Mechanism for the destabilization of GO-H2O colloid is established. Surface to surface attachment of SnS on graphene sheet is achieved by solvothermal solution phase assembly of graphene sheets and SnS nanoparticles in DMF solvent. Graphene plays role in nanoparticle formation in composite. Such confined composite has been cycled reversibly at current rate of 160 mA g-1 , in voltage region of 0.01 V-2.5 V and exhibit a superior discharge capacity of 630 mAh g-1 after 50 th cycle. Ex-situ TEM analysis of used electrode reveal that the SnS nanoparticle-graphene composite with CMC binder perform better due to proper shape retention of electroactive materials during electrochemical cycling.

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“…probably tyrosine 201, is ionized (pfca = 1.1-1.9).32 Furthermore, the mutant Tyr-201 -Phe was found to have only 6% of the catalytic activity of the wild-type enzyme and to lack the ionization of the substrate. The aim of the present ab initio model assembly study is to investigate the proton transfer from the 4-OH site of the ligand to the ionized Tyr-201 in the complexes of PHBH with substrate p-OHB (1,2), with 3-OH radical adducts (5,6) and 8) of the substrate (these adducts being possible structures of p-OHB in the intermediate II) and with product 3,4-DOHB (3,4). To shed light on the mechanism of the hydroxylation, the calculated energetics of the proton-transfer reactions are compared with the experimental results.…”

Section: Introductionmentioning

confidence: 99%

Ab initio models for receptor-ligand interactions in proteins. 3. Model assembly study of the proton transfer in the hydroxylation step of the catalytic mechanism of p-hydroxybenzoate hydroxylase

Peräkylä¹,

Pakkanen²

1993

J. Am. Chem. Soc.

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Proton transfer in the hydroxylation step of the catalytic mechanism of p-hydroxybenzoate hydroxylase was investigated using the ab initio model assembly approach. In the hydroxylation step the hydroxy group is introduced at the ortho position ofp-hydroxybenzoate. The calculations showed, in accordance with the experimental observations, that ionization of the p-hydroxybenzoate is energetically feasible. The role of individual amino acid residues forming hydrogen bonds with the ligand was investigated energetically, and the residues were calculated to stabilize the ionized form of p-hydroxybenzoate. The calculations also supported the conclusion that the intermediate in the hydroxylation is the radical O H adduct of p-hydroxybenzoate.

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Ab initio models for receptor–ligand interactions in proteins. Part 1. Models for asparagine, glutamine, serine, threonine and tyrosine

Cited by 6 publications

References 43 publications

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Solvent transfer of graphene oxide for synthesis of tin mono-sulfide graphene composite and application as anode of lithium-ion battery

Ab initio models for receptor-ligand interactions in proteins. 3. Model assembly study of the proton transfer in the hydroxylation step of the catalytic mechanism of p-hydroxybenzoate hydroxylase

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