Ion-pairs in proteins

Barlow, D. J.; Thornton, Janet M.

doi:10.1016/s0022-2836(83)80079-5

Cited by 672 publications

(439 citation statements)

References 22 publications

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“…Salt bridges within these geometric ranges are generally stronger interactions than hydrogen bonds. Our identification of such salt bridges follows previous studies [11][12][13] by extending the maximum distance between donor and acceptor to 4.6Å and including all such salt bridges as constraints.…”

Section: Statics Modeling the Forces Within Proteinsmentioning

confidence: 70%

Protein flexibility and dynamics using constraint theory

Thorpe

Lei

Rader

et al. 2001

Journal of Molecular Graphics and Modelling

112

114

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Section: Statics Modeling the Forces Within Proteinsmentioning

confidence: 70%

Protein flexibility and dynamics using constraint theory

Thorpe

Lei

Rader

et al. 2001

Journal of Molecular Graphics and Modelling

112

114

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“…Because the amount of nonpolar surface area calculated in RdPf to be buried upon folding is similar to other proteins of comparable size, AC, associated with hydrophobic effects should also be similar (Livingston et al, 1991). Furthermore, the observation that only approximately two intramolecular salt bridges are present in the different rubredoxins (about that expected for a typical protein the size of rubredoxin) (Barlow & Thornton, 1983) indicates that exposure of charged groups during unfolding will not make a significant contribution to AC,.…”

Section: Acmentioning

confidence: 95%

X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

et al. 1992

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The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100 °C, have been determined by X‐ray crystallography to a resolution of 1.8 å. Crystals of this rubredoxin grow in space group P212121 with room temperature cell dimensions a = 34.6 å, b = 35.5 å, and c = 44.4 å. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X‐PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 å and 2.06°, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 å and in bond angles of 1.95°. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen‐bonding network in the β‐sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino‐terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.

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“…We defined SDS to be in contact with an amino acid if any of SDS atoms were within 4 Å of any amino acid atom, because this distance entails for hydrophobic interactions of the SDS tails as well as salt bridge interactions to the sulphate head-group. 28 This was calculated for every snapshot collected for each of the 12 simulations and the results averaged. From Figure 8 it is evident that SDS is in contact with the two loops (amino acids 64-75 and 160-176) situated on either side of the catalytic triad.…”

Section: Studiesmentioning

confidence: 99%

“…Native HiC was inhibited with diethyl-p-nitrophenyl-phosphate (DNPP: purchased from Sigma) with the aim of preparing a complex with DEP by methods previously established for the Humicola lanuginosa 28,46 and Rhizomucor miehei 47 lipases. The enzyme was washed and concentrated to 30 mg mL 21 and subjected to crystallization screening.…”

Section: Crystallization and X-ray Data Collectionmentioning

confidence: 99%

“…Cutinases (EC 3.1.1.74, Pfam family PF01083) are small (20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30) lipolytic enzymes capable of hydrolyzing a wide variety of esters, including triglycerides of varying size. To date, the threedimensional (3D) structure has been reported for three cutinases, from Fusarium solani (FsC), 1 Glomerella cingulata (GcC), 2,3 and Aspergillus oryzae (AoC).…”

Section: Introductionmentioning

confidence: 99%

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Thermodynamic and structural investigation of the specific SDS binding of humicola insolens cutinase

et al. 2014

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The interaction of lipolytic enzymes with anionic surfactants is of great interest with respect to industrially produced detergents. Here, we report the interaction of cutinase from the thermophilic fungus Humicola insolens with the anionic surfactant SDS, and show the enzyme specifically binds a single SDS molecule under nondenaturing concentrations. Protein interaction with SDS was investigated by NMR, ITC and molecular dynamics simulations. The NMR resonances of the protein were assigned, with large stretches of the protein molecule not showing any detectable resonances. SDS is shown to specifically interact with the loops surrounding the catalytic triad with medium affinity (K a % 10 5 M 21 ). The mode of binding is closely similar to that seen previously for binding of amphiphilic molecules and substrate analogues to cutinases, and hence SDS acts as a substrate mimic. In addition, the structure of the enzyme has been solved by X-ray crystallography in its apo form and after cocrystallization with diethyl p-nitrophenyl phosphate (DNPP) leading to a complex with monoethylphosphate (MEP) esterified to the catalytically active serine. TheAbbreviations: AA, all-atom; AoC, Aspergillus oryzae cutinase; AOT, sodium bis(2-ethylhexyl) sulfosuccinate; cmc, critical micelle concentration; DEP, diethylphosphate; DNPP, diethyl p-nitrophenyl phosphate; EDTA, ethylene diamine tetraacetate; FsC, Fusarium solani cutinase; GcC, Glomerella cingulata cutinase; HiC, Humicola insolens cutinase; HSQC, heteronuclear singlequantum coherence; IPTG, isopropyl b-D-1-thiogalactopyranoside; ITC, isothermal titration calorimetry; MD, molecular dynamics; MEP, monoethylphosphate; MWCO, molecular weight cut-off; PAGE, polyacrylamide gel electrophoresis; RMSD, root mean square deviation; RMSF, root mean square fluctuation; TES, N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonic acid; SANS, small-angle neutron scattering; SDS, sodium dodecyl sulfate.Additional Supporting Information may be found in the online version of this article.An interactive view is available in the electronic version of the article. enzyme has the same fold as reported for other cutinases but, unexpectedly, esterification of the active site serine is accompanied by the ethylation of the active site histidine which flips out from its usual position in the triad.

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Ion-pairs in proteins

Cited by 672 publications

References 22 publications

Protein flexibility and dynamics using constraint theory

Protein flexibility and dynamics using constraint theory

X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

Thermodynamic and structural investigation of the specific SDS binding of humicola insolens cutinase

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