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Biomedical subjects

W Saenger

Publications and source records attributed to W Saenger.

At least 181 records · Page 10Linked to original sources
PubMed1985

X-ray studies on triclinic crystals of fatty acid binding protein. Examples of an extremely X-ray-resistant protein.

Fatty acid binding protein (pI 7.0) from bovine liver cytosol was crystallized using polyethylene glycol 4000 and 6000 as precipitating agents. The crystals are triclinic, space group P1. One molecule of 14 kDa occupies the unit cell with constants a = 33.5 A, b = 39.4 A, c = 30.6 A, alpha = 113.6 degrees, beta = 113.8 degrees, gamma = 88.8 degrees. Crystal diffraction extends to at least 2.25 A resolution and the crystals are stable in the X-ray beam for more than 450 h. One native data set to 2.5 A resolution has been collected.

Animals↗
PubMed1985

Three-dimensional structure of the ribonuclease T1 X 3'-guanylic acid complex at 2.6 A resolution.

The mother enzyme of RNase T1 was co-crystallized with its natural product, 3'-GMP at pH 4.0. The X-ray structure of this complex was refined with 2432 reflections in the 5.4-2.6 A range using a stereochemical restrained method (conventional R = 27.4%). The overall polypeptide chain folding is very similar in the secondary structure elements to the RNase T1 in the complex with 2'-GMP crystallized also at pH 4.0, but larger conformational changes occur in the loop regions. The base recognition scheme is identical in both complexes but in RNase T1 X 3'-GMP, the ribose phosphate is not seen in the electron density, probably due to static disorder.

Chemical Phenomena↗
PubMed1984

Crystallization of and preliminary X-ray diffraction data for TET-repressor and the TET-repressor-tetracycline complex.

The TET-repressor encoded by the transposon Tn10 has been crystallized along with the repressor-tetracycline complex. Both crystals belong to the space group P43212 (or P41212) with cell dimensions a = b = 74.3(1) A, c = 94.2(2) A and a = b = 73.3(1) A, c = 94.6(2) A for the free and complexed repressor, respectively. There is one molecule of molecular weight 23,000 per asymmetric unit, and the biologically active dimer therefore consists of two identically formed subunits which are related by a crystallographic 2-fold axis. This isomorphism of TET-repressor and its tetracycline complex suggests that only minor, subtle changes in structure trigger binding to or release of the operator. The crystals of the native protein permit X-ray data collection to 3.2 A and those of the complexed repressor to 2.8 A.

Crystallization↗
PubMed1984

Small angle x-ray study on the structure of active and inactive ribulose bisphosphate carboxylase from Alcaligenes eutrophus. Evidence for a configurational change.

Two small angle x-ray scattering curves have been obtained from active and inactive ribulose 1,5-bisphosphate carboxylase from Alcaligenes eutrophus. The radius of gyration was calculated to be R = 47.8 +/- 0.1 nm for the active enzyme and R = 49.2 +/- 0.1 nm for the inactive enzyme. The maximum particle dimension amounts to 13.5 +/- 0.5 nm for the active and 15.7 +/- 0.5 nm for the inactive enzyme. A model of the active carboxylase is presented. It is in good agreement with models derived from electron microscopical data. Model calculations for the inactive enzyme show some evidence for a configurational change.

Alcaligenes↗
PubMed1984

Three-dimensional structure of fungal proteinase K reveals similarity to bacterial subtilisin.

The three-dimensional structure of the fungal serine protease proteinase K has been determined at 3.3 A resolution by single crystal X-ray diffraction analysis. The enzyme crystallizes in the tetragonal space group P4(3)2(1)2 with cell constants a = b = 68.3 A, c = 108.5 A. The asymmetric unit consists of one monomer of 27 000 daltons mol. wt., approximately 50% higher than the so far assumed value of 18 500 daltons. The main chain fold of proteinase K shows a high degree of tertiary homology with the corresponding bacterial subtilisin BPN'. Proteinase K is the second enzyme in this family of serine proteases to be studied by X-ray diffraction, thus confirming the existence of two unrelated families of serine proteases in pro-and eukaryotes.

Bacteria↗
PubMed1984

Neutron diffraction of alpha, beta and gamma cyclodextrins: hydrogen bonding patterns.

Cyclodextrins (CD's) have proved useful as model systems for the study of hydrogen bonding. They are torus-shaped molecules composed of six(alpha), seven(beta) or eight(gamma) (1----4) linked glucoses. Because of their particular geometry, they are able to act as a "host" to form inclusion complexes with "guest" molecules very much like enzymes. Cyclodextrins have been shown to exert catalytic activity on suitable included-substrate molecules; they catalyze the hydrolysis of phenylacetates, of organic pyrophosphates and of penicillin derivatives. They also accelerate aromatic chlorinations and diazo coupling by means of their primary and/or secondary hydroxyl groups, so that the rates of hydrolysis are enhanced by up to a factor of 400. In order to understand the hydrogen bonding in these enzyme models, neutron diffraction data were collected to unambiguously determine the hydrogen atom positions, which could not be done from the x-ray diffraction data. alpha-CD has been shown to have two different structures with well-defined hydrogen bonds, one "tense" and the other "relaxed". An "induced-fit"-like mechanism for alpha-CD complex formation has been proposed. Circular hydrogen bond networks have also been found for alpha-CD due to the energetically favored cooperative effect. beta-CD with a disordered water structure possesses an unusual flip-flop hydrogen bonding system of the type O-H...H-O representing an equilibrium between two states: O-H...O in equilibrium O...H-O. gamma-CD with a disordered water structure similar to beta-CD also possesses the flip-flop hydrogen bond. This study demonstrates that hydrogen bonds are operative in disordered systems and display dynamics even in the solid state.

Crystallography↗
PubMed1983

Molecular structure of deoxyadenylyl-3'-methylphosphonate-5'-thymidine dihydrate, (d-ApT x 2H2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study.

dApT, a modified deoxyribose dinucleoside phosphate with an uncharged methylphosphonate group, crystallizes as dihydrate in space group P2(1)2(1)2, a = 9.629(3), b = 20.884(6) and c = 14.173(4)A, Z = 4. The structure has been determined using 2176 X-ray diffractometer reflections and refined to a final R of 0.105. Torsion angles about P-O(5') and P-O(3') bonds are -91.8 degrees and 117.8 degrees. The former is in the normal (-)gauche range while the latter is eclipsed. Bases are oriented anti, the sugar of adenosine is puckered 2T3 (C(2')endo) whereas that of thymidine displays puckering disorder with major and minor occupancy sites. Major site is a half-chair 2T (C(2')endo-C(1')exo) and minor site an envelope 3T2 (C(3(1)endo). Adenine and thymine bases of symmetry related molecules form reversed Hoogsteen type base pairs, water molecules are disordered in the crystal lattice.

Crystallography↗
PubMed1983

Interactions of biotin with metal ions. X-ray crystal structure of the polymeric biotin--silver(I) nitrate complex: metal bonding to thioether and ureido carbonyl groups.

X-ray structure analysis of the silver(I) complex of d-(+)-biotin, [Ag(biotin)(NO3)] X 0.5H2O, shows the complex to be polymeric with the silver ion coordinated tetrahedrally to nitrate and to three different biotin molecules. Binding to the latter involves two thioether sulfur atoms in the cis and trans direction with respect to the ureido ring, and one ureido carbonyl oxygen atom. The biotin carboxylate group is probably protonated and not coordinated with the silver ion.

Biotin↗
PubMed1983

Crystallographic study of mechanism of ribonuclease T1-catalysed specific RNA hydrolysis.

Ribonuclease T1 (RNase T1) cleaves the phosphodiester bond of RNA specifically at the 3'-end of guanosine. 2'-guanosinemonophosphate (2'-GMP) acts as inhibitor for this reaction and was cocrystallized with RNase T1. X-Ray analysis provided insight in the geometry of the active site and in the parts of the enzyme involved in the recognition of guanosine. RNase T1 is globular in shape and consists of a 4.5 turns alpha-helix lying "below" a four-stranded antiparallel beta-sheet containing recognition center as well as active site. The latter is indicated by the position of phosphate and sugar residues of 2'-GMP and shows that Glu58, His92 and Arg77 are active in phosphodiester hydrolysis. Guanine is recognized by a stretch of protein from Tyr42 to Tyr45. Residues involved in recognition are peptide NH and C = O, guanine O6 and N1H which form hydrogen bonds and a stacking interaction of Tyr45 on guanine. Although, on a theoretical basis, many specific amino acid-guanine interactions are possible, none is employed in the RNase T1.guanine recognition.

Amino Acid Sequence↗
PubMed1982

Crystal and molecular structure of the sulfhydryl protease calotropin DI at 3.2 A resolution.

The three-dimensional structure of the sulfhydryl protease calotropin DI from the madar plant, Calotropis gigantea, has been determined at 3.2 A resolution using the multiple isomorphous replacement method with five heavy atom derivatives. A Fourier synthesis based on protein phases with a mean figure of merit of 0.857 was used for model building. The polypeptide backbone of calotropin DI is folded to form two distinct lobes, one of which is comprised mainly of alpha-helices, while the other is characterized by a system of all antiparallel pleated sheets. The overall molecular architecture closely resembles those found in the sulfhydryl proteases papain and actinidin. Despite the unknown amino acid sequence of calotropin DI a number of residues around its active center could be identified. These amino acid side-chains were found in a similar arrangement as the corresponding ones in papain and actinidin. The polypeptide chain between residues 1 and 18 of calotropin DI folds in a unique manner, providing a possible explanation for the unusual inability of calotropin DI to hydrolyze those synthetic substrates that papain and actinidin act upon.

Binding Sites↗
PubMed1982

Specific protein-nucleic acid recognition in ribonuclease T1-2'-guanylic acid complex: an X-ray study.

RNase T1 is folded into an alpha-helix of 4.5 turns, covered by a four-strand antiparallel beta-sheet. Specific recognition of 2'-guanylic acid arises from hydrogen bonding between main chain peptide groups and the O-6 and N-1-H of guanine, as well as from stacking of Tyr 45 on guanine. At the active site, Glu 58, His 92 and Arg 77 are involved in phosphodiester hydrolysis.

Amino Acid Sequence↗
PubMed1982

Crystallization and preliminary X-ray investigation of avidin.

Hen egg-white avidin was crystallized at pH 6 from solutions containing 8-9% (w/v) poly(ethyleneglycol) 6000 as precipitant. X-ray investigation showed that the crystals are orthorhombic with cell constants a = 7.47 nm, b = 8.00 nm, c = 4.31 nm and belong to space group P21212. They contain half of a tetrameric molecule in the asymmetric unit.

Animals↗
PubMed1981

Six polymorphic crystal forms of alpha-cobratoxin.

Six different crystal forms of the long neurotoxin alpha-cobratoxin isolated from the venom of Naja naja siamensis have been obtained and the conditions for their crystallisation are described. Heavy atom derivatives for two of these forms have been prepared and have proven suitable for high-resolution X-ray studies and, with one of them, a 0.28-nm resolution structure has been determined. All but one of the crystal forms were grown between pH 2 and pH 3. Two novel suggestions are made which may be applicable to other protein crystallisation studies. One involves cocrystallisation with mercurous iodide and the other describes a two-step microdialysis procedure, first against salt solution, followed by dialysis against poly(ethylene glycol).

1-Propanol↗