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C Betzel

Publications and source records attributed to C Betzel.

At least 73 records · Page 4Linked to original sources
PubMed1995

Stability of subtilisins and related proteinases (subtilases).

The stability towards thermal and chemical (guanidine hydrochloride, GnHCl) denaturation of six inhibited subtilases (mesentericopeptidase, subtilisins BPN', Carlsberg and DY, proteinase K and thermitase) has been investigated by kinetic and equilibrium studies. The unfolding processes were monitored by circular dichroic and fluorescence spectroscopy. Experiments in the absence and presence of extraneous calcium in the concentration range 2 x 10(-3)-10(-1) M were performed. The presence of calcium in the weak calcium binding site changes the denaturation drastically. The heat- (or GnHCl-) induced unfolding curves obtained using CD spectroscopy show two independent transitions which seem not to have been resolved before. The presence of Ca2+ in the second (third in the case of thermitase) binding site increases the Tm values by 11-21 degrees C and the delta GD(H2O) values obtained from denaturation experiments in GnHCl by 6.7-7.2 kcal/mol when an extraneous Ca2+ concentration of 2 x 10(-2) M was used. One interpretation is that the initial step of denaturation in the presence of added calcium is the formation of a partially unfolded intermediate form, retaining a highly ordered structure with 60-85% of the alpha-helix structure of the native enzyme. This intermediate then unfolds at a temperature considerably higher than that of the same proteinases in the absence of added Ca2+. The free energy of stabilization of the intermediates is increased by 1.8-2.8 times in comparison with that for the unfolding reactions of the subtilases with empty Ca2/Ca3 binding sites. A second interpretation is that the two steps in the unfolding curves correspond to enzyme without and with calcium in the weak binding site. Fluorescence experiments confirm the mechanism involving the formation of intermediate states. The results are discussed in relation to the X-ray models of the six subtilases.

Binding Sites↗
PubMed1994

Crystal structure of beta-D-cellotetraose hemihydrate with implications for the structure of cellulose II.

The crystal structure of beta-D-cellotetraose shows the same molecule packing as cellulose II, with two antiparallel molecules in the unit cell: For cellulose II, the orientation of the C6-O6 bonds has been described as gauche-trans and trans-gauche, respectively, for the two antiparallel molecules, which otherwise have identical conformations. In contrast, in beta-D-cellotetraose all C6-O6 bonds are gauche-trans, but the conformations of the two antiparallel molecules are different. Energy minimization and molecular dynamics studies suggest that the structure of cellulose II should be reinvestigated in light of these findings.

Carbohydrate Conformation↗
PubMed1994

Cavity mutants of Savinase. Crystal structures and differential scanning calorimetry experiments give hints of the function of the buried water molecules in subtilisins.

The subtilisin molecule possesses several internal water molecules, which may be characterised as an integral part of the protein structure. We have introduced specific mutations (T71I, T71S, T71V, T71A and T71G) at position 71 in the subtilisin variant Savinase from Bacillus lentus. This position is involved in a hydrogen bonded network with several internal water molecules, forming a water channel. The water channel and most of the other internal water molecules are positioned in the interface between two half-domains of the subtilisin molecule. The data presented here indicate that the internal water molecules are structural, and may be the result of trapping during the folding process.

Amino Acids↗
PubMed1994

Protein microheterogeneity and crystal habits: the case of epidermal growth factor receptor isoforms as isolated in a multicompartment electrolyzer with isoelectric membranes.

A purified, soluble form of the epidermal growth factor receptor (sEGFR) was found, by isoelectric focusing in immobilized pH gradients, to consist of three major isoforms (with pI values 6.45, 6.71 and 6.96, respectively) and ca. a dozen minor components. This wild-type sEGFR, while producing crystals, has so far defied any attempt at decoding the structure, due to the very poor diffraction pattern. When the wild-type sEGFR was purified in a multicompartment electrolyzer with isoelectric Immobiline membranes, it yielded the three major isoforms as single-pI components, collected in three separate chambers of the recycling electrolyzer. The pI 6.71 and the pI 6.96 isoforms produced large crystals of apparent good quality. However, while the former produced a high-quality diffraction pattern, which may lead to decoding of three-dimensional structure, the pI 6.96 produced crystals which did not diffract at all. It is concluded that, in the case of "tough" proteins (large size, heterogeneous glycosylation, high water content of crystals), purification to single-charge components might be an essential step for growing proper crystals. The unique advantage of purification via isoelectric membranes is that the protein is collected both isoelectric and isoionic, i.e. uncontaminated by soluble buffers (such as the carrier ampholytes used in conventional focusing).

Animals↗
PubMed1994

Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure.

This is the first high resolution crystal structure of an RNA molecule made by solid phase chemical synthesis and representing a natural RNA. The structure of the domain A of Thermus flavus ribosomal 5S RNA is refined to R = 18% at 2.4 A including 159 solvent molecules. Most of the 2'-hydroxyl groups as well as the phosphate oxygens are involved either in specific hydrogen bonds in intermolecular contacts or to solvent molecules. The two U-G and G-U base-pairs are stabilized by H-bonds supplied via three water molecules to compensate for the lack of base-pair hydrogen bonds. The structure shows for the first time in detail the importance of highly ordered internal water in stabilizing an RNA structure.

Base Sequence↗
PubMed1994

Crystallographic studies of Savinase, a subtilisin-like proteinase, at pH 10.5.

The effect of high pH (pH 10.5) on Savinase, a subtilisin-like serine proteinase, has been investigated using X-ray crystallography. The structures of two Savinase mutants were determined at two different pH values, namely pH 6.0, where the enzyme is inactive (this is the pH at which most of the structural work has been carried out on other serine proteinases), and pH 10.5, where Savinase is active. Comparison of these high resolution (0.16 nm) structures showed four related sets of changes between the two pH values. First, the difference in protonation state of the active-site histidine leads to a change in conformation of the active-site triad. Secondly, there are resulting changes in the water structure around this histidine residue with much increased mobility of the water in the active-site at pH 10.5. Thirdly, the two substrate-binding loops on either side of the binding site are less well linked by ordered water molecules at pH 10.5 and show substantially increased flexibility. Finally, the first substrate-binding loop, residues at positions 99-104, moves slightly so as to widen the substrate channel.

Amino Acid Sequence↗
PubMed1993

Crystallization and preliminary X-ray analysis of leukemia inhibitory factor.

Leukemia inhibitory factor (LIF) is a polyfunctional molecule with significant and diverse biological activities. LIF is a glycoprotein secreted by a number of different cell types in vitro. It is induced in fibroblasts, lymphocytes, monocytes and astrocytes by various inducers such as serum, TNF, interleukin-IP and EGF. Due to extensive and variable glycosylation the molecular weight can range from 38 to 67 kDA. The biological functions of LIF are mediated through a receptor and a signal transducer, gp130, which is also used by factors like interleukin-6 (IL-6), cilliary neurotropic factor (CNTF), and oncostatin M (OSM). Here, we report the crystallization of the non-glycosylated human-like LIF expressed in E. coli. The present crystals diffract to 2.0 A using synchrotron radiation. They belong to the monoclinic space group C2, and the cell dimensions are a = 61.5 A, b = 45.3 A, c = 77.7 A and beta = 112.3 degrees.

Cloning, Molecular↗
PubMed1993

Structure of the complex of proteinase K with a substrate analogue hexapeptide inhibitor at 2.2-A resolution.

The crystal structure of a transition state/product complex formed by the interaction between proteinase K and the substrate analogue N-Ac-L-Pro-L-Ala-L-Pro-L-Phe-D-Ala-L-Ala-NH2 has been determined at a resolution of 2.2 A and refined to an R-factor of 0.165 for 12,725 reflections. The inhibitor forms a stable complex through a series of hydrogen bonds with protein atoms and water molecules. The inhibitor is hydrolyzed between Phe 4I and D-Ala5I (I indicates inhibitor). The two fragments are separated by a distance of 3.07 A between the carbonyl carbon and the main chain nitrogen. Both fragments remain bound to the protein. The N-terminal fragment occupies subsites S5 to S1, whereas the C-terminal part is bound in S1' and S2', the first time that electron density for a substrate analogue has been observed in the P1' and P2' sites of a subtilisin-like enzyme. The flexible segments of the substrate recognition sites Gly100-Tyr104 and Ser132-Gly136 move appreciably to accommodate the inhibitor. Biochemical results indicate an inhibition by this specifically designed peptide of 95%.

Amino Acid Sequence↗
PubMed1993

Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form.

. An active recombinant preparation of the carboxy-terminal ribonuclease H (RNase H) domain of HIV-I reverse transcriptase has produced crystals of several different forms, including a trigonal prism form (P3(1); a = b = 52.03, c = 113.9 A with two molecules per asymmetric unit) and a hexagonal tablet form (P6(2)22 or P6(4)22; a = b = 93.5, c = 74.1 A with one molecule per asymmetric unit). The former appears to be isomorphous with crystals of a similar, but inactive, version of the enzyme that was used for a prior crystal structure determination [Davies, Hostomska, Hostomsky, Jordan & Matthews (1991). Science, 252, 88-95]. We have also obtained a structure solution for this crystal form and have refined it with 2.8 A resolution data (R = 0.216). We report here details of our crystallization studies and some initial structural results that verify that the preparation of active HIV-1 RNase H yields a protein that is not just enzymatically, but also structurally, distinguishable from the inactive form. Evidence suggests that region 538-542, which may be involved in the catalytic site and which is disordered in both molecules in the prior structure determination, is ordered in the crystal structure of the active enzyme, although the ordering may include more than one conformation for this loop. It should also be noted that, in the crystal structure of the trigonal form, RNase H monomers associate to form noncrystallographic twofold-symmetric dimers by fusing five-stranded mixed beta sheets into a single ten-stranded dimerwide sheet, an assembly that was not remarked upon by previous investigators.

Journal Article↗
PubMed1993

Crystallization and preliminary X-ray analysis of vipoxin, a complex between a toxic phospholipase A2 and its natural polypeptide inhibitor.

The toxin vipoxin, which is a complex between a basic toxic phospholipase A2 and an acidic non-toxic protein inhibitor, is found in the venom of the Bulgarian viper (Vipera ammodytes ammodytes), the most toxic snake in Europe. The two polypeptide chains each consist of 122 residues and are highly homologous (62%). The vipoxin complex is the first reported example of a high degree of structural homology between an enzyme and its natural inhibitor. The present crystals diffract in the X-ray beam to 1.8 A resolution. The space group is P2(1)2(1)2(1). The cell dimensions are a = 45.80 A, b = 55.36 A and c = 107.69 A. Native data to a resolution of 2.8 A have been recorded.

Animals↗
PubMed1993

Three-dimensional structure of neurotoxin-1 from Naja naja oxiana venom at 1.9 A resolution.

Neurotoxin-1 from Naja naja oxiana venom (NTX-1) has been crystallized by vapor diffusion in sitting drops. The crystals have cell dimensions of a = 25.2 A, b = 75.6 A, c = 35.9 A, and are in space group P2(1)2(1)2(1). Three-dimensional data to 1.9 A have been recorded by a Syntex P2(1) automatic diffractometer. The atomic structure of the toxin has been determined by molecular replacement using the alpha-cobratoxin (alpha-CTX) as the search model. The position of 534 non-hydrogen protein atoms have been determined. The model contains 65 water molecules. Refinement has led to an R-factor of 19.3% at 1.9 A resolution. The secondary and tertiary structures of NTX-1 have been analyzed and a comparison with structure of the alpha-CTX has been made.

Amino Acid Sequence↗
PubMed1993

Structure of the proteinase inhibitor eglin c with hydrolysed reactive centre at 2.0 A resolution.

The inhibition of serine proteinases by both synthetic and natural inhibitors has been widely studied. Eglin c is a small thermostable protein isolated from the leech, Hirudo medicinalis. Eglin c is a potent serine proteinase inhibitor. The three-dimensional structure of native eglin and of its complexes with a number of proteinases are known. We here describe the crystal structure of hydrolysed eglin not bound to a proteinase. The body of the eglin has a conformation remarkably similar to that in the known complexes with proteinases. However, the peptide chain has been cut at the 'scissile' bond between residues 45 and 46, presumed to result from the presence of subtilisin DY in the crystallisation sample. The residues usually making up the inhibiting loop of eglin take up a quite different conformation in the nicked inhibitor leading to stabilising contacts between neighbouring molecules in the crystal. The structure was solved by molecular replacement techniques and refined to a final R-factor of 14.5%.

Hydrolysis↗
PubMed1993

Actinomycins as proteinase inhibitors.

A novel actinomycin (Act SG3) from a strain of Streptomyces galbus var. C-72, as well as actinomycin D (Act D) were found to act as competitive inhibitors of serine proteinases from microorganisms. The inhibitory properties of Act SG3 and Act D are compared with these of other peptide antibiotics, namely bacitracin A (Bac A) and gramicidin S (Gr S). The last compound has only a weak inhibitory effect. The following order of affinity for the four peptide antibiotics towards subtilisin DY and proteinase K was observed: Bac A > Act D > Act SG3 = Gr S. The affinity towards thermitase changes as follows: Act SG3 = Act D > Bac A > Gr S.

Amino Acids↗
PubMed1993

Fluorescence properties of subtilisins and related proteinases (subtilases): relation to X-ray models.

The fluorescence properties of six subtilases with known X-ray structure were determined using the same experimental conditions and instrumentation. The steady state and nanosecond lifetime measurements were performed on purified samples of phenylmethanesulphonyl-inhibited proteinases in the presence of 20 mM CaCl2 which stabilizes the molecules. The tryptophan emission quantum yield strongly depends on the local environment and varies from 0.02 to 0.10. The efficiency of tyrosine-to-tryptophan energy transfer also varies (0%-70%) in the different enzymes; the most efficient transfer was observed for thermitase. Experiments with nanosecond excitation indicated that the tryptophan fluorescence of subtilases decays with two exponential components. The X-ray models of the six proteinases were analysed in the region of the tryptophyl residues and were used to explain the observed properties.

Endopeptidases↗
PubMed1993

The sequence and X-ray structure of the trypsin from Fusarium oxysporum.

The trypsin from Fusarium oxysporum is equally homologous to trypsins from Streptomyces griseus, Streptomyces erythraeus and to bovine trypsin. A DFP (diisopropylfluorophosphate) inhibited form of the enzyme has been crystallized from 1.4 M Na2SO4, buffered with citrate at pH 5.0-5.5. The crystals belong to space group P2(1) with cell parameters a = 33.43 A, b = 67.65 A, c = 39.85 A and beta = 107.6 degrees. There is one protein molecule in the asymmetric unit. X-ray diffraction data to a resolution of 1.8 A were collected on film using synchrotron radiation. The structure was solved by molecular replacement using models of bovine and S. griseus trypsins and refined to an R-factor of 0.141. The overall fold is similar to other trypsins, with some insertions and deletions. There is no evidence of the divalent cation binding sites seen in other trypsins. The covalently bound inhibitor molecule is clearly visible.

Amino Acid Sequence↗
PubMed1992

Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution.

The X-ray crystal structure of the molecular complex of penicillin G with a deacylation-defective mutant of the RTEM-1 beta-lactamase from Escherichia coli shows how these antibiotics are recognized and destroyed. Penicillin G is covalently bound to Ser 70 0 gamma as an acyl-enzyme intermediate. The deduced catalytic mechanism uses Ser 70 0 gamma as the attacking nucleophile during acylation. Lys 73 N zeta acts as a general base in abstracting a proton from Ser 70 and transferring it to the thiazolidine ring nitrogen atom via Ser 130 0 gamma. Deacylation is accomplished by nucleophilic attack on the penicilloyl carbonyl carbon by a water molecule assisted by the general base, Glu 166.

Acylation↗
PubMed1992

A TIM barrel protein without enzymatic activity? Crystal-structure of narbonin at 1.8 A resolution.

The major protein component in seeds is storage protein. These have no known enzymatic activity and act to provide amino acids as a source of metabolites in the developing seedling. We report here the first three dimensional crystal structure of a seed storage globulin at high resolution. The molecule of the 2S globulin, narbonin, from Vicia narbonensis L., consists of an eight-stranded parallel alpha/beta barrel structure similar to that observed in triose phosphate isomerase (TIM). Narbonin is the first protein with this topology possessing no known enzymatic activity. Because of the lack of sequence information most of the primary structure was determined directly from the electron density.

Amino Acid Sequence↗