Irreversible thermal denaturation of bovine pancreatic ribonuclease-A. Physico-chemical characterization of initial products

The isolation and characterization of the products formed during the irreversible thermal denaturation of enzyme RNAase-A are described. RNAase-A, when maintained in aqueous solution at pH 7.0 and 70 degrees for 2 h, gives soluble products which have been fractionated by gel filtration on Sephadex G-75 into four components. These components are designated RNAase-At1, RNAase-At2, RNAase-At3 and RNAase-At4 according to the order of their elution from Sephadex G-75. RNAase-At4 shows the same specific activity towards yeast RNA as native RNAase-A and is virtually indistinguishable from it by the physical methods employed. However, chromatography on CM-cellulose separates it into three components that show the same u.v. spectra and specific activity towards yeast RNA as native RNAase-A. RNAase-At1, RNAase-At2 and RNAase-At3 are all structurally altered derivatives of RNAase-A and they exhibit low specific activity (5-10%) towards yeast RNA. In the presence of added S-protein, all these derivatives show greatly enhanced enzymic activity. RNAase-At1 and RNAase-At2 are polymers, covalently crosslinked by intermolecular disulfide bridges; whereas RNAase-At3 is a monomer. Physical studies such as 1H-n.m.r., sedimentation analysis, u.v. absorption spectra and CD spectra reveal that RNAase-At3 is a unfolded derivative of RNAase-A. However, it is seen to possess sufficient residual structure which gives rise to a low but easily detectable enzymic activity.     

An X-ray diffraction study of poly-L-homoarginine hydrochloride.

An X-ray study of the synthetic polypeptide poly(L -homoarginine hydrochloride) has been made to investigate whether, like the chemically related polypeptides poly(L -lysine hydrochloride), poly(L -arginine hydrochloride), and poly(L -ornithine hydrobromide), it can undergo conformational transitions merely from variations in its degree of hydration. X-ray photographs of powder and oriented specimens containing one to 15 molecules of water per L -homoarginine hydrochloride residue showed that this polymer forms only a β-pleated-sheet structure. The pleated sheets, formed by antiparallel polypeptide chains hydrogen-bonded to each other, are piled up along the b axis in an alternating sequence (“sandwich structure”). This structure did not appreciably change with variations of the degree of hydration, and the observed reflections at 56% relative humidity (1.8 molecules of water per residue) could be indexed satisfactorily in terms of a monoclinic unit cell, of space group P2₁, with a = 9.34 Å, b = 40.07 Å, c = 6.94 Å, and γ = 106°. These dimensions are shown by models to be compatible with the proposed structure, and the calculated density of 1.27 g/cm³ agrees well with the experimental value of 1.29 g/cm³. Removal of the last molecule of water results in a very diffuse pattern, while specimens containing 20 molecules of water per residue show only reflections due to water.     

Crystallization and preliminary X-ray study of subunit III of the bovine pancreatic procarboxypeptidase A-S6 ternary complex

Subunit III of the bovine pancreatic procarboxypeptidase A-S6 ternary complex was dissociated from the complex, purified and crystallized using the hanging- or sitting-drop method of vapour diffusion, with ammonium sulphate as the precipitant. The assays were carried out at pH 4.2 (20 mM-acetate buffer). An X-ray examination of the crystals shows that they are monoclinic, with a space group P21 and cell dimensions a = 47.9 A, b = 61.3 A, c = 39.0 A and beta = 95.0 degrees. The asymmetric unit contains one molecule of 25,800 Mr. The crystals are suitable for structure determination to at least 2.8 A resolution.     

Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.

The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) that was soaked with the substrate maltopentaose showed electron density corresponding to two independent carbohydrate recognition sites on the surface of the molecule. Both binding sites are distinct from the active site described in detail in our previous high-resolution study of a complex between PPA and a carbohydrate inhibitor (Qian M, Buisson G, Duée E, Haser H, Payan F, 1994, Biochemistry 33:6284-6294). One of the binding sites previously identified in a 5-A-resolution electron density map, lies at a distance of 20 A from the active site cleft and can accommodate two glucose units. The second affinity site for sugar units is located close to the calcium binding site. The crystal structure of the maltopentaose complex was refined at 2.1 A resolution, to an R-factor of 17.5%, with an RMS deviation in bond distances of 0.007 A. The model includes all 496 residues of the enzyme, 1 calcium ion, 1 chloride ion, 425 water molecules, and 3 bound sugar rings. The binding sites are characterized and described in detail. The present complex structure provides the evidence of an increased stability of the structure upon interaction with the substrate and allows identification of an N-terminal pyrrolidonecarboxylic acid in PPA.     

Crystallization and preliminary X-ray study of horse pancreatic lipase

Horse (Equus caballus) pancreatic lipase (EC 3.1.1.3) has been crystallized using the hanging drop method of vapour diffusion at 20 degrees C. The best crystals were grown from an 8 mg/ml solution in 10 to 20% (w/v) polyethylene glycol 8000, 10 mM-MgCl2, 0.1 M-NaCl, 0.1 M-Mes buffer (pH 5.6). They reach dimensions of 0.8 mm x 0.4 mm x 0.6 mm. X-ray examination of the lipase crystals shows that they are orthorombic with a space group P2(1)2(1)2(1). Their cell dimensions are a = 79.8 A, b = 97.2 A c = 145.3 A. Two molecules per asymmetric unit give a Vm value of 2.82 A3/dalton (56% water content). Lipase crystals strongly diffract to at least 1.8 A resolution. Some molecular properties of horse lipase compared to those of the better-known porcine enzyme are also presented.     

Crystallization and preliminary X-ray crystallographic study of the leech protease inhibitor guamerin and its complex with bovine pancreatic chymotrypsin

Guamerin, a small peptide inhibitor of the serine protease from Hirudo nipponia, was expressed in yeast and crystallized using the vapor diffusion method, with MPD as precipitant. The crystal was found to belong to the monoclinic P2(1) space group with unit cell parameters a=136.06, b=206.59, c=227.39 A, beta=105.03 degrees. The guamerin/bovine pancreatic chymotrypsin complex was also crystallized using PEG 8K as precipitant. The space group was identified as P2(1)2(1)2(1) with unit cell parameters of a=44.01, b=44.30, c=122.47 A. The diffraction data of the complex were collected up to a resolution of 2.4 A using a synchrotron-radiation source under cryogenic condition.     

X-ray analysis of a thrombin inhibitor-trypsin complex

The three-dimensional structure of a thrombin inhibitor-trypsin complex has been determined by an X-ray analysis at 2.5 A resolution. The result has given experimental support to the mechanisms previously proposed by the authors for the selective inhibition of trypsin, thrombin, factor Xa, and plasmin by inhibitors with an arginine or lysine backbone. The differences in the amino acid sequences at the positions corresponding to Ilc63, Leu99, and Ser190 of trypsin give each enzyme different binding affinities toward inhibitors and result in the selective inhibition. Furthermore, the X-ray analysis has revealed a novel type of interaction between the inhibitor and trypsin. The hydrogen bonds between the inhibitor main chain and trypsin Gly216 play an essential role in the complex formation.     

An X-ray diffraction study of poly-L-arginine hydrochloride

An x-ray study has been made of polyarginine hydrochloride to investigate whether, like polylysine hydrochloride, it can undergo conformational changes merely from variations in the degree of hydration. X-ray powder and fiber photographs of specimens containing up to about five molecules of water per arginine residue show features characteristic of α-helical structures including a 5.4-Å layer line and a meridional 1.5-Å reflection. Increasing the water content from ¹/₂ to 6¹/₂ molecules per residue causes the a axis of the hexagonal unit cell to increase from 14.4 Å to 15.8 Å, with no appreciable change in the 27.0 Å c axis. Removal of the last half molecule of water results in a very diffuse α pattern, but on rehydration the sharp pattern reappears. Specimens containing five to twenty water molecules per residue show quite a different pattern, the spacing of which do not vary appreciably with hydration. This pattern includes a meridional 3.4-Å reflection, a feature commonly shown by β structures, and indeed all the reflections can be satisfactorily indexed in terms of a monoclinic unit cell with a = 9.26 Å, b = 22.05 Å, c = 6.76 Å, and γ = 108.9°. These dimensions are shown by models to be compatible with a β pleated-sheet structure.     

An X-ray diffraction and X-ray absorption spectroscopy joint study of neuroglobin

Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, involved in neuroprotection. A combined approach of X-ray diffraction (XRD) on single crystal and X-ray absorption spectroscopy (XAS) in solution, allows to determine the oxidation state and the structure of the Fe-heme both in the bis-histidine and the CO-bound (NgbCO) states. The overall data demonstrate that under X-ray the iron is photoreduced fairly rapidly, and that the previously reported X-ray structure of ferric Ngb [B. Vallone, K. Nienhaus, M. Brunori, G.U. Nienhaus, Proteins 56 (2004) 85-92] very likely refers to a photoreduced species indistinguishable from the dithionite reduced protein. Results from the XAS analysis of NgbCO in solution are in good agreement with XRD data on the crystal. However prolonged X-ray exposure at 15 K determines CO release. This preliminary result paves the way to experiments aimed at the characterization of pentacoordinate ferrous Ngb, the only species competent in binding external ligands such as O₂, CO or NO.     

The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study.

Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.     

Craniofacial changes in unilateral microtia: II. An X-ray study

Roentgenocephalometry was used for studies into the extent and character of craniofacial changes in 45 adult males with unilateral (right-sided) microtia. Out of the whole complex of changes associated with this malformation the mandibular ramus showed the most marked involvement and represented the main cause of the accompanying deviations and asymmetries. On the average, the affected half of the face was compressed toward the level of the external auditory meatus both from above and below, but there was a marked variability in individual patients examined. No signs of asymmetry were disclosed in one third of the patients while severe asymmetry was present in one fifth of the patients. Facial hemihypoplasia exerted no substantial influence on the facial profile (when no retrusion of the lower jaw was present) on the sagittal maxillomandibular relations or on the occlusion of incisors, while in transverse direction a laterosuperior deviation of the mandible towards the affected side was clearly visible. A branchiogenic malformation affected the neighboring structures, the cranial base (a more marked curving), frontonasal segment (septum and premaxillar deviation), and the neurocranium (posterior rotation of the cranial vault). The inner ear structures (semicircular canals) were affected only rarely (in 4% of patients). These findings complemented the results obtained in the first part of our study and confirmed the complex character of this inborn anomaly.     

Blood groups antigens distribution in pancreatic cancer. An immunohistochemical study

Distribution and immunolocalization of blood groups antigens ABO were investigated in pancreatic cancer with the use of immunoperoxidase method. In contrast to earlier investigations no correlation was found between histological differentiation of pancreatic cancers and maintenance of the blood groups antigens in tumor cells.