Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution

Secondary and conformational specificities of trypsin and chymotrypsin

Specific and non-specific trypsin substrates of known structure have been examined for common features. This analysis suggests that trypsin has a specificity for a particular conformation near the scissile bond which I denote as a conformational specificity. This conformation is a bent left-handed helix at the third and fourth (P3 and P4) amino acid positions toward the amino terminus from the scissile bond which I denote as a conformational specificity. This conformation is a bent left-handed show a high frequency of proline and glycine at these positions consistent with the left-handed helical conformation. This apparent secondary specificity for a particular substrate residue other than that at the primary position is not related to the nature of the residues at the third and fourth positions. Rather, these residues determine the bend of left-handed helix which has the effect of exposing main chain hydrogen-bonding groups of the substrate peptide chain to hydrogen-bonding groups on the enzyme. Thus, the secondary specificity of trypsin is not sequence-specific, but is for peptide main chain in the third and fourth positions and is determined by the tertiary structure of the substrate. This hypothesis for conformational and secondary specificity in trypsin can be extended to chymotrypsin. It also provides a means for the regulation of certain processes in vivo catalyzed by other proteases.

Crystallographic structure studies of an IgG molecule and an Fc fragment

The crystal structures of a human IgG antibody molecule Kol and a human Fc fragment have been determined at 4-A and 3.4-A resolution respectively, by isomorphous replacement. The electron-density maps were interpreted in terms of immunoglobulin domains based on the Rei and McPC 603 models (Kol) and by model-building (Fc). The Fab parts of Kol have a different quaternary structure from that observed in isolated crystalline Fab fragments, there being no longitudinal V-C contact in Kol. The Fc part C terminal to the hinge is disordered in the Kol crystals. It is suggested that the Kol molecule is flexible in solution, whereas fragments are rigid. In the Fc fragment both CH3 and CH2 show the immunoglobulin fold. The CH3 dimer aggregates as CH1-CL while CH2 are widely separated from each other. The carbohydrate bound to Fc is in fixed position. From these structures a hypothetical liganded antibody molecule has been constructed, which is assumed to be rigid.

Structural domains of transfer RNA molecules

In this article, we have described various detailed features of the conformation of yeast tRNA(Phe) revealed by recent refinement analysis of x-ray diffraction data at 2.5 A resolution. The gross features of the molecule observed in the unrefined version have been largely confirmed and a number of new features found. The unique role of the ribose 2' hydroxyl groups in maintaining a series of nonhelical conformations in this RNA molecule has become apparent. Many of these features are a direct consequence of the geometry of the ribose phosphate backbone of RNA molecules, and these may also be found in structured regions of other RNA species as well. Special attention has been directed toward two conformational motifs revealed by this analysis. These include the striking similarity between the TpsiC and anticodon hairpin turns in the polynucleotide chain, which are stabilized by the participation of uridine in the U turn. In addition, there is frequent occurrence of an arch conformation in the polynucleotide chian which is stabilized by hydrogen bonds from 2' hydroxyl residues to phosphate groups across the base of the arch. The importance of the 2' hydroxyl interactions in defining tertiary structure is illustrated by the fact that, in the nonhelical regions, almost half of the ribose residues are involved in O2' hydrogen-bonding interactions which stabilize the conformation of the molecule.

Induction of the bovine trypsinogen-trypsin transition by peptides sequentially similar to the N-terminus of trypsin

A technique using commercially available B-mode gray scale ultrasonography for imaging the head in the newborn and young infant is described. Serial scans were performed at several angles from the canthomeatal line. Images of technical quality previously unobtainable are shown. Normal anatomic structures such as ventricles, cerebral peduncles, pons, cerebellum, sulci, gyri, choroid plexus, falx cerebri, and tentorium cerebelli can be demonstrated. From April 1978 through December 1978, 165 gray scale ultrasonograms of the head on 111 children younger than 2 years were performed; 63 normal and 48 abnormal patients were studied, with hydrocephalus of various etiologies the most common abnormality. Porencephalic cysts, developmental anomalies, intraventricular and intracerebral hemorrhages, cephalohematoma, subdural hematomas, and arteriovenous malformations were demonstrated. Because of its safety and relatively low cost, ultrasonography proved to be an excellent method for following ventricular size and shunt function.

Binding of chloromethyl ketone substrate analogues to crystalline papain

Papain (EC 3.4.22.2) is a proteolytic enzyme, the three-dimensional structure of which has been determined by x-ray diffraction at 2.8 A resolution (Drenth, J., Jansonius, J.N., Koekoek, R., Swen, H. M., and Wothers, B.G. (1968), Nature (London) 218, 929-932). The active site is a groove on the molecular surface in which the essential sulfhydryl group of cysteine-25 is situated next to the imidazole ring of histidine-159. The main object of this study was to determine by the difference-Fourier technique the binding mode for the substrate in the groove in order to explain the substrate specificity of the enzyme (P2 should have a hydrophobic side chain (Berger and Schechter, 1970) and to contribute to an elucidation of the catalytic mechanism. To this end, three chloromethyl ketone substrate analogues were reacted with the enzyme by covalent attachment to the sulfur atom of cysteine-25. The products crystallized isomorphously with the parent structure that is not the native, active enzyme but a mixture of oxidized papain (probably papain-SO2-) and papain with an extra cysteine attached to cysteine-25. Although this made the interpretation of the difference electron density maps less easy, it provided us with a clear picture of the way in which the acyl part of the substrate binds in the active site groove. The carbonyl oxygen of the P1 residue is near two potential hydrogen-bond donating groups, the backbone NH of cysteine-25 and the NH2 of glutamine-19. Valine residues 133 and 157 are responsible for the preference of papain in its substrate splitting. By removing the methylene group that covalently attaches the inhibitor molecules to the sulfur atom of cysteine-25 we obtained acceptable models for the acyl-enzyme structure and for the tetrahedral intermediate. The carbonyl oxygen of the P1 residue, carrying a formal negative charge in the tetrahedral intermediate, is stabilized by formation of two hydrogen bonds with the backbone NH of cysteine-25 and the NH2 group of glutamine-19. This situation resembles that suggested for the proteolytic serine enzymes (Henderson, R., Wright, C. S., Hess, G. P., and Blow, D. M. (1971), Cold Spring Harbor Symp. Quant. Biol. 36, 63-70; Robertus, J. D., Kraut, J., Alden, R. A., and Birktoft, J. J. (1972b), Biochemistry 11, 4293-4303). The nitrogen atom of the scissile peptide bond was found close to the imidazole ring of histidine-159, suggesting a role for this ring in protonating the N atom of the leaving group (Lowe, 1970). This proton transfer would be facilitated by a 30 degrees rotation of the ring around the C beta-Cgamma bond from an in-plane position with the sulfur atom to an in-plane position with the N atom. The possibility of this rotation is derived from a difference electron-density map for fully oxidizied papain vs. the parent protein.

Homologous inhibitors from potato tubers of serine endopeptidases and metallocarboxypeptidases

A potent polypeptide inhibitor of chymotrypsin has been purified from Russett Burbank potatoes. The inhibitor has no effect on bovine carboxypeptidases A or B but exhibits homology with a carboxypeptidase inhibitor that is also present in potato tubers. The chymotrypsin inhibitor has a molecular weight of approximately 5400 as estimated by gel filtration, amino acid analysis, and titration with chymotrypsin. The polypeptide chain consists of 49 amino acid residues, of which six are half-cystine, forming three disulfide bonds. Its size is similar to that of the carboxypeptidase inhibitor, which contains 39 amino acid residues and also has three disulfide bridges. In immunological double diffusion assays, the chymotrypsin inhibitor and the carboxypeptidase inhibitor do not crossreact; however, automatic Edman degradation of reduced and alkylated derivatives of the chymotrypsin inhibitor, yielding a partial sequence of 18 amino acid residues at the NH2-terminus, reveals a similarity in sequence to that of the carboxypeptidase inhibitor. Thus, inhibitors directed toward two distinct classes of proteases, the serine endopeptidases and the metallocarboxypeptidases, appear to have evolved from a common ancestor.

Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles

The atomic coordinates of yeast phenylalanine transfer RNA (tRNA) as well as the torsion angles of the polynucleotide chain are presented as derived from an x-ray diffraction analysis of orthorhombic crystals. A comparison is made between the coordinates obtained from analysis of monoclinic crystals of the same material. It is concluded that the molecule has substantially the same form in the orthorhombic and the monoclinic lattices, except for differences found between residues at the 3' end of the polynucleotides chain. A number of observations are made concerning hydrogen bonding interactions which may account for many of the residues conserved in all tRNA sequences.

Principles of protein-protein recognition

The formation of the protein-protein interface by the insulin dimer, the trypsin-PTI complex and the alphabeta oxyhaemoglobin dimer removes 1,130-1,720 A2 of accessible surface from contact with water. The residues forming the interface are close packed: each occupies the same volume as it does in crystals of amino acids. These results indicate that hydrophobicity is the major factor stabilising protein-protein association, while complementarily plays a selective role in deciding which proteins may associate.

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor

Conformational potentials of sidechains in the bovine pancreatic trypsin inhibitor have been studied with an empirical energy function. Calculated minimumenergy positions are in excellent agreement with the x-ray structure for sidechains in the core or at the surface of the protein; as expected, angles for sidechains that are directed out into the solvent do not agree with the calculated values. The contributions to the potentials are analyzed and compared with the potentials for the free amino acid. Although there is a large restriction in the available conformational space due to nonbonded interactions, the minimum energy positions in the protein are close to those of the free amino acid; the significance of this result is discussed. To estimate the effective barriers for rotation of the aromatic rings (tyrosine and phenylalanine), calculations are done in which the protein is permitted to relax as a function of the ring orientation. Thr resulting barriers, which are much lowere than the rigid rotation barriers, are used to evaluate the rotation rates; comparison is made with the available nuclear magnetic resonance data.

The structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor III. Structure of the anhydro-trypsin-inhibitor complex

The structure of the complex between anhydro-trypsin and pancreatic trypsin inhibitor has been determined by difference Fourier techniques using phases obtained from the native complex (Huber et al., 1974). It was refined independently by constrained crystallographic refinement at 1.9 A resolution. The anhydro-complex has Ser 195 converted to dehydro-alanine. There were no other significant structural changes. In particular, the high degree of pyramidalization of the C atom of Lys 15 (I) of the inhibitor component observed in the native complex in maintained in the anhydro-species.

The structure determination of the variable portion of the Bence-Jones protein Au

The structure of a pi-type Bence-Jones protein variable fragment Au has been determined by molecular replacement methods using the known structure of an other Bence-Jones variable fragment Rei (Epp et al., Eur J. Biochem. 45, 513 (1974). The crystallographic R factor is 0.31 for about 4000 significantly measured reflections between 6.8 to 2.5 A. The Au protein forms a dimer across a crystallographic two fold axis. The spatial relationship of the two monomers, the conformation of the backbones and of the internal residues is extremely similar to that found in Rei.