Diazabicyclononanones, a potent class of kappa opioid analgesics.

The 1,5-dimethyl 3,7-diaza-3,7-dimethyl-9-oxo-2,4-di-2-pyridine-bicyclo[3.3.1]nonane-1,5-dicarboxylate, HZ2, has a high and selective affinity for the kappa opioid receptor and an antinociceptive activity comparable to morphine. In addition, it is characterized by a long duration of action and a high oral bioavailability. QSAR studies within series of kappa agonists revealed a chair-boat conformation of a double protonated HZ2 characterized by an almost parallel orientation of the C9 carbonyl group and the N7-H group and at least one aromatic ring to be the pharmacophoric arrangement. Structural variations showed that the pyridine rings in 2 and 4 position can be replaced with p-methoxy-, m-hydroxy- and m-fluoro-substituted phenyl rings. However, all other substituents have to be kept the same for a high affinity to the kappa receptor.

A strong thrombin-inhibitory prourokinase derivative with sequence elements from hirudin and the human thrombin receptor.

In order to design plasminogen activators with improved thrombolytic properties, bifunctional proteins with both plasminogen-activating and anticoagulative activity were constructed by fusing a thrombin-inhibitory moiety itself comprises four elements: linker 1, a motif directed to thrombin's active site, linker 2 and a fragment of hirudin which binds to the fibrinogen-recognition site of thrombin. In order to improve further the anticoagulative activity, the thrombin-inhibitory domain was modified by substituting linker 2. Introduction of a linker (FLLRNP) from the human thrombin receptor conferred about a 10-fold increase in anticoagulative activity in protein M37 compared with the parent molecule M23 carrying an aliphatic linker. The increase in anticoagulative activity was also reflected in the shift of the Ki value from 159 +/- 20 nM for M23 to 2.0 +/- 0.5 nM for M37. The increased thrombin-inhibitory activity of M37 may be due to the presence of an arginine in the linker from the thrombin receptor which may interact with one of two glutamic acid residues located at the exit of the thrombin substrate binding pocket. This explanation is supported by the observation that another chimera (M35) carrying a linker sequence with two acidic residues has relatively weak thrombin-inhibitory activity. The thrombin-inhibitory activity of M37 may be strong enough to substitute anticoagulative co-medication during fibrinolytic treatment.

Models of G-protein coupled receptors revised for family-wide compliance with experimental data. A new sequence accommodation suggested for helix G.

The G-protein coupled receptors form a vast superfamily. The hydrophobic sequences of the transmembrane regions can be consistently and unambiguously aligned for nearly all, even distantly related, members owing to striking conserved patterns. As the fold is highly conserved in evolution, a model of the structure of the transmembrane helix bundle built for any individual receptor will thus be of family-wide relevance. Consequently the model must comply with key results experimentally obtained for other individual receptors. Meeting this demand can greatly reduce the uncertainties in modelling G-protein coupled receptors. This present communication shows how our recent template model based on the backbone structure of bacteriorhodopsin is revised according to that demand. Although it turns out to be in accordance with the experimental data in most of its parts, this revision suggests a sequence accommodation to helix G that is different from all other published models.

Modeling of G-protein coupled receptors with bacteriorhodopsin as a template. A novel approach based on interaction energy differences.

The structure of bacteriorhodopsin was used as a template to generate a model for G-protein coupled receptors. However, these receptors and the template are not related by sequence homology. Therefore a pragmatic and reproducible approach was developed to achieve an energetically favourable accommodation of receptor sequences to the backbone structure of bacteriorhodopsin. Improved interaction energy differences are used in a two step procedure analogous to a hypothetical folding mechanism for integral membrane proteins. The resulting model is in good agreement with existing data from structure-function studies.

High expression vectors for the production of recombinant single-chain urinary plasminogen activator from Escherichia coli.

An expression cassette containing a synonymous gene for human single-chain urokinase-type plasminogen activator (Rscu-PA) 5'-flanked by a trp promoter and the Shine-Dalgarno sequence of the xyl A operon of Bacillus subtilis and terminated by the terminators trp A and Tn10 was constructed and inserted into a pBR322 derivative to yield pBF160. When compared to pUK54 trp 207-1 containing the natural scu-PA gene without the Shine-Dalgarno sequence and terminator, the expression efficiency of pBF160 in Escherichia coli strains was improved by one order of magnitude. Replacement of the trp by the tac promoter (pBF171) did not affect expression. Inserting the Shine-Dalgarno sequence and Tn10 terminator into pUK54 trp 207-1 (pWH1320) slightly increased the expression level, whereas elimination of the Shine-Dalgarno sequence and the terminators from pBF160 with almost complete conservation of the synonymous structural gene (pBF191) significantly reduced the expression. Variation of the distance between the Shine-Dalgarno sequence and the start codon between 8 and 10 bp (pBF163) proved irrelevant. In conclusion, poor expression of mammalian genes in E. coli may result from both improperly designed regulatory elements and structural features of the coding region and therefore de-novo synthesis of the gene may be required to obtain satisfactory expression.

A model for the C5a receptor and for its interaction with the ligand [corrected].

A model of the C5a receptor was built based on the assumption that the seven membrane-spanning helices of known inward/outward direction are in an arrangement roughly similar to that in bacteriorhodopsin. Guidelines for the positioning of the helices were cysteine pairing, 'ridges into grooves' interdigitation of side chains and aromatic cluster formation. The chain segments protruding from the membrane are too short for folding into an independent ectodomain. The only longer segment (179-202) is tied down in its centre onto the membrane by a disulphide bridge and, thereby, made into two short loops as well. Ideas of the interaction of the C5a receptor with its ligand were derived mainly from the search for accommodation of the functionally essential arginine residues 40 and 74 of C5a. Asp82 is the only charged residue in a pocket approximately 20 A below the receptor surface and is conserved in the rhodopsin superfamily. It commends itself for binding Arg74 which is the tip of the flexible C-terminal chain of C5a, and rules out Arg40 in the structurally well-defined part of the molecule. The latter may bind to Glu180 at the bottom of a more shallow pocket which happens to resemble the substrate-binding site of trypsin.

Phospholipid hydroperoxide glutathione peroxidase is a selenoenzyme distinct from the classical glutathione peroxidase as evident from cDNA and amino acid sequencing.

The primary structure of phospholipid hydroperoxide glutathione peroxidase (PHGPx) was partially elucidated by sequencing peptides obtained by cyanogen bromide cleavage and tryptic digestion and by isolating and sequencing corresponding cDNA fragments covering about 75% of the total sequence. Based on these data PHGPx can be rated as a selenoprotein homologous, but poorly related to classical glutathione peroxidase (GPx). Peptide loops constituting the active site in GPx are, however, strongly conserved in PHGPx. This suggests that the mechanism of action involving an oxidation/reduction cycle of a selenocysteine residue is essentially identical in PHGPx and GPx.

Interaction of parvalbumin of pike II with calcium and terbium ions.

Fluorimetric titrations of parvalbumin II (pI 4.2) of pike (Pike II) with Ca2+ and Tb3+ show the CD and EF binding sites to be non-equivalent. The intrinsic binding constants of the strong and the weak sites obtained for Ca2+ are: KsCa = 1.6.10(8) M-1; KwCa = 6.6.10(5) M-1. Differences of the order of 100% were encountered between the Tb3+ binding constants obtained with four different versions of titration. Their average values are: KsTb = 1.9.10(11) M-1; KwTb = 1.0.10(7) M-1. The distances of the strong and the weak sites from the singular Tyr-48, rs = 9.5 A and r2 = 11.5 A, were derived from Förster-type energy transfer and proved compatible with the X-ray structure of parvalbumin III (pI 4.2) of carp (CarpIII). From the distances, it is suggested that CD is the strong and EF the weak metal-binding site of PikeII. Tb3+ was shown by CD spectroscopy to have the same structural effect on PikeII as Ca2+. Removal of the metal ions from PikeII results in a decrease of helix content as monitored by CD spectroscopy. This decrease is larger than that in CarpIII. A concomitant decrease of the fluorescence quantum yield at nearly constant decay time is indicative of mainly static quenching, probably by the non-coordinating carboxylate groups. The maximum helix content is almost completely reestablished upon binding of the first metal ion. However, small changes of the energy transfer in PikeII with one terbium ion bound to the strong site indicate fine structural rearrangements of the strong binding site when Ca2+ is bound to the weak one.

The simulated dynamics of the insulin monomer and their relationship to the molecule's structure.

Insulin crystallizes in different forms, some of which show different conformations for the different molecules in the asymmetric unit. This observation leads to the question as to which conformation the molecule will adopt in solution. Molecular dynamics computer simulations of rhombohedral 2 Zn pig insulin have been carried out for both monomers (1 and 2) independently in order to study their behaviour in the absence of quaternary structure and crystal packing forces. These preliminary 120 ps simulations suggest that both monomers converge in solution to very similar conformations which differ from the X-ray structures of both monomer 1 and 2 (Chinese nomenclature), but are closer to the former, as has previously been suggested by an analysis of the crystal packing (Chothia et al. 1983) and by energy minimization (Wodak et al. 1984). The secondary structure of the molecules is basically preserved, as expected. A detailed description of the conformational changes is given.

Primary structure of Cu-Zn superoxide dismutase of Brassica oleracea proves homology with corresponding enzymes of animals, fungi and prokaryotes.

The complete amino-acid sequence of Cu-Zn superoxide dismutase from white cabbage (Brassica oleracea) is reported. The polypeptide chain consists of 151 amino acids and has a molecular mass of 15,604 Da. The primary structure of the reduced and S-carboxymethylated protein was determined by automated solid phase sequence analysis of tryptic fragments and peptides obtained by digestion with Staphylococcus aureus proteinase V8. The protein shows a free amino terminus as was found for all non-mammalian Cu-Zn enzymes so far sequenced. Comparison of the amino-acid sequence from the plant Cu-Zn enzyme with those from nine eukaryotic enzymes reveals a high degree of homology (50-64%) among these enzymes. As already described for all the eukaryotic Cu-Zn superoxide dismutases also the plant enzyme shows a low homology (about 28%) with the bacteriocuprein of Photobacterium leiognathi. However, the amino-acid residues involved in metal binding, the half-cystine residues forming the intermolecular disulfide bridge, one of the arginine and some glycine and proline residues are conserved in all eleven Cu-Zn superoxide dismutases. Although the precise role of the 23 completely conserved residues is not yet completely understood, they appear to almost define the minimum structural requirements for optimizing the superoxide dismutation at the catalytic site, since functional differences between the eleven enzymes are not detectable.

A comparison of the structure and dynamics of avian pancreatic polypeptide hormone in solution and in the crystal.

A molecular dynamics simulation was carried out with avian pancreatic polypeptide hormone (aPP) as an isolated monomer explicitly including the solvent (MDS). The simulation and the resulting mean structure are compared with the results of a corresponding crystal simulation (MDC) with 4 aPP molecules plus interstitial water in a periodic boundary unit cell and with the X-ray structure (van Gunsteren, Haneef et al., manuscript in preparation). Comparison is based on the time span 5 to 15 ps and considering cartesian coordinates, dihedral angles, H-bond length, and accessible surface area. While in the MDC simulation equilibration is fast and complete, it does occur in MDS for most but not all parts of the molecule; the turn region starts moving away from the X-ray structure after 9 ps. Only minor differences result when dimer-forming side chains, e.g. tyrosines 7 and 21, are exposed to solvent. The largest rms fluctuations are encountered in exposed polar side chains of Asp 11, Glu 15, Arg 19, and Arg 33, but also in the hydrophobic core residue Phe 20, the only phenylalanine residue present. The latter undergoes an abrupt reorientation suitable for verification by NMR spectroscopy, which is possibly related to the motion of the turn region. The main-chain dihedral angles of the alpha-helix are shifted from values generally found in crystal structures towards those of the ideal Pauling helix. There is concomitant H-bond elongation. The effects are most pronounced and consistent in the MDS simulation.

Conformational studies on the pancreatic polypeptide hormone family.

Pancreatic polypeptide has been extracted and sequenced from a wide range of species. The 36-residue polypeptides have some hormonal characteristics, and show a high degree of sequence homology. Two recently isolated polypeptides, from porcine gut and brain, also show a high degree of sequence homology with the pancreatic polypeptides. It was proposed that these polypeptides were members of a related family. The X-ray determined structure of one member of the family, turkey pancreatic polypeptide, is known to high resolution, but there is no structural information for the others. Studies designed to give an insight into the tertiary structure of these related molecules have been carried out, including model building using interactive computer graphics, circular dichroic spectroscopy and secondary structure prediction using a variety of algorithms. The results indicate that a compact globular conformation, similar to that observed in turkey pancreatic polypeptide may be adopted by all molecules and that this may be more highly conserved than the individual amino acid sequences.

A solution equivalent of the 2Zn----4Zn transformation of insulin in the crystal.

Circular dichroic spectroscopy clearly reveals a solvent-induced conformational change of insulin in the presence of zinc ions. The spectral change corresponds to an increase in helix content. The transition observed in solution is an equivalent of the 2Zn----4Zn insulin transformation in the crystal. This is inferred from a series of observations. (1) The spectral effects are compatible with the refolding of the B-chain N-terminus into a helix known from crystal studies. (2) The spectral effects are induced by the very same conditions which are known to induce the 2Zn----4Zn insulin transformation in the crystal (i.e. threshold concentrations of NaCl, KSCN, NaI, for example). (3) They fail to be induced by the same conditions that fail to induce the crystal transformation (e.g. Ni2+ instead of Zn2+). It is concluded that the potential to undergo the transition resides in the hexamer since neither insulin dimers nor monomeric des-pentapeptideB26-30-insulin respond detectably to high halide concentration. Secondly the ability of zinc ions to accommodate tetrahedral coordination allows the transition which is not permitted by other divalent metal ions. Thirdly the transition is independent of the off-axial tetrahedral zinc coordination sites since it occurs in [AlaB5]insulin which lacks the B5 histidine necessary for their formation. A symmetrically rearranged hexamer thus appears possible with two tetrahedrally coordinated zinc ions on the threefold axis; this is consistent with the observation that in native insulin two zinc ions per hexamer are sufficient to produce the full spectral effect. The amount of additional helix derived from the circular dichroic spectral change, however, cannot settle whether the transition comprises only three or all six of the subunits to yield a symmetrical hexamer. Finally the transformation in solution evidently still occurs in an intramolecularly A1-B29-cross-linked insulin in spite of the partially reduced flexibility.

Adaptation of plasminogen activator sequences to known protease structures.

The sequences of urokinase (UK) and tissue-type plasminogen activator (TPA) were aligned with those of chymotrypsin, trypsin, and elastase according to their 'structurally conserved regions'. In spite of its trypsin-like specificity UK was model-built on the basis of the chymotrypsin structure because of a corresponding disulfide pattern. The extra disulfide bond falls to cysteines 50 and 111d. Insertions can easily be accommodated at the surface. As they occur similarly in both, UK and TPA, a role in plasminogen recognition may be possible. Of the functional positions known to be involved in substrate or inhibitor binding, Asp 97, Lys 143 and Arg 217 (Leu in TPA) may contribute to plasminogen activating specificity. PTI binding may in part be impaired by structural differences at the edge of the binding pocket.

Two mutant forms of human insulin. Structural consequences of the substitution of invariant B24- or B25-phenylalanine by leucine.

In 1979 the first abnormal human insulin was discovered. With the minute samples from the patient a Phe leads to Leu replacement could be established in either position B24 or B25. For the unequivocal localization of the substitution both the Leu analogues had to be prepared by semisynthesis. While another laboratory did this with the sequence of porcine insulin, here we are dealing with the true analogues of human insulin. In the present paper the structural consequences of the substitutions are investigated. Human insulin obtained by total synthesis served as a reference. Its CD spectral properties are herewith documented. According to the substantial deviations of the CD spectrum of [Leu B24]insulin, the introduction of the new side-chain forces conformational changes to occur not only in its immediate surrounding but also in the peptide chain. The failure to give the typical CD spectral response to variations of protein and zinc concentration indicates that the ability to form quaternary structure is impaired. Though dimerization was confirmed by gel chromatography to be largely reduced, it is concluded that, in addition, interactions normally responsible for the increase in tyrosine-CD with association are weakened. [Leu B25]insulin, on the other hand, does exhibit all CD spectral effects characteristic of the native hormone, though quantitatively somewhat reduced. The CD spectroscopic results are in full agreement with the computergraphic analysis of the sterical consequences of the substitutions. For B24-leucine an acceptable packing without movements of the mainchain and/or B15-leucine and without affecting dimerization is impossible, whereas B25-leucine can be accommodated without causing bad contacts either in the monomer or in the dimer. The structural results do not explain why [Leu B25]-insulin should have a lower biological activity than the B24 analogue, 2.1 +/- 0.3% versus 20.9 +/- 2.8%, in the fat cell test. They suggest, however, an important but not critical stereospecific role for the B25-phenylalanine in binding.

Calculation of the circular dichroism of Chironomus hemoglobin in the light of the quality of its X-ray structure.

For the larval hemoglobin III of the insect Chironomus thummi thummi, the rotational strength of the B (Soret) and Q band is calculated with a monopole/monopole and a dipole/dipole approximation applied to the atomic co-ordinates of the X-ray structures at 2.5 and 1.4 A resolution. In previous calculations using the 2.5 A co-ordinates and with perturbing groups being restricted to aromatic side-chains, the dipole/dipole approximation clearly confirmed the negative sign observed by experiment. The predominant interactions were those of phenylalanine residues. Recalculation with X-ray data refined to the present limits of performance corroborates the negativity of the rotational strength, but now the most important contributions are due to the peptide bonds formerly neglected. Also for the 2.5 A coordinates it is learned that in contrast to earlier expectation the influence of the backbone in this hemoglobin is rather strong. A substantial contribution is further obtained for the perturbation by one of the propionic acid carboxylate groups of the heme. Perspectives and problems of the approach are outlined.

Side-chain mobility and the calculation of tyrosyl circular dichroism of proteins. Implications of a test with insulin and des-B1-phenylalanine insulin.

Previous calculations using crystal structure coordinates (Strickland and Mercola [1976], Biochemistry. 15: 3857) have predicted that about 40 percent of the calculated tyrosyl circular dichroism of hexameric insulin is due to one of the four tyrosine residues: viz. the A14-tyrosine interacting with the nearby B1-phenylalanine ring group. We have tested this prediction by measuring the tyrosyl circular dichroism of an isomorphous analogue of insulin, des-B1-phenylalanine-insulin. Contrary to expectation, the resulting circular dichroism was the same as that of insulin. It is concluded that the B1-phenylalanine residue does not in fact make a large contribution to the circular dichroism of A14-tyrosine. This result is probably due to the thermal motion of the B1 and A14 ring groups not taken into account by the calculations. An example of the effects of thermal motion on the calculated circular dichroism is given and improvements that do take into account thermal motion are discussed.