In situ proteolysis for protein crystallization and structure determination

We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.     

Effects on protease inhibition by modifying of helicase residues in hepatitis C virus nonstructural protein 3

This study of the full-length bifunctional nonstructural protein 3 from hepatitis C virus (HCV) has revealed that residues in the helicase domain affect the inhibition of the protease. Two residues (Q526 and H528), apparently located in the interface between the S2 and S4 binding pockets of the substrate binding site of the protease, were selected for modification, and three enzyme variants (Q526A, H528A and H528S) were expressed, purified and characterized. The substitutions resulted in indistinguishable K(m) values and slightly lower k(cat) values compared to the wild-type. The K(i) values for a series of structurally diverse protease inhibitors were affected by the substitutions, with increases or decreases up to 10-fold. The inhibition profiles for H528A and H528S were different, confirming that not only did the removal of the imidazole side chain have an effect, but also that minor differences in the nature of the introduced side chain influenced the characteristics of the enzyme. These results indicate that residues in the helicase domain of nonstructural protein 3 can influence the protease, supporting our hypothesis that full-length hepatitis C virus nonstructural protein 3 should be used for protease inhibitor optimization and characterization. Furthermore, the data suggest that inhibitors can be designed to interact with residues in the helicase domain, potentially leading to more potent and selective compounds.     

Redox-sensitive loops D and E regulate NADP(H) binding in domain III and domain I-domain III interactions in proton-translocating Escherichia coli transhydrogenase.

Membrane-bound transhydrogenases are conformationally driven proton-pumps which couple an inward proton translocation to the reversible reduction of NADP+ by NADH (forward reaction). This reaction is stimulated by an electrochemical proton gradient, Delta p, presumably through an increased release of NADPH. The enzymes have three domains: domain II spans the membrane, while domain I and III are hydrophilic and contain the binding sites for NAD(H) and NADP(H), respectively. Separately expressed domain I and III together catalyze a very slow forward reaction due to tightly bound NADP(H) in domain III. With the aim of examining the mechanistic role(s) of loop D and E in domain III and intact cysteine-free Escherichia coli transhydrogenase by cysteine mutagenesis, the conserved residues beta A398, beta S404, beta I406, beta G408, beta M409 and beta V411 in loop D, and residue beta Y431 in loop E were selected. In addition, the previously made mutants betaD392C and betaT393C in loop D, and beta G430C and beta A432C in loop E, were included. All loop D and E mutants, especially beta I406C and beta G430C, showed increased ratios between the rates of the forward and reverse reactions, thus approaching that of the wild-type enzyme. Determination of values indicated that the former increase was due to a strongly increased dissociation of NADPH caused by an altered conformation of loops D and E. In contrast, the cysteine-free G430C mutant of the intact enzyme showed the same inhibition of both forward and reverse rates. Most domain III mutants also showed a decreased affinity for domain I. The results support an important and regulatory role of loops D and E in the binding of NADP(H) as well as in the interaction between domain I and domain III.     

Temperature sensitivity of nitrogen productivity for Scots pine and Norway spruce

Environmental conditions control physiological processes in plants and thus their growth. The predicted global warming is expected to accelerate tree growth. However, the growth response is a complex function of several processes with both direct and indirect effects. To analyse this problem we have used needle nitrogen productivity, which is an aggregate parameter for production of new foliage. Data on needle dry matter, production, and nitrogen content in needles of Scots pine ( Pinus sylvestris) and Norway spruce ( Picea abies) from a wide range of climatic conditions were collected and needle nitrogen productivities, defined as dry matter production of needles per unit of nitrogen in the needle biomass, were calculated. Our results show that the nitrogen productivity for spruce is insensitive to temperature. However, for pine, temperature affects both the magnitude of nitrogen productivity at low needle biomass and the response to self-shading but the temperature response is small at the high end of needle biomass. For practical applications it may be sufficient to use a species-specific nitrogen productivity that is independent of temperature. Because temperature affects tree growth indirectly as well as through soil processes, the effects of temperature change on tree growth and ecosystem carbon storage should mainly be derived from effects on nitrogen availability through changes in nitrogen mineralization. In addition, this paper summarises data on dry matter, production and nitrogen content of needles of conifers along a temperature gradient.     

Thrombin inhibitor reduces myocardial infarction in apoE-/- x LDLR-/- mice

We have previously shown that atherosclerotic apolipoprotein E-deficient (apoE(-/-)) x LDL receptor-deficient (LDLR(-/-)) mice develop myocardial infarction when exposed to hypoxic stress. This study was performed to assess the role of thrombin and thrombosis in this process. ApoE(-/-) x LDLR(-/-) mice were fed a cholesterol-rich diet for 8 mo and were then subjected to hypoxic stress while receiving isoflurane anesthesia. One group received a bolus dose (5.6 micromol/kg) of the thrombin inhibitor melagatran, and control animals received PBS 10 min before the hypoxic stress. The mice were exposed to 10 min of hypoxia followed by normoxia. Ten minutes after the stress, Alzet pumps delivering melagatran (20 nmol x kg x (-1)min(-1)) or PBS were implanted, and the mice were allowed to recover for 48 h. The cardiac response was analyzed by histology, immunohistochemistry, and serum troponin T assay. All animals showed reversible ECG changes as a sign of ischemia during hypoxic stress, and 50% developed infarctions afterward as judged by troponin T levels. The group that received thrombin inhibitor had significantly lower troponin T and smaller myocardial infarctions than the PBS-treated group. These data show that thrombin generation is an important pathogenetic factor and suggest that coronary thrombosis is involved in myocardial infarction in atherosclerotic mice. Exposure of atherosclerotic mice to hypoxia leads to myocardial infarction through a two-phase pathway in which acute transient ischemia is followed by thrombin-dependent, irreversible, myocardial ischemia and myocardial cell death.     

Four new species of Gyrodactylus von Nordmann, 1832 (Monogenea,Gyrodactylidae) on gobiid fishes: combined DNA and morphological analyses

Four Gyrodactylus species parasitising four closely related gobiid species in European coastal waters were studied and compared with G. arcuatus Bychowsky sensu Bychowsky & Poljansky (1953) from Gasterosteus aculatus . These were G. gondae n. sp. from Pomatoschistus minutus and P. lozanoi , G. flavescensis n. sp. from Gobiusculus flavescens , G. arcuatoides n. sp. from P. minutus and G. branchialis n. sp. from P. microps. Combined molecular and morphological analyses, as well as morphometric and statistical methods, were used. The ssrRNA V4 region and the complete ITS rDNA region were sequenced. Genetically the four new species are clearly distinct from G. arcuatus . From a morphological point of view, the haptoral hard parts of G. gondae n. sp., G. flavescensis n. sp. and G. arcuatoides n. sp. are related to those of G. arcuatus, while these parts of G. branchialis n. sp. are different, but related to those of G. quadratidigitus Longshaw, Pursglove & Shinn, 2003. For the latter two species, a new species group is formed. The V4 and ITS sequence analyses, however, indicate a close relationship between G. branchialis and the three G. arcuatus-like species.     

Bone and joint neuropathy in rats with type-2 diabetes

We have previously demonstrated that Goto-Kakizaki (GK) rats with spontaneous type-2 diabetes and peripheral neuropathy exhibit regional osteopathic changes. In the present study on 18 GK rats and 21 control Wistar rats, the occurrence of the sensory neuropeptides substance P (SP) and calcitonin gene-related peptide (CGRP), and the autonomic neuropeptide Y (NPY) was analysed in bone and joints, dorsal root ganglia and lumbar spinal cord by immunohistochemistry and radioimmunoassay (RIA). Immunohistochemistry disclosed a predominance of immunoreactivities in vessel-related nerve fibers, although some were also seen in free terminals. While SP, CGRP and NPY in periosteum, cortical bone and synovium was confined to neuronal tissue, the bone marrow in addition exhibited an abundance of NPY-positive megakaryocytes. Apart from this cellular source of NPY, the observations suggest that the three neuropeptides analysed in bone and joints are of neuronal origin. Quantification by RIA showed a significant decrease of NPY in cortical bone (-36%), bone marrow (-66%) and ankle (-29%) of GK rats. CGRP was decreased in the spinal cord (-19%) and dorsal root ganglia (-26%) but was unchanged in bone and joints, as with SP. Given the suggested anabolic role of NPY and CGRP on bone, neuropeptidergic deficit in diabetes may prove to be an important factor underlying the development of regional osteopenia.     

Towards a new concept of lignin condensation in kraft pulping. Initial results

In kraft pulping, a comparatively large amount of lignin remains in the fibres after the cook. Based on various analytical techniques for lignin, such as thioacidolysis, GPC and NMR, it is suggested that lignin condensation reactions take place during the cook. The reaction seems, however, not to involve ionic intermediates as has been suggested previously but rather a one-electron mechanism with elemental sulphur as the initiator. Support for such a reaction has been found through kraft cooks in the presence of an added phenol, 2,6-xylenol, as well as through NMR analysis of kraft lignin. It was found that the added phenol is incorporated in the pulp lignin with linkages indicative of radical coupling. Furthermore, kraft lignin was found to contain substantial amounts of chemically linked fatty acids. By complementary analyses of sulphur and polysulphide in an industrial black liquor, the presence of these compounds throughout a kraft cook was demonstrated.