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It is no surprise to anyone who has tried to memorize clotting and complement cascades that there are a great many trypsin-like proteases-too many, it may seem. This fecund enzyme family encompasses such a range of biological roles that other important members and functions are sure to await discovery. Of known trypsin-like proteases, few, if any, are lung-specific. Nonetheless, many contribute in ways critical to lung function, such as fighting microbial invaders, regulating the formation and removal of polymerized fibrin, and rejecting tumors or transplanted tissues. Some of these enzymes, such as plasminogen activators and mast cell tryptases, are native to the lung and live where they work; identical enzymes live and work in other tissues. Other enzymes, such as most complement and hemostatic proteases, are migrants, typically born elsewhere (e.g., the liver). They pass through the lung, looking for something to do; if nothing is found, they pass on, circulating, perhaps to return later. Still others are unwanted, uninvited intruders, such as dust mite proteases. This minireview provides a selective glimpse of the lives of some of the trypsin-like enzymes at work in the lung and airways.
Am J Respir Cell Mol Biol 1997 Jun
PMID:Of mites and men: trypsin-like proteases in the lungs. 919 63

Heat-shock proteins (Hsp) or stress proteins are strong candidates for biomarkers of environmental pollution since they are activated very early in the cascade of cellular events that follow toxic exposure and at concentrations below the lethal dose. Included in a test battery comprised of different bioassays, Hsp induction could provide a general purpose tier I indicator of pollution. Still, little is known on the induction of Hsp under different environmental conditions. In the present study we have made use of an Enzyme Linked Immunosorbent Assay (ELISA) to detect the synthesis of Hsp70 in Raphidocelis subcapitata in response to changes in pH, temperature, humic acids, nitrates and phosphates. The results show that algae respond to these changes in the environment by a transient increase in Hsp70 levels, the extend of which is dependent on the actual parameter under investigation. Out of these five parameters studied, only temperature and possibly pH were able to induce acquired tolerance, i.e. algae grown at a pH or at a temperature different from control conditions were shown to have acquired resistance to a subsequent challenge with Zn (10(-5) M). Adjustment of the pH and temperature in two physico-chemically different natural surface waters was demonstrated to be sufficient to obtain similar induction patterns of Hsp70 upon exposure to zinc. These results qualify Hsp70 as a good biomonitor for environmental pollution provided essential environmental parameters such as pH and temperature are kept constant.
Comp Biochem Physiol A Mol Integr Physiol 1998 May
PMID:Effect of different environmental variables on the synthesis of Hsp70 in Raphidocelis subcapitata. 977 96

Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible. As a result, in the last few years researchers have started to address the "inverse folding problem": Identifying and aligning a sequence to the fold with which it is most compatible, a process known as "threading". In two meetings in which protein folding predictions were objectively evaluated, it became clear that threading as a concept promises a real breakthrough, but that much improvement is still needed in the technique itself. Threading is a NP-hard problem, and thus no general polynomial solution can be expected. Still a practical approach with demonstrated ability to find optimal solutions in many cases, and acceptable solutions in other cases, is needed. We applied the technique of Genetic Algorithms in order to significantly improve the ability of threading algorithms to find the optimal alignment of a sequence to a structure, i.e. the alignment with the minimum free energy. A major progress reported here is the design of a representation of the threading alignment as a string of fixed length. With this representation validation of alignments and genetic operators are effectively implemented. Appropriate data structure and parameters have been selected. It is shown that Genetic Algorithm threading is effective and is able to find the optimal alignment in a few test cases. Furthermore, the described algorithm is shown to perform well even without pre-definition of core elements. Existing threading methods are dependent on such constraints to make their calculations feasible. But the concept of core elements is inherently arbitrary and should be avoided if possible. While a rigorous proof is hard to submit yet an, we present indications that indeed Genetic Algorithm threading is capable of finding consistently good solutions of full alignments in search spaces of size up to 10(70).
Proc Int Conf Intell Syst Mol Biol 1998
PMID:Genetic algorithms for protein threading. 978 25

The nucleotide excision repair (NER) pathway is able to remove a wide variety of structurally unrelated lesions from DNA. NER operates throughout the genome, but the efficiencies of lesion removal are not the same for different genomic regions. Even within a single gene or DNA strand repair rates vary, and this intragenic heterogeneity is of considerable interest with respect to the mutagenic potential of carcinogens. In this study, we have analyzed the removal of the two major types of genotoxic DNA adducts induced by UV light, i.e., the pyrimidine (6-4)-pyrimidone photoproduct (6-4PP) and the cyclobutane pyrimidine dimer (CPD), from the Saccharomyces cerevisiae URA3 gene at nucleotide resolution. In contrast to the fast and uniform removal of CPDs from the transcribed strand, removal of lesions from the nontranscribed strand is generally less efficient and is modulated by the chromatin environment of the damage. Removal of 6-4PPs from nontranscribed sequences is also profoundly influenced by positioned nucleosomes, but this type of lesion is repaired at a much higher rate. Still, the transcribed strand is repaired preferentially, indicating that, as in the removal of CPDs, transcription-coupled repair predominates in the removal of 6-4PPs from transcribed DNA. The hypothesis that transcription machinery operates as the rate-determining damage recognition entity in transcription-coupled repair is supported by the observation that this pathway removes both types of UV photoproducts at equal rates without being profoundly influenced by the sequence or chromatin context.
Mol Cell Biol 1999 Jan
PMID:RNA polymerase II transcription suppresses nucleosomal modulation of UV-induced (6-4) photoproduct and cyclobutane pyrimidine dimer repair in yeast. 985 17

Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent.
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PMID:Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model. 1035 44

Two modes of evolution of repeated domains in proteins have been described: (1) a conservative mode, whereby individual domains are conserved across gene duplication and speciation events, and (2) a concerted mode, whereby repeat domains become homogenized within a gene, presumably by intragenic partial duplication and/or gene conversion. The evolution of repeated EGF-like and fibronection-type-III-like (Fn-III) domains in the vertebrate extracellular matrix proteins tenascin-X (TNX) and tenascin-C (TNC) was studied by comparisons between human and mouse orthologs and between the paralogous TNC and TNX genes. The EGF-like repeats have largely been homogenized within each gene by concerted evolution since the duplication of the two genes but have been conserved since the divergence of rodents and primates. The Fn-III domains of TNC have likewise mainly evolved in a conservative fashion since the divergence of rodents and primates. In contrast, the Fn-III repeats of TNX fall into three distinct categories with regard to mode of evolution: (1) The three C-terminal repeats have been conserved since before duplication of the TNX and TNC genes. (2) Certain other repeats have been homogenized within each gene since gene duplication but have been conserved since the divergence of rodents and primates. (3) Still other repeats have evolved in a concerted fashion in rodent and primate lineages since their divergence. Remarkably, certain introns adjacent to the exons encoding these concertedly evolving Fn-III repeats have themselves evolved in a concerted fashion. This is the first known example of concerted evolution of repeated introns within a protein-coding gene.
Mol Biol Evol 1999 Nov
PMID:Concerted evolution of exons and introns in the MHC-linked tenascin-X gene of mammals. 1055 87

Proteasomal cleavage of proteins is the first step in the processing of most antigenic peptides that are presented to cytotoxic T cells. Still, its specificity and mechanism are not fully understood. To identify preferred sequence signals that are used for generation of antigenic peptides by the proteasome, we performed a rigorous analysis of the residues at the termini and flanking regions of naturally processed peptides eluted from MHC class I molecules. Our results show that both the C terminus (position P1 of the cleavage site) and its immediate flanking position (P1') possess significant signals. The N termini of the peptides show these signals only weakly, consistent with previous findings that antigenic peptides may be cleaved by the proteasome with N-terminal extensions. Nevertheless, we succeed to demonstrate indirectly that the N-terminal cleavage sites contain the same preferred signals at position P1'. This reinforces previous findings regarding the role of the P1' position of a cleavage site in determining the cleavage specificity, in addition to the well-known contribution of position P1. Our results apply to the generation of antigenic peptides and bare direct implications for the mechanism of proteasomal cleavage. We propose a model for proteasomal cleavage mechanism by which both ends of cleaved fragments are determined by the same cleavage signals, involving preferred residues at both P1 and P1' positions of a cleavage site. The compatibility of this model with experimental data on protein degradation products and generation of antigenic peptides is demonstrated.
J Mol Biol 2000 Jan 28
PMID:Sequence signals for generation of antigenic peptides by the proteasome: implications for proteasomal cleavage mechanism. 1065 97

Various phthalate compounds are used as softeners and plasticizers in a wide range of plastic materials. There has been a growing concern regarding a possible health hazard to humans. The mucosa of the upper aerodigestive tract is the organ of first contact for the majority of xenobiotics, such as phthalates, entering the body. Still, there is a lack of information concerning possible carcinogenicity of phthalates in the upper aerodigestive tract. This motivated us to investigate their genotoxic effects on human epithelia: human mucosal cells derived from biopsies harvested during surgery of the oropharynx and the inferior nasal turbinate, respectively. The alkaline version of the microgel electrophoresis assay was used to detect single-strand breaks in the DNA following incubation with dibutylphthalate (DBP) and diisobutylphthalate (DiBP). DNA damage was induced by both DBP and DiBP in oropharyngeal and nasal mucosa, though the effect of DiBP was more pronounced than that of DBP. Nasal mucosa proved to be more sensitive than oropharyngeal epithelia. The results demonstrate genotoxic effects of phthalates on human mucosal cells of the upper aerodigestive tract, in contrast to earlier findings in animal models.
Environ Mol Mutagen 2000
PMID:Phthalates demonstrate genotoxicity on human mucosa of the upper aerodigestive tract. 1069 22

Representatives of the genus Salamandra occur in Europe, Northern Africa and the Near East. Many local variants are known but species and subspecies status of these is still a matter of dispute. We have analysed samples from locations covering the whole expansion range of Salamandra by sequence analysis of mitochondrial D-loop regions. In addition, we have calibrated the rate of divergence of the D-loop on the basis of geologically dated splits of the closely related genus Euproctus. Phylogenetic analysis of the sequences suggests that six major monophyletic groups exist (S. salamandra, S. algira, S. infraimmaculata, S. corsica, S. atra and S. lanzai) which have split between 5 and 13 million years ago (Ma). We find that each of the Salamandra species occupies a distinct geographical area, with the exception of S. salamandra. This species occurs all over Europe from Spain to Greece, suggesting that it was the only species that has recolonized Central Europe after the last glaciation. The occurrence of specific east and west European haplotypes, as well as allozyme alleles in the S. salamandra populations suggests that this recolonization has started from at least two source populations, possibly originating in the Iberian peninsula and the Balkans. Two subpopulations of S. salamandra were found that are genetically very distinct from the other populations. One lives in northern Spain (S. s. bernardezi) and one in southern Italy (S. s. gigliolii). Surprisingly, the mitochondrial lineages of these subpopulations group closer together than the remainder S. salamandra lineages. We suggest that these populations are remnants of a large homogeneous population that had colonized Central Europe in a previous interglacial period, approximately 500 000 years ago. Animals from these populations were apparently not successful in later recolonizations. Still, they have maintained their separate genetic identity in their areas, although they are not separated by geographical barriers from very closely related neighbouring populations.
Mol Ecol 2000 Apr
PMID:Mitochondrial sequence analysis of Salamandra taxa suggests old splits of major lineages and postglacial recolonizations of central Europe from distinct source populations of Salamandra salamandra. 1073 43

Cellobiohydrolase Cel7A (previously called CBH 1), the major cellulase produced by the mould fungus Trichoderma reesei, has been successfully exploited as a chiral selector for separation of stereo-isomers of some important pharmaceutical compounds, e.g. adrenergic beta-blockers. Previous investigations, including experiments with catalytically deficient mutants of Cel7A, point unanimously to the active site as being responsible for discrimination of enantiomers. In this work the structural basis for enantioselectivity of basic drugs by Cel7A has been studied by X-ray crystallography. The catalytic domain of Cel7A was co-crystallised with the (S)-enantiomer of a common beta-blocker, propranolol, at pH 7, and the structure of the complex was determined and refined at 1. 9 A resolution. Indeed, (S)-propranolol binds at the active site, in glucosyl-binding subsites -1/+1. The catalytic residues Glu212 and Glu217 make tight salt links with the secondary amino group of (S)-propranolol. The oxygen atom attached to the chiral centre of (S)-propranolol forms hydrogen bonds to the nucleophile Glu212 O(epsilon1) and to Gln175 N(epsilon2), whereas the aromatic naphthyl moiety stacks with the indole ring of Trp376 in site +1. The bidentate charge interaction with the catalytic glutamate residues is apparently crucial, since no enantioselectivity has been obtained with the catalytically deficient mutants E212Q and E217Q. Activity inhibition experiments with wild-type Cel7A were performed in conditions close to those used for crystallisation. Competitive inhibition constants for (R)- and (S)-propranolol were determined at 220 microM and 44 microM, respectively, corresponding to binding free energies of 20 kJ/mol and 24 kJ/mol, respectively. The K(i) value for (R)-propranolol was 57-fold lower than the highest concentration, 12.5 mM, used in co-crystallisation experiments. Still several attempts to obtain a complex with the (R)-enantiomer have failed. By using cellobiose as a selective competing ligand, the retention of the enantiomers of propranolol on the chiral stationary phase (CSP) based on Cel7A mutant D214N were resolved into enantioselective and non- selective binding. The enantioselective binding was weaker for both enantiomers on D214N-CSP than on wild-type-CSP.
J Mol Biol 2001 Jan 05
PMID:Structural basis for enantiomer binding and separation of a common beta-blocker: crystal structure of cellobiohydrolase Cel7A with bound (S)-propranolol at 1.9 A resolution. 1111 49


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