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Martin Petrek

Publications and source records attributed to Martin Petrek.

15 recordsLinked to original sources
PubMed2007

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles.

The knowledge of the access paths connecting interior of molecular systems with surrounding environment is important for the understanding of structurefunction relationships and engineering of molecules for biotechnological applications. CAVER is a computer program developed for calculations of tunnels, channels or pores in the biomolecules, inorganic materials and molecular ensembles. The algorithm performs a skeleton search based on a reciprocal distance function grid. The algorithm is implemented in the stand-alone version, web version and as plug-in for PyMol. CAVER is available from the website http://loschmidt.chemi.muni.cz/caver.

Algorithms↗
PubMed2006

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.

1,2,3-Trichloropropane (TCP) is a highly toxic, recalcitrant byproduct of epichlorohydrin manufacture. Haloalkane dehalogenase (DhaA) from Rhodococcus sp. hydrolyses the carbon-halogen bond in various halogenated compounds including TCP, but with low efficiency (k (cat)/K (m )= 36 s(-1) M(-1)). A Cys176Tyr-DhaA mutant with a threefold higher catalytic efficiency for TCP dehalogenation has been previously obtained by error-prone PCR. We have used molecular simulations and quantum mechanical calculations to elucidate the molecular mechanisms involved in the improved catalysis of the mutant, and enantioselectivity of DhaA toward TCP. The Cys176Tyr mutation modifies the protein access and export routes. Substitution of the Cys residue by the bulkier Tyr narrows the upper tunnel, making the second tunnel "slot" the preferred route. TCP can adopt two major orientations in the DhaA enzyme, in one of which the halide-stabilizing residue Asn41 forms a hydrogen bond with the terminal halogen atom of the TCP molecule, while in the other it bonds with the central halogen atom. The differences in these binding patterns explain the preferential formation of the (R)- over the (S)-enantiomer of 2,3-dichloropropane-1-ol in the reaction catalyzed by the enzyme.

Hydrolases↗
PubMed2006

CAVER: a new tool to explore routes from protein clefts, pockets and cavities.

BACKGROUND: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS: The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version. CONCLUSION: The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web site http://loschmidt.chemi.muni.cz/caver/.

Algorithms↗
PubMed2006

Protein profiles of bronchoalveolar lavage fluid from patients with pulmonary sarcoidosis.

BACKGROUND: Pulmonary sarcoidosis is a multisystem granulomatous disease with various clinical phenotypes. So far, there has been little information on protein patterns (PPs) of bronchoalveolar lavage fluid (BALF) from patients with sarcoidosis and no data are available on PPs in clinical disease subtypes. OBJECTIVES: To investigate the PP of BALF from patients with pulmonary sarcoidosis, to evaluate whether PPs reflect disease course as assessed by chest X-ray (CXR), and to compare PPs between patients with/without Löfgren's syndrome. METHODS: Surface-enhanced laser desorption/ionization-time-of-flight mass spectroscopy was applied to investigate PPs in unconcentrated BALF from 65 patients (CXR stage I, n = 32; CXR stage II, n = 22, CXR stage III, n = 11) and 23 healthy control subjects. The Mann-Whitney U test was used to detect differentially expressed protein peaks. After reversed-phase fractionation, peptide fingerprint mapping and immunodepletion were used to identify deregulated (up-regulated or down-regulated) proteins. RESULTS: Forty differentially expressed protein entities (2.75-185.62 kD) were detected in patients with pulmonary sarcoidosis versus control subjects (p < 0.05). Whereas 13 peaks (33%) were present across all CXR stages, 27 (67%) were specific for particular CXR stages. Comparison of PPs between CXR stage I patients with or without Löfgren's syndrome revealed 25 differentially expressed peaks. The total number of deregulated peaks and also of those associated with sarcoidosis as a whole were markedly lower in patients with Löfgren's syndrome in comparison with other sarcoid phenotypes. Human serum albumin, alpha1-antitrypsin, and protocadherin-2 precursor were identified from sarcoidosis-associated PP. CONCLUSION: Surface-enhanced laser desorption/ionization-time-of-flight mass spectroscopy enables determination of protein patterns in sarcoid BALF and allows detection of protein patterns linked to a particular disease course.

Adult↗
PubMed2004

Monocyte chemoattractant protein-1 in patients with peripheral arterial disease.

BACKGROUND: Chemokine-driven migration of inflammatory cells has been implicated in the pathogenesis of atherosclerotic conditions including peripheral arterial disease (PAD). Monocyte chemoattractant protein-1 (MCP-1) is elevated in patients with coronary artery disease and in hypertensive patients. This study therefore investigated MCP-1 in patients with PAD. METHODS: Serum MCP-1 was determined by enzyme-linked immunosorbent assay in 36 healthy, control subjects and in 19 patients with PAD. Statistical analysis utilised the Mann-Whitney test and Spearman correlation (p < 0.05). RESULTS: MCP-1 (pg/ml) was increased in patients compared with in controls (mean+/-standard error of the mean: PAD group, 748+/-60; control group, 459+/-27; p=0.0001). MCP-1 levels tended to decrease with progressing disease. From atherosclerosis risk factors, diabetes inclined to increase MCP-1 levels; hypertension had no effect. Serum MCP-1 correlated with cholesterol, triglycerides, low-density lipoprotein but not high-density lipoprotein. CONCLUSION: Elevation of MCP-1 in the circulation of PAD patients shown in the present pilot study implicates this CC chemokine ligand 2 in inflammatory processes contributing to PAD clinical symptomatology. Further investigations are necessary to evaluate whether MCP-1 can be used as a potential marker of peripheral arterial disease follow-up and/or prognosis.

Aged↗
PubMed2004

Interleukin 1alpha single-nucleotide polymorphism associated with systemic sclerosis.

OBJECTIVE: In systemic sclerosis (SSc), constitutive expression of the proinflammatory and fibrogenic cytokine interleukin 1alpha (IL-1alpha) by dermal fibroblasts from the affected skin has been observed. We investigated the association of a single-nucleotide polymorphism at position -889 in the IL-1alpha gene in patients with SSc. METHODS: Genotyping of IL-1alpha-889 polymorphism was performed in 46 patients with SSc and in 150 healthy controls by polymerase chain reaction with sequence-specific primers. All subjects were unrelated Slovak Caucasians. RESULTS: In SSc patients, carriers of the IL-1alpha-889 T allele were significantly overrepresented in comparison with controls (63.0% vs 42.0%; p = 0.01, OR 2.3, 95% CI 1.2-4.6). The frequency of the IL-1alpha-889 T allele was increased in SSc patients (38.0%) in comparison with controls (25.7%; p = 0.02). CONCLUSION: The IL-1alpha-889 polymorphism, previously shown to predispose to increased IL-1 protein expression, may be involved in susceptibility to SSc.

Case-Control Studies↗
PubMed2003

CC chemokine receptor (CCR)2 polymorphism in Czech patients with myocardial infarction.

Examining an association between myocardial infarction (MI) and the Val/Ile polymorphism in the gene for CC chemokine receptor (CCR)2 at the position 64 (CCR2-V64I), 122 MI Czech patients and 277 unrelated control (C) subjects were genotyped by PCR-SSP. The frequency of the VI genotype of CCR2-V64I was increased in MI patients in comparison with the control population (P=0.03). Further analysis revealed that relationship between the VI genotype and MI is specific only for females and, strikingly, this genotype was associated to an early MI onset (before or at the age of 50 years). Females with the VI genotype were seven times more prone to suffer from MI before 50 years than those with the VV genotype (P<0.01). If the VI genotype of the CCR2-V64I is indeed a risk factor for an earlier MI onset in females must be checked by independent studies in other centres and/or populations.

Case-Control Studies↗
PubMed2003

Expression of macrophage inflammatory protein-3 beta/CCL19 in pulmonary sarcoidosis.

In this study, messenger RNA (mRNA) expression for novel T lymphocyte chemoattractants, leukotactin-1, macrophage inflammatory protein (MIP)-3 alpha and MIP-3 beta was investigated in bronchoalveolar lavage fluid (BALF) cells from patients with sarcoidosis, a T cell-mediated disease with typical CD4+ lymphocyte alveolitis. Of these three chemokines, only MIP-3 beta mRNA was upregulated in sarcoidosis, and therefore, protein levels of this chemokine, its pharmacologic regulation, and association with disease clinical course were explored. MIP-3 beta protein concentrations were elevated in BALF from sarcoid patients compared with control subjects (p = 0.001) and in patients with chest X-ray stage II chemokine protein levels were increased compared with stage I (p = 0.003). MIP-3 beta protein was associated predominantly with alveolar macrophages and correlated with BALF lymphocytes and T cell subsets. mRNA expression for the MIP-3 beta receptor, CC chemokine receptor 7, was increased in sarcoidosis and correlated with MIP-3 beta protein levels. MIP-3 beta mRNA and protein expression in BALF cells was suppressed by dexamethasone and cyclosporine A in vitro. In conclusion, MIP-3 beta is implicated in T lymphocyte recruitment in sarcoidosis, is associated with disease progression, and is downregulated by drugs used for sarcoidosis treatment. This novel chemokine, therefore, represents a candidate for studies of sarcoidosis pathobiologic mechanisms.

Adult↗
PubMed2003

In vitro pharmacoregulation of CC chemokine ligand 5 and its receptor CCR5 in diffuse lung diseases.

BACKGROUND: CC chemokine ligand (CCL)5 and its receptor CCR5 contribute to leukocyte migration into lungs of patients with diffuse lung diseases (DLD). Pharmacological regulation of CCL5 and CCR5 expression was therefore explored in bronchoalveolar cells obtained from patients with DLD. METHODS: Cells from 21 patients were co-cultivated in vitro with tumour necrosis factor-alpha and dexamethasone, cyclosporin A (CyA) or pentoxifylline. Chemokine mRNA expression and protein production was assessed by reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. RESULTS: Dexamethasone altered CCL5 mRNA expression and suppressed its protein levels. CyA inhibited chemokine mRNA expression but not protein production. Pentoxifylline did not affected chemokine expression. Both dexamethasone and CyA suppressed CCR5 mRNA transcripts. CONCLUSION: In conclusion, while dexamethasone downregulates the CCL5 functional form, CyA and pentoxifylline have no effects on CCL5 protein. These data provide in vitro correlation for clinical applications of immunomodulators in therapy of DLD.

Adult↗
PubMed2003

Characterization of p40 and IL-10 in the BALF of patients with pulmonary sarcoidosis.

This study investigated cytokine protein levels (interleukin-12 p70 [IL-12p70], p40, and IL-10) in bronchoalveolar lavage fluid (BALF) from patients with pulmonary sarcoidosis (n = 59), healthy control subjects (n = 17), and patients with idiopathic pulmonary fibrosis (IPF) (n = 30). The relationship between cytokine levels and clinical course of sarcoidosis was also examined. Overall, p40 was far more abundant than IL-12p70. p40 levels (pg/ml, mean +/- SEM) were significantly higher in the BALF from patients with sarcoidosis (2.97 +/- 3.69) than in IPF patients (0.83 +/- 1.57) and healthy subjects (0.78 +/- 1.00). Size exclusion chromatography indicated that p40 detected in BALF from sarcoidosis patients corresponded to p40 monomers or (p40)(2) homodimers. Further, p40 levels were associated with (paralleled) the clinical course of sarcoidosis, with the highest levels detected in BALF from patients with persistent disease. Higher p40 levels were also found in the BALF from sarcoid patients who required corticosteroid treatment compared with patients with spontaneous regression (3.51 +/- 3.83 vs. 2.01 +/- 3.43, p = 0.03). IL-10 concentrations paralleled p40 changes. No similar association was found for IL-12p70 levels. In conclusion, this report shows that the BALF from patients with sarcoidosis contains elevated levels of p40, (p40)(2), and IL-10 protein but not of IL-12p70. The present data also suggest that BALF p40 concentrations may be indicative of the sarcoidosis clinical course.

Adult↗
PubMed2002

Expression of the chemokine PARC mRNA in bronchoalveolar cells of patients with sarcoidosis.

BACKGROUND: Chemotactic cytokines (chemokines) have been recently implicated in the pathogenesis of interstitial lung diseases. A novel chemokine called pulmonary and activation-regulated chemokine (PARC/CCL18), which attracts lymphocytes in vitro, has been detected in the human lung. We have, therefore, investigated PARC mRNA expression in bronchoalveolar lavage fluid (BALF) cells of patients with pulmonary sarcoidosis-a disease characterised by a lymphocytic infiltrate. Further, because several immunomodulators are used in the treatment of sarcoidosis, we have determined the effects of selected drugs on PARC mRNA expression in vitro. SUBJECTS AND METHODS: BALF cells were obtained by standard bronchoalveolar lavage (BAL) from 30 patients with pulmonary sarcoidosis (S) and 16 control subjects (C). BALF cells from seven subjects were cultured in the presence of dexamethasone (Dx), cyclosporin A (CyA) and pentoxifylline (Px). PARC mRNA expression was semiquantitated by reverse-transcription polymerase chain reaction (RT-PCR) using normalisation to the expression of the beta-actin gene. RESULTS: PARC mRNA transcripts were detected in 87% of all investigated BALF samples. The expression (ODR PARC/beta-actin; median, the first to the third quartile range) was similar in both groups tested (S, 0.60 (0.50-0.95); C, 0.59 (0.36-0.93); S vs. C: P>0.05). PARC mRNA expression was not associated with the number of lymphocytes in bronchoalveolar space. PARC mRNA expression was significantly suppressed by Dx (P=0.02); CyA and Px showed a moderate inhibitory effect which did not attain significance. CONCLUSION: mRNA for the chemokine PARC is expressed in the lower respiratory tract in both healthy subjects and patients with pulmonary sarcoidosis. Out of the three immunomodulatory drugs tested, Dx downregulates PARC mRNA expression in BALF cells in vitro.

Adjuvants, Immunologic↗
PubMed2002

CC chemokine receptor 5 (CCR5) mRNA expression in pulmonary sarcoidosis.

The CC chemokine receptor 5 (CCR5) binds the chemokine ligands RANTES (CCL5) and MIP-1alpha (CCL3), which have been implicated in the development of alveolitis in sarcoidosis. We have, therefore, investigated CCR5 mRNA expression in bronchoalveolar lavage fluid (BALF) cells from patients with sarcoidosis. Further, we explored whether there was any association between CCR5 mRNA expression and the presence of the CCR5Delta32 DNA polymorphism. Semiquantitative RT-PCR was used to determine CCR5 mRNA expression from BALF cells from 16 control subjects (C) and 39 patients with sarcoidosis (S). The data on the CCR5Delta32 polymorphism, determined by PCR-SSP, were available for 37 patients. CCR5 mRNA expression was significantly upregulated in sarcoidosis (median+/-SEM, C, 0.00+/-0.07; S, 0.12+/-0.07; P<0.05). When patients were evaluated according to their CCR5Delta32 genotype, an interesting trend emerged with Delta32 positive patients (wt, mt) expressing less mRNA than the patients with both wild-type alleles (wt, wt): 0.00+/-0.09, and 0.26+/-0.09, respectively; P>0.05). In conclusion, upregulation of CCR5 mRNA in BALF of patients with sarcoidosis is consistent with its chemokine ligands RANTES and MIP-1alpha playing a pivotal role in inflammatory cell recruitment to disease sites. Though the data from this pilot study had no clinical correlations we suggest that further studies are warranted on the role of this Th1 subset marker in the pathogenesis of sarcoidosis.

Adult↗
PubMed2002

Interleukin-1 gene cluster polymorphisms in sarcoidosis and idiopathic pulmonary fibrosis.

Members of the interleukin-1 (IL-1) family are implicated in the pathogenesis of sarcoidosis and idiopathic pulmonary fibrosis (IPF). We have, therefore, performed a case-control study to investigate a plausible association between sarcoidosis and the polymorphisms in the IL-1alpha, IL-1beta, and IL-1 receptor antagonist (IL-1Ra) genes. Further, as a separate question, we explored whether the aforementioned genes of the IL-1 cluster are associated with IPF. Using PCR with sequence-specific primers, IL-1alpha -889, IL-1beta -511, IL-1beta +3953, and IL-1Ra intron 2 VNTR polymorphisms were determined in 348 white subjects of West Slavonic ancestry (95 patients with sarcoidosis, 54 patients with IPF, and 199 healthy control subjects). The IL-1alpha -889 1.1 genotype was significantly overrepresented in patients with sarcoidosis in comparison with control subjects (60.0 versus 44.2%, p = 0.012, p(corr) = 0.047). The distribution of IL-1beta -511, IL-1beta +3953, and IL-1Ra VNTR genotypes and alleles did not significantly differ between the cases and controls. No association between IPF and the investigated polymorphisms was found. Strong linkage disequilibrium between pairs of polymorphic loci was observed. Further population studies are warranted to confirm the observed association between sarcoidosis and the IL-1alpha polymorphism and also to explore mechanisms of IL-1alpha -889 participation in aberrant immune response in sarcoidosis.

Adolescent↗
PubMedDate not supplied

Clara cell protein (CC16) in serum and bronchoalveolar lavage fluid of subjects exposed to asbestos.

The Clara cell protein (CC16) is a small and readily diffusible protein of 16 kDa secreted by bronchiolar Clara cells in the distal airspaces. These epithelial cells are altered in several pulmonary pathological processes induced by various lung toxicants. In the search for a new biomarker of asbestos-induced lung impairment, we used a sensitive immunoassay to determine the levels of CC16 in bronchoalveolar fluid (BALF) and serum of subjects exposed to asbestos compared with a group of healthy controls. In the BALF of asbestos-exposed subjects there was an insignificant trend towards CC16 elevation compared with controls, with a (mean +/- SD of 0.81 +/- 0.65 mg l-1 for asbestos-exposed subjects (n = 23) versus 0.39 +/- 0.19 mg l-1 for controls (n = 11) (p = 0.09). In serum, CC16 concentration was significantly increased among asbestos-exposed subjects, with values of 27.2 +/- 24.0 micrograms l-1 for asbestos-exposed subjects (n = 34) versus 16.1 +/- 7.6 micrograms l-1 for controls (n = 34) (p = 0.01). Regarding the effects of smoking, there were significant differences between generally lower CC16 levels in serum and BALF (p = 0.05 and 0.001, respectively) of smokers compared with the higher levels in non-smokers. Serum CC16 levels positively correlated with those in BALF, which is consistent with a diffusional transfer of CC16 from the bronchoalveolar space into the serum. No association, however, emerged between the levels of CC16 in serum or BALF and either the duration of asbestos exposure or the severity of the lung impairment as assessed by chest X-ray. These findings suggest that exposure to asbestos elicits early changes in the local and, importantly, also the systemic levels of CC16. This pneumoprotein therefore appears as a promising non-invasive biomarker of asbestos-induced lung injury and occupational disease in both smoking and non-smoking exposed subjects.

Adult↗