Reduction of hexavalent chromium by Ochrobactrum intermedium BCR400 isolated from a chromium-contaminated soil

Hexavalent chromium-resistant Ochrobactrum intermedium BCR400 was isolated from chromium contaminated soil collected from Vadodara, Gujarat. It reduced 100 mg Cr(VI)/L completely in 52 h with initial Cr(VI) reduction rate of 1.98 mg/L/h. The Cr(VI) reduction rate decreased with increase in Cr(VI) concentration from 100 to 500 mg/L. The addition of anthraquinone-2-sulphonic acid (AQS) to culture O. intermedium BCR400 significantly enhanced its chromium reduction rate. The activation energy of AQS-mediated Cr(VI) reduction (120.69 KJ/mol) was 1.1-fold lower than non-mediated Cr(VI) reduction. An increase in the activities of quinone reductase and chromate reductase in cells grown in presence of AQS/AQS + Cr(VI) suggests their role in reduction of Cr(VI) by O. intermedium. Both chromate reductase and quinone reductase activities were FAD independent, required NADH as reductant, displayed maximum activity at pH (7.0) and temperature (30 °C). Thus Cr(VI) bioremediation potential of O. intermedium can be enhanced by augmentation of system with AQS as redox mediator

Tissue inhibitors of metalloproteinases: evolution, structure and function.

The matrix metalloproteinases (MMPs) play a key role in the normal physiology of connective tissue during development, morphogenesis and wound healing, but their unregulated activity has been implicated in numerous disease processes including arthritis, tumor cell metastasis and atherosclerosis. An important mechanism for the regulation of the activity of MMPs is via binding to a family of homologous proteins referred to as the tissue inhibitors of metalloproteinases (TIMP-1 to TIMP-4). The two-domain TIMPs are of relatively small size, yet have been found to exhibit several biochemical and physiological/biological functions, including inhibition of active MMPs, proMMP activation, cell growth promotion, matrix binding, inhibition of angiogenesis and the induction of apoptosis. Mutations in TIMP-3 are the cause of Sorsby's fundus dystrophy in humans, a disease that results in early onset macular degeneration. This review highlights the evolution of TIMPs, the recently elucidated high-resolution structures of TIMPs and their complexes with metalloproteinases, and the results of mutational and other studies of structure-function relationships that have enhanced our understanding of the mechanism and specificity of the inhibition of MMPs by TIMPs. Several intriguing questions, such as the basis of the multiple biological functions of TIMPs, the kinetics of TIMP-MMP interactions and the differences in binding in some TIMP-metalloproteinase pairs are discussed which, though not fully resolved, serve to illustrate the kind of issues that are important for a full understanding of the interactions between families of molecules

Identification of the (183)RWTNNFREY(191) region as a critical segment of matrix metalloproteinase 1 for the expression of collagenolytic activity.

Matrix metalloproteinase 1 (MMP-1) cleaves types I, II, and III collagen triple helices into (3/4) and (1/4) fragments. To understand the structural elements responsible for this activity, various lengths of MMP-1 segments have been introduced into MMP-3 (stromelysin 1) starting from the C-terminal end. MMP-3/MMP-1 chimeras and variants were overexpressed in Escherichia coli, folded from inclusion bodies, and isolated as zymogens. After activation, recombinant chimeras were tested for their ability to digest triple helical type I collagen at 25 degrees C. The results indicate that the nine residues (183)RWTNNFREY(191) located between the fifth beta-strand and the second alpha-helix in the catalytic domain of MMP-1 are critical for the expression of collagenolytic activity. Mutation of Tyr(191) of MMP-1 to Thr, the corresponding residue in MMP-3, reduced collagenolytic activity about 5-fold. Replacement of the nine residues with those of the MMP-3 sequence further decreased the activity 2-fold. Those variants exhibited significant changes in substrate specificity and activity against gelatin and synthetic substrates, further supporting the notion that this region plays a critical role in the expression of collagenolytic activity. However, introduction of this sequence into MMP-3 or a chimera consisting of the catalytic domain of MMP-3 with the hinge region and the C-terminal hemopexin domain of MMP-1 did not express any collagenolytic activity. It is therefore concluded that RWTNNFREY, together with the C-terminal hemopexin domain, is essential for collagenolytic activity but that additional structural elements in the catalytic domain are also required. These elements probably act in a concerted manner to cleave the collagen triple helix

Collagenase unwinds triple-helical collagen prior to peptide bond hydrolysis.

Breakdown of triple-helical interstitial collagens is essential in embryonic development, organ morphogenesis and tissue remodelling and repair. Aberrant collagenolysis may result in diseases such as arthritis, cancer, atherosclerosis, aneurysm and fibrosis. In vertebrates, it is initiated by collagenases belonging to the matrix metalloproteinase (MMP) family. The three-dimensional structure of a prototypic collagenase, MMP-1, indicates that the substrate-binding site of the enzyme is too narrow to accommodate triple-helical collagen. Here we report that collagenases bind and locally unwind the triple-helical structure before hydrolyzing the peptide bonds. Mutation of the catalytically essential residue Glu200 of MMP-1 to Ala resulted in a catalytically inactive enzyme, but in its presence noncollagenolytic proteinases digested collagen into typical 3/4 and 1/4 fragments, indicating that the MMP-1(E200A) mutant unwinds the triple-helical collagen. The study also shows that MMP-1 preferentially interacts with the alpha2(I) chain of type I collagen and cleaves the three alpha chains in succession. Our results throw light on the basic mechanisms that control a wide range of biological and pathological processes associated with tissue remodelling

Collagenase unwinds triple-helical collagen prior to peptide bond hydrolysis.

Breakdown of triple-helical interstitial collagens is essential in embryonic development, organ morphogenesis and tissue remodelling and repair. Aberrant collagenolysis may result in diseases such as arthritis, cancer, atherosclerosis, aneurysm and fibrosis. In vertebrates, it is initiated by collagenases belonging to the matrix metalloproteinase (MMP) family. The three-dimensional structure of a prototypic collagenase, MMP-1, indicates that the substrate-binding site of the enzyme is too narrow to accommodate triple-helical collagen. Here we report that collagenases bind and locally unwind the triple-helical structure before hydrolyzing the peptide bonds. Mutation of the catalytically essential residue Glu200 of MMP-1 to Ala resulted in a catalytically inactive enzyme, but in its presence noncollagenolytic proteinases digested collagen into typical 3/4 and 1/4 fragments, indicating that the MMP-1(E200A) mutant unwinds the triple-helical collagen. The study also shows that MMP-1 preferentially interacts with the alpha2(I) chain of type I collagen and cleaves the three alpha chains in succession. Our results throw light on the basic mechanisms that control a wide range of biological and pathological processes associated with tissue remodelling

Proteins in Scalp Hair of Preschool Children

Background. Early childhood experiences have long-lasting effects on subsequent mental and physical health, education, and employment. The measurement of these effects relies on insensitive behavioral signs, subjective assessments by adult observers, neuroimaging or neurophysiological studies, or retrospective epidemiologic outcomes. Despite intensive research, the underlying mechanisms of these long-term changes in development and health status remain unknown. Methods. We analyzed scalp hair from healthy children and their mothers using an unbiased proteomics platform combining tandem mass spectrometry, ultra-performance liquid chromatography, and collision-induced dissociation to reveal commonly observed hair proteins with a spectral count of 3 or higher. Results. We observed 1368 non-structural hair proteins in children and 1438 non-structural hair proteins in mothers, with 1288 proteins showing individual variability. Mothers showed higher numbers of peptide spectral matches and hair proteins compared to children, with important age-related differences between mothers and children. Age-related differences were also observed in children, with differential protein expression patterns between younger (2 years and below) and older children (3–5 years). We observed greater similarity in hair protein patterns between mothers and their biological children compared with mothers and unrelated children. The top 5% of proteins driving population variability represented biological pathways associated with brain development, immune signaling, and stress response regulation. Conclusions. Non-structural proteins observed in scalp hair include promising biomarkers to investigate the long-term developmental changes and health status associated with early childhood experiences

Proteins observed in scalp hair from preschool children

ABSTRACTEarly childhood experiences have long-lasting effects on subsequent mental and physical health, education, and employment. Measurement of these effects relies on insensitive behavioral signs, subjective assessments by adult observers, neuroimaging and neurophysiological studies, or remote epidemiologic outcomes. Despite intensive search, no biomarkers for developmental changes in the brain have been identified. We analyzed scalp hair from healthy children and their mothers using an unbiased proteomics platform to reveal 1368 hair proteins commonly observed in children, 1438 proteins commonly observed in mothers, and 1288 proteins observed sporadically in individual subjects. Mothers showed higher numbers of peptide spectral matches and hair proteins compared to children, with important age-related differences between mothers and children. Age-related differences were also observed in children, with differential protein expression patterns between younger (2 years and below) and older children (3-5 years). Boolean analyses showed greater conservation of hair protein patterns between mothers and their biological children as compared to mothers and unrelated children. The top 5% proteins driving population variability represent biological pathways associated with brain development, immune signaling, and stress response regulation. Non-structural proteins observed in scalp hair may include promising biomarkers to investigate the developmental changes associated with early childhood experiences.One Sentence SummaryThe non-structural proteins observed in scalp hair from preschool children show evidence for heritability, reflect biological functions such as brain development, or immune function and regulation of stress responses, and exhibit age- and sex-related differences across periods of early childhood development.</jats:sec

MachineProse: an Ontological Framework for Scientific Assertions

Objective: The idea of testing a hypothesis is central to the practice of biomedical research. However, the results of testing a hypothesis are published mainly in the form of prose articles. Encoding the results as scientific assertions that are both human and machine readable would greatly enhance the synergistic growth and dissemination of knowledge. Design: We have developed MachineProse (MP), an ontological framework for the concise specification of scientific assertions. MP is based on the idea of an assertion constituting a fundamental unit of knowledge. This is in contrast to current approaches that use discrete concept terms from domain ontologies for annotation and assertions are only inferred heuristically. Measurements: We use illustrative examples to highlight the advantages of MP over the use of the Medical Subject Headings (MeSH) system and keywords in indexing scientific articles. Results: We show how MP makes it possible to carry out semantic annotation of publications that is machine readable and allows for precise search capabilities. In addition, when used by itself, MP serves as a knowledge repository for emerging discoveries. A prototype for proof of concept has been developed that demonstrates the feasibility and novel benefits of MP. As part of the MP framework, we have created an ontology of relationship types with about 100 terms optimized for the representation of scientific assertions. Conclusion: MachineProse is a novel semantic framework that we believe may be used to summarize research findings, annotate biomedical publications, and support sophisticated searches