Estructura y propiedades de macromoléculas biológicas

Facultad de Ciencias Exacta

Estructura y propiedades de macromoléculas biológicas

Facultad de Ciencias Exacta

Theoretical study of the mechanisms of substrate recognition by catalase

A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H2O2 is only slightly larger than that for H2O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.This work has been supported by the Centre de Supercomputació de Catalunya (CESCA; Mol. Recog. Project) and by the Spanish Ministerio de Ciencia y Tecnología PM99-0046 and BIO099-0865Peer Reviewe

Theoretical study of the mechanisms of substrate recognition by catalase

A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H2O2 is only slightly larger than that for H2O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.This work has been supported by the Centre de Supercomputació de Catalunya (CESCA; Mol. Recog. Project) and by the Spanish Ministerio de Ciencia y Tecnología PM99-0046 and BIO099-0865Peer Reviewe

The need for a shared database infrastructure: Combining X-ray crystallography and electron microscopy

Advances in structural biology are opening greater opportunities for understanding biological structures from the cellular to the atomic level. Particularly promising are the links that can be established between the information provided by electron microscopy and the atomic structures derived from X-ray crystallography and nuclear magnetic resonance spectroscopy. Combining such different kinds of structural data can result in novel biological information on the interaction of biomolecules in large supramolecular assemblies. As a consequence, the need to develop new databases in the field of structural biology that allow for an integrated access to data from all the experimental techniques is becoming critical. Pilot studies performed in recent years have already established a solid background as far as the basic information that an integrated macromolecular structure database should contain, as well as the basic principles for integration. These efforts started in the context of the BioImage project, and resuited in a first complete database prototype that provided a versatile platform for the linking of atomic models or X-ray diffraction data with electron microscopy information. Analysis of the requirements needed to combine data at different levels of resolution have resulted in sets of specifications that make possible the integration of all these different types in the context of a web environment. The case of a structural stuffy linking electron microscopy and X-ray data, which is already contained within the BioImage data base and in the Protein Data Bank, is used here to illustrate the current approach, while a general discussion highlights the urgent need for integrated databases.Work on this project has been supported by the European Union through grant PL 960472. Special actions or extensions are being made possible by core national grants (BIO95-0768, BIO97-1485-CE and BIO98-0761, to J.C., and PB95218 to I.F.)Peer Reviewe

Reports and information RPEiS 37(4), 1975

Digitalizacja i deponowanie archiwalnych zeszytów RPEiS sfinansowane przez MNiSW w ramach realizacji umowy nr 541/P-DUN/201

Systemic Inflammatory Response to Smoking in Chronic Obstructive Pulmonary Disease: Evidence of a Gender Effect

<div><p>Background</p><p>Tobacco smoking is the main risk factor of chronic obstructive pulmonary disease (COPD) but not all smokers develop the disease. An abnormal pulmonary and systemic inflammatory response to smoking is thought to play a major pathogenic role in COPD, but this has never been tested directly.</p><p>Methods</p><p>We studied the systemic biomarker and leukocyte transcriptomic response (Affymetrix microarrays) to smoking exposure in 10 smokers with COPD and 10 smokers with normal spirometry. We also studied 10 healthy never smokers (not exposed to smoking) as controls. Because some aspects of COPD may differ in males and females, and the inflammatory response to other stressors (infection) might be different in man and women, we stratified participant recruitment by sex. Differentially expressed genes were validated by q-PCR. Ontology enrichment was evaluated and interaction networks inferred.</p><p>Results</p><p>Principal component analysis identified sex differences in the leukocyte transcriptomic response to acute smoking. In both genders, we identified genes that were differentially expressed in response to smoking exclusively in COPD patients (COPD related signature) or smokers with normal spirometry (Smoking related signature), their ontologies and interaction networks.</p><p>Conclusions</p><p>The use of an experimental intervention (smoking exposure) to investigate the transcriptomic response of peripheral leukocytes in COPD is a step beyond the standard case-control transcriptomic profiling carried out so far, and has facilitated the identification of novel COPD and Smoking expression related signatures which differ in males and females.</p></div

Median (and IQR) values of blood carboxy-hemoglobin (<i>panel A</i>), circulating leukocytes (<i>panel B</i>), C-reactive protein serum levels (<i>panel C</i>) and IL-6 (<i>panel D</i>) in COPD patients, smoker (S) and non-smoker (NS) controls, before (T0) and 30 min.

<p>(T30) or 180 min. (T180) later. For further explanations, see text.</p

Characterization of participants by sex (mean±SD).

<p>Asterisk indicate p<0.05 between COPD males and females, § indicates p<0.05 between COPD patients and smoker controls.</p

Gene ontology enrichment analysis, by sex. Females ontologies/genes associated with COPD.

<p>Bold italic text indicates up regulated genes and normal text indicates down regulated genes in response to smoking.</p