PROMPT: a protein mapping and comparison tool

BACKGROUND: Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or sequence properties compared to another group, and whether this enrichment is statistically significant. In order to conduct such comparisons it is often required to integrate molecular sequence data and experimental information from disparate incompatible sources. While many specialized programs exist for comparisons of this kind in individual problem domains, such as expression data analysis, no generic software solution capable of addressing a wide spectrum of routine tasks in comparative proteomics is currently available. RESULTS: PROMPT is a comprehensive bioinformatics software environment which enables the user to compare arbitrary protein sequence sets, revealing statistically significant differences in their annotation features. It allows automatic retrieval and integration of data from a multitude of molecular biological databases as well as from a custom XML format. Similarity-based mapping of sequence IDs makes it possible to link experimental information obtained from different sources despite discrepancies in gene identifiers and minor sequence variation. PROMPT provides a full set of statistical procedures to address the following four use cases: i) comparison of the frequencies of categorical annotations between two sets, ii) enrichment of nominal features in one set with respect to another one, iii) comparison of numeric distributions, and iv) correlation of numeric variables. Analysis results can be visualized in the form of plots and spreadsheets and exported in various formats, including Microsoft Excel. CONCLUSION: PROMPT is a versatile, platform-independent, easily expandable, stand-alone application designed to be a practical workhorse in analysing and mining protein sequences and associated annotation. The availability of the Java Application Programming Interface and scripting capabilities on one hand, and the intuitive Graphical User Interface with context-sensitive help system on the other, make it equally accessible to professional bioinformaticians and biologically-oriented users. PROMPT is freely available for academic users from

Structural adaptation of enzymes to low temperatures

A systematic comparative analysis of 21 psychrophilic enzymes belonging to different structural families from pokaryotic and eukaryotic organisms is reported. Our results show a clear tendency for the charged residues Arg and Glu to be replaced at exposed sites on alpha-helices by Lys and Ala, respectively, in the direction from "hot" to "cold" enzymes. Possible implications of the observed structural variations for protein stability and engineering are discussed

ADATTAMENTO STRUTTURALE DEGLI ENZIMI ALLE BASSE TEMPERATURE

Si stima che circa il 90% della biosfera si trovi a temperature inferiori a 10°C. Infatti la superficie terrestre è dominata da ambienti quali i continenti Artici e Antartici, le regioni montane, e le profondità marine che al di sotto dei 1000 m mostrano temperature non superiori a 5°C. Gli organismi psicrofili vivono a queste basse temperature. In generale questi organismi sono rappresentati da organismi unicellulari la cui temperatura è prossima a quella ambientale. Per sopravvivere, devono produrre enzimi con sufficiente attività catalitica in quelle condizioni ambientali. Alle stesse temperature, gli enzimi da organismi mesofili e termofili sono incapaci di sostenere un metabolismo vitale. Per questi motivi, gli enzimi sintetizzati dagli organismi psicrofili hanno un considerevole potenziale biotecnologico

Structural adaptation of enzymes to low temperatures

A systematic comparative analysis of 21 psychrophilic enzymes belonging to different structural families from prokaryotic and eukaryotic organisms is reported. The sequences of these enzymes were multiply aligned to 427 homologous proteins from mesophiles and thermophiles. The net flux of amino acid exchanges from meso/thermophilic to psychrophilic enzymes was measured. To assign the observed preferred exchanges to different structural environments, such as secondary structure, solvent accessibility and subunit interfaces, homology modeling was utilized to predict the secondary structure and accessibility of amino acid residues for the psychrophilic enzymes for which no experimental three-dimensional structure is available. Our results show a clear tendency for the charged residues Arg and Glu to be replaced at exposed sites on alpha-helices by Lys and Ala, respectively, in the direction from 'hot' to 'cold' enzymes. Val is replaced by Ala at buried regions in alpha-helices. Compositional analysis of psychrophilic enzymes shows a significant increase in Ala and Asn and a decrease in Arg at exposed sites. Buried sites in beta-strands tend to be depleted of VAL: Possible implications of the observed structural variations for protein stability and engineering are discussed

Improvement in prediction of solvent accessibility by probability profiles

The capability of predicting folding and conformation of a protein from its primary structure is probably one of the main goals of modern biology. An accurate prediction of solvent accessibility is an intermediate step along this way. A new method for predicting solvent accessibility from single sequence and multiple alignment data is described. The method is based on probability profiles calculated on an amino acid sequence centred on the residue whose accessibility has to be predicted. A profile is constructed for each exposure category considered so as to calculate the probability of a sequence being generated by the different profiles. Prediction accuracy was tested on a variety of protein sets with two- and three-state models. Different thresholds were used according to those adopted by the authors proposing the data sets. The prediction accuracy is significantly improved over existing methods

STRUCTURAL PLASTICITY OF THERMOPHILIC SERINE HYDROXYMETHYLTRANSFERASES

Serine hydroxymethyltransferase (SHMT) catalyzes the reversible cleavage of serine to form glycine and monocarbonic groups, essential in several biosynthetic pathways. The availability of crystallographic structures of SHMT from mesophilic organisms and information produced by the genomic projects, prompted the analysis of the adaptatgoin of SHMT to 'extreme' environments, such as high temperatures, by exploitation of structural data from thermophilic organisms

Structural plasticity of thermophilic serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT) catalyzes the reversible cleavage of serine to form glycine and monocarbonic groups, essential in several biosynthetic pathways. The availability of crystallographic structures of SHMT from mesophilic organisms and information produced by the genomic projects prompted the analysis of the adaptation of SHMT to "extreme" environments, such as high temperatures, by exploitation of structural data from thermophilic organisms. The sequences of 10 thermophilic/hyperthermophilic SHMTs were multiply aligned to 53 mesophilic homologs and analyzed by a comparative approach, examining the amino acid compositions and preferred residue exchanges between mesophiles and extremophiles. The structural basis of the observed exchanges was further investigated through the application of homology modeling to the 10 extremophilic SHMTs. The results of this study indicate that, in SHMT, thermal stability can be achieved mainly through three strategies: (i) increased number of charged residues at the protein surface; (ii) increased hydrophobicity of the protein core; and (iii) substitution of thermolabile residues exposed to the solvent. Additional features of the archaeal SHMTs, for which no structural data are available yet, were also investigated to explain their quaternary assemblage and the interaction with modified folates

Granulomatous Lymphocytic Interstitial Lung Disease (GLILD) in Common Variable Immunodeficiency (CVID): A Multicenter Retrospective Study of Patients From Italian PID Referral Centers

Background: Granulomatous and Lymphocytic Interstitial Lung Diseases (GLILD) is a severe non-infectious complication of Common Variable Immunodeficiency (CVID), often associated with extrapulmonary involvement. Due to a poorly understood pathogenesis, GLILD diagnosis and management criteria still lack consensus. Accordingly, it is a relevant cause of long-term loss of respiratory function and is closely associated with a markedly reduced survival. The aim of this study was to describe clinical, immunological, laboratory and functional features of GLILD, whose combination in a predictive model might allow a timely diagnosis.Methods: In a multicenter retrospective cross-sectional study we enrolled 73 CVID patients with radiologic features of interstitial lung disease (ILD) associated to CVID (CVID-ILD) and 125 CVID patients without ILD (controls). Of the 73 CVID-ILD patients, 47 received a definite GLILD diagnosis while 26 received a clinical-radiologic diagnosis of CVID related ILD defined as uILD.Results: In GLILD group we found a higher prevalence of splenomegaly (84.8 vs. 39.2%), autoimmune cytopenia (59.6 vs. 6.4%) and bronchiectasis (72.3 vs. 28%), and lower IgA and IgG serum levels at CVID diagnosis. GLILD patients presented lower percentage of switched-memory B cells and marginal zone B cells, and a marked increase in the percentage of circulating CD21lo B cells (14.2 vs. 2.9%). GLILD patients also showed lower total lung capacity (TLC 87.5 vs. 5.0%) and gas transfer (DLCO 61.5 vs. 5.0%) percent of predicted. By univariate logistic regression analysis, we found IgG and IgA levels at CVID diagnosis, presence of splenomegaly and autoimmune cytopenia, CD21lo B cells percentage, TLC and DCLO percent of predicted to be associated to GLILD. The joint analysis of four variables (CD21lo B cells percentage, autoimmune cytopenia, splenomegaly and DLCO percent of predicted), together in a multiple logistic regression model, yielded an area under the ROC curve (AUC) of 0.98 (95% CI: 0.95-1.0). The AUC was only slightly modified when pooling together GLILD and uILD patients (0.92, 95% CI: 0.87-0.97).Conclusions: we propose the combination of two clinical parameters (splenomegaly and autoimmune cytopenia), one lung function index (DLCO%) and one immunologic variable (CD21lo%) as a promising tool for early identification of CVID patients with interstitial lung disease, limiting the use of aggressive diagnostic procedures