A dynamic model of the proteins that form the initial iron-sulfur cluster biogenesis machinery in yeast mitochondria

The assembly of iron-sulfur clusters (ISCs) in eukaryotes involves the protein Frataxin. Deficits in this protein have been associated with iron inside the mitochondria and impair ISC biogenesis as it is postulated to act as the iron donor for ISCs assembly in this organelle. A pronounced lack of Frataxin causes Friedreich's Ataxia, which is a human neurodegenerative and hereditary disease mainly affecting the equilibrium, coordination, muscles and heart. Moreover, it is the most common autosomal recessive ataxia. High similarities between the human and yeast molecular mechanisms that involve Frataxin have been suggested making yeast a good model to study that process. In yeast, the protein complex that forms the central assembly platform for the initial step of ISC biogenesis is composed by yeast frataxin homolog, Nfs1-Isd11 and Isu. In general, it is commonly accepted that protein function involves interaction with other protein partners, but in this case not enough is known about the structure of the protein complex and, therefore, how it exactly functions. The objective of this work is to model the protein complex in order to gain insight into structural details that end up with its biological function. To achieve this goal several bioinformatics tools, modeling techniques and protein docking programs have been used. As a result, the structure of the protein complex and the dynamic behavior of its components, along with that of the iron and sulfur atoms required for the ISC assembly, have been modeled. This hypothesis will help to better understand the function and molecular properties of Frataxin as well as those of its ISC assembly protein partners.

The peptide-binding motif of HLA-DR8 shares important structural features with other type 1 diabetes-associated alleles

The objective of this study was to characterize the peptide-binding motif of the major histocompatibility complex (MHC) class II HLA-DR8 molecule included in the type 1 diabetes-associated haplotype DRB1(*)0801-DQA1(*)0401/DQB1(*)0402 (DR8-DQ4), and compare it with that of other diabetes-associated MHC class II alleles; DR8-bound peptides were eluted from an HLA-DR homozygous lymphoblastoid cell line. The repertoire was characterized by peptide sequencing using a LTQ ion trap mass spectrometer coupled to a multidimensional liquid chromatography system. After validation of the spectra identification, the definition of the HLA-DR8 peptide-binding motif was achieved from the analysis of 486 natural ligands, based on serial alignments of all possible HLA-DR-binding cores. The DR8 motif showed a strong similarity with the peptide-binding motifs of other MHC class II diabetes-associated alleles, HLA-DQ8 and H-2 I-A(g7). Similar to HLA-DQ8 and H-2 I-A(g7), HLA-DR8 preferentially binds peptides with an acidic residue at position P9 of the binding core, indicating that DR8 is the susceptibility component of the DR8-DQ4 haplotype. Indeed, some DR8 peptides were identical to peptides previously identified as DQ8- or I-A(g7) ligands, and several diabetes-specific peptides associated with DQ8 or I-A(g7) could theoretically bind to HLA-DR8. These data further strengthen the association of HLA-DR8 with type I diabetes.

Interest of non-invasive and semi-invasive testings in asymptomatic children with pre-excitation syndrome

AIMS

To determine the feasibility and the results of exercise testing (ET) and electrophysiological study (EPS) in outpatient asymptomatic children with a Wolff-Parkinson-White (WPW) syndrome.

METHODS AND RESULTS

Exercise testing and transesophageal EPS were performed in 55 outpatient asymptomatic children aged 6 to 19 years old (14 +/- 3) with WPW. Wolff-Parkinson-White persisted during maximal exercise. Isoproterenol was not required in five children younger than 10 years old, because they developed a catecholaminergic sinus tachycardia. Maximal rate conducted through accessory pathway (AP) was higher in children younger than 16 years old than in teenagers (P < 0.05). Atrioventricular re-entrant tachycardia (AVRT) was induced in six children; atrial fibrillation (AF) in 12 children. The induction of tachycardias and the dangerous forms (18%) were not influenced by age. After 5 +/- 1 years, one child, 12 year old with inducible rapid AF, had a sudden cardiac arrest; two children became symptomatic after ablation.

CONCLUSIONS

Transesophageal EPS was required to determine the prognosis of asymptomatic WPW in children. The maximal rate conducted in AP was higher in children younger than 16 years old than in teenagers; other data did not differ. AVRT was rare; 71% of children had no inducible arrhythmia and were authorized to resume physical activities.

Cloning, expression and purification of human epidermal growth factor using different expression systems

Epidermal growth factor (EGF) is a protein that belongs to the family of growth factors that bind the ErbB receptors, which play a prominent role in the development of carcinomas. We had demonstrated that potato carboxypeptidase inhibitor (PCI) acts as an EGF antagonist. Because of the low affinity of PCI for the epidermal growth factor receptor, it was decided to design EGF mutants with PCI abilities. In order to achieve this we have first cloned, expressed and purified the native protein, EGF. Different expression systems with different locations of the recombinant protein were designed and a purification protocol was designed with those which allowed expression of EGF. Finally, the sample needed folding. Differences in the amount of EGF obtained and its activity were observed depending on the expression system used.

The gene causing the Best's macular dystrophy (BMD) encodes a putative ion exchanger

Best's macular dystrophy (BMD), also known as vitelliform macular degeneration type 2, is an autosomal dominant disease that causes loss of vision. The causative gene encodes a 585 amino acids protein called bestrophin with unknown function. From bioinformatics analysis, a putative ion exchanger function for bestrophin can be suggested.

'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins

MOTIVATION

Genomic sequences from different organisms, even prokaryotic, have plenty of orphan ORFs, making necessary methods for the prediction of protein structure and function. The prediction of the presence of hydrophobic transmembrane (HTM) stretches is a valuable clue for this.

RESULTS

The program. TransMem, based on a neural network and running on personal computers (either Apple Macintosh or PC, using Excel worksheets), for the prediction and distribution of amino acid residues in transmembrane segments of integral membrane proteins is reported. The percentage of residue predictive accuracy obtained for the set of proteins tested is 93%, ranging from 99.9% for the best to 71.7% for the worst prediction. The segment-based accuracy is 93.6%; 63.6% of the protein set match any of the predicted and observed segment locations.

AVAILABILITY

TransMem is available upon request or by anonymous up: IP address: luz.uab.es, directory/pub/ TransMem. It is also placed on the EMBL file server (ftp:/(/)ftp.ebi.ac.uk/pub/software/mac/TransMem ).

Relation between amino acid composition and cellular location of proteins

A correlation analysis of the amino acid composition and the cellular location of a protein is presented. The statistical analysis discriminates among the following five protein classes: integral membrane proteins, anchored membrane proteins, extracellular proteins, intracellular proteins and nuclear proteins. This segregation into protein classes related to their location can help researchers to design experimental work for testing hypotheses in order to find out the functionality of a reading frame in search of function. A program (ProtLock) to predict the cellular location of a protein has been designed.

An Excel spreadsheet computer program combining algorithms for prediction of protein structural characteristics

A program running on personal computers (either Apple Macintosh or PC, using Excel worksheets) for the prediction of some protein structural characteristics is reported. The program runs according to the Chou and Fasman algorithm, with some modifications, for secondary structure prediction. The program also incorporates several complementary analyses for secondary structure prediction to help the user in the decision-making process: rules for amino acid preferences in the N-cap and C-cap of alpha-helices; prediction of the protein structural class and search of sequential motifs related to secondary structure. Additional algorithms performed by the program are: prediction of domain boundaries, prediction of loops, prediction of the state of cysteines (reduced or in disulfide bridge), hydropathy profiles according to Kyte and Doolittle, Hoop and Woods, and flexibility plot according to Karplus and Schulz.