Protein Structure and Bioinformatics Group

Trieste, Italy

Protein Structure and Bioinformatics Group

Trieste, Italy
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Popovic M.,Protein Structure and Bioinformatics Group | Zlatev V.,Protein Structure and Bioinformatics Group | Hodnik V.,University of Ljubljana | Anderluh G.,University of Ljubljana | And 4 more authors.
Biochimica et Biophysica Acta - Biomembranes | Year: 2012

Human Jagged-1, one of the ligands of Notch receptors, is a transmembrane protein composed of a large extracellular region and a 125-residue cytoplasmic tail which bears a C-terminal PDZ recognition motif. To investigate the interaction between Jagged-1 cytoplasmic tail and the inner leaflet of the plasma membrane we determined, by solution NMR, the secondary structure and dynamics of the recombinant protein corresponding to the intracellular region of Jagged-1, J1-tmic, bound to negatively charged lysophospholipid micelles. NMR showed that the PDZ binding motif is preceded by four α-helical segments and that, despite the extensive interaction between J1-tmic and the micelle, the PDZ binding motif remains highly flexible. Binding of J1-tmic to negatively charged, but not to zwitterionic vesicles, was confirmed by surface plasmon resonance. To study the PDZ binding region in more detail, we prepared a peptide corresponding to the last 24 residues of Jagged-1, J1C24, and different phosphorylated variants of it. J1C24 displays a marked helical propensity and undergoes a coil-helix transition in the presence of negatively charged, but not zwitterionic, lysophospholipid micelles. Phosphorylation at different positions drastically decreases the helical propensity of the peptides and abolishes the coil-helix transition triggered by lysophospholipid micelles. We propose that phosphorylation of residues upstream of the PDZ binding motif may shift the equilibrium from an ordered, membrane-bound, interfacial form of Jagged-1 C-terminal region to a more disordered form with an increased accessibility of the PDZ recognition motif, thus playing an indirect role in the interaction between Jagged-1 and the PDZ-containing target protein. © 2012 Elsevier B.V. All rights reserved.


Reiz B.,Protein Structure and Bioinformatics Group | Reiz B.,Hungarian Academy of Sciences | Reiz B.,University of Szeged | Kertesz-Farkas A.,Protein Structure and Bioinformatics Group | And 4 more authors.
Bioinformatics | Year: 2013

Motivation: Identification of proteins by mass spectrometry-based proteomics requires automated interpretation of peptide tandem mass spectrometry spectra. The effectiveness of peptide identification can be greatly improved by filtering out extraneous noise peaks before the subsequent database searching steps.Results: Here we present a novel chemical rule-based filtering algorithm, termed CRF, which makes use of the predictable patterns (rules) of collision-induced peptide fragmentation. The algorithm selects peak pairs that obey the common fragmentation rules within plausible limits of mass tolerance as well as peak intensity and produces spectra that can be subsequently submitted to any search engine. CRF increases the positive predictive value and decreases the number of random matches and thus improves performance by 15-20% in terms of peptide annotation using search engines, such as X!Tandem. Importantly, the algorithm also achieves data compression rates of ∼75%. © 2013 The Author. Published by Oxford University Press. All rights reserved.


Kertesz-Farkas A.,Protein Structure and Bioinformatics Group | Reiz B.,Institute of Biophysics | Vera R.,Protein Structure and Bioinformatics Group | Myers M.P.,Protein Networks Group | And 2 more authors.
Bioinformatics | Year: 2014

Motivation: Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins. Algorithmic searches for PTMs from tandem mass spectrum data (MS/MS) tend to be hampered by noisy data as well as by a combinatorial explosion of search space. This leads to high uncertainty and long search-execution times.Results: To address this issue, we present PTMTreeSearch, a new algorithm that uses a large database of known PTMs to identify PTMs from MS/MS data. For a given peptide sequence, PTMTreeSearch builds a computational tree wherein each path from the root to the leaves is labeled with the amino acids of a peptide sequence. Branches then represent PTMs. Various empirical tree pruning rules have been designed to decrease the search-execution time by eliminating biologically unlikely solutions. PTMTreeSearch first identifies a relatively small set of high confidence PTM types, and in a second stage, performs a more exhaustive search on this restricted set using relaxed search parameter settings. An analysis of experimental data shows that using the same criteria for false discovery, PTMTreeSearch annotates more peptides than the current state-of-the-art methods and PTM identification algorithms, and achieves this at roughly the same execution time. PTMTreeSearch is implemented as a plugable scoring function in the X!Tandem search engine. © 2013 The Author.


Marini B.,International Center for Genetic Engineering and Biotechnology | Kertesz-Farkas A.,Protein Structure and Bioinformatics Group | Ali H.,International Center for Genetic Engineering and Biotechnology | Lucic B.,International Center for Genetic Engineering and Biotechnology | And 15 more authors.
Nature | Year: 2015

Long-standing evidence indicates that human immunodeficiency virus type 1 (HIV-1) preferentially integrates into a subset of transcriptionally active genes of the host cell genome. However, the reason why the virus selects only certain genes among all transcriptionally active regions in a target cell remains largely unknown. Here we show that HIV-1 integration occurs in the outer shell of the nucleus in close correspondence with the nuclear pore. This region contains a series of cellular genes, which are preferentially targeted by the virus, and characterized by the presence of active transcription chromatin marks before viral infection. In contrast, the virus strongly disfavours the heterochromatic regions in the nuclear lamin-associated domains and other transcriptionally active regions located centrally in the nucleus. Functional viral integrase and the presence of the cellular Nup153 and LEDGF/p75 integration cofactors are indispensable for the peripheral integration of the virus. Once integrated at the nuclear pore, the HIV-1 DNA makes contact with various nucleoporins; this association takes part in the transcriptional regulation of the viral genome. These results indicate that nuclear topography is an essential determinant of the HIV-1 life cycle. ©2015 Macmillan Publishers Limited. All rights reserved.


Petric I.,University of Nova Gorica | Petric I.,Protein Structure and Bioinformatics Group | Ligeti B.,Pázmány Péter Catholic University | Gyorffy B.,Hungarian Academy of Sciences | And 2 more authors.
Protein and Peptide Letters | Year: 2014

Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database. © 2014 Bentham Science Publishers.


Popovic M.,Protein Structure and Bioinformatics Group | Bella J.,University of Edinburgh | Zlatev V.,Protein Structure and Bioinformatics Group | Hodnik V.,University of Ljubljana | And 4 more authors.
Journal of Molecular Recognition | Year: 2011

Jagged-1, one of the five Notch ligands in man, is a membrane-spanning protein made of a large extracellular region and a 125-residue cytoplasmic tail bearing a C-terminal PDZ recognition motif ( 1213RMEYIV 1218). Binding of Jagged-1 intracellular region to the PDZ domain of afadin, a protein located at cell-cell adherens junctions, couples Notch signaling with the adhesion system and the cytoskeleton. Using NMR chemical shift perturbation and surface plasmon resonance, we studied the interaction between the PDZ domain of afadin (AF6-PDZ) and a series of polypeptides comprising the PDZ-binding motif. Chemical shift mapping of AF6-PDZ upon binding of ligands of different length (6, 24, and 133 residues) showed that the interaction is strictly local and involves only the binding groove in the PDZ. The recombinant protein corresponding to the entire intracellular region of Jagged-1, J1-ic, is mainly disordered in solution, and chemical shift mapping of J1-ic in the presence of AF6-PDZ showed that binding is not coupled to folding. Binding studies on a series of 24-residue peptides phosphorylated at different positions showed that phosphorylation of the tyrosine at position -2 of the PDZ-binding motif decreases its affinity for AF6-PDZ, and may play a role in the modulation of this interaction. Finally, we show that the R1213Q mutation located in the PDZ-binding motif and associated with extrahepatic biliary atresia increases the affinity for AF6-PDZ, suggesting that this syndrome may arise from an imbalance in the coupling of Notch signaling to the cytoskeleton. © 2010 John Wiley & Sons, Ltd.


PubMed | Protein Structure and Bioinformatics Group, International Center for Genetic Engineering and Biotechnology, University of Trieste and University of Modena and Reggio Emilia
Type: Journal Article | Journal: Nature | Year: 2015

Long-standing evidence indicates that human immunodeficiency virus type 1 (HIV-1) preferentially integrates into a subset of transcriptionally active genes of the host cell genome. However, the reason why the virus selects only certain genes among all transcriptionally active regions in a target cell remains largely unknown. Here we show that HIV-1 integration occurs in the outer shell of the nucleus in close correspondence with the nuclear pore. This region contains a series of cellular genes, which are preferentially targeted by the virus, and characterized by the presence of active transcription chromatin marks before viral infection. In contrast, the virus strongly disfavours the heterochromatic regions in the nuclear lamin-associated domains and other transcriptionally active regions located centrally in the nucleus. Functional viral integrase and the presence of the cellular Nup153 and LEDGF/p75 integration cofactors are indispensable for the peripheral integration of the virus. Once integrated at the nuclear pore, the HIV-1 DNA makes contact with various nucleoporins; this association takes part in the transcriptional regulation of the viral genome. These results indicate that nuclear topography is an essential determinant of the HIV-1 life cycle.


Popovic M.,Protein Structure and Bioinformatics Group | Wienk H.,University Utrecht | Coglievina M.,Protein Structure and Bioinformatics Group | Boelens R.,University Utrecht | And 2 more authors.
Proteins: Structure, Function and Bioinformatics | Year: 2014

Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an N-terminal segment, b1, containing functionally important phosphorylation sites, the basic region b2, required for binding to DNA, and the HLH domain. We show that a proline residue in the sequence divides the protein in two parts, a flexible and disordered N-terminal region including b1 and a structured, mainly helical region comprising b2 and the HLH domain. Binding of H1H to a double strand DNA oligonucleotide was monitored through the chemical shift perturbation of backbone amide resonances, and showed that the interaction surface involves not only the b2 segment but also several residues in the b1 and HLH regions. © 2014 Wiley Periodicals, Inc.


Coglievina M.,Protein Structure and Bioinformatics Group | Guarnaccia C.,Protein Structure and Bioinformatics Group | Zlatev V.,Protein Structure and Bioinformatics Group | Pongor S.,Protein Structure and Bioinformatics Group | Pintar A.,Protein Structure and Bioinformatics Group
Biochemical and Biophysical Research Communications | Year: 2013

Ectodomain shedding of membrane receptors and ligands carried out by ADAMs (A disintegrin and metalloprotease) plays a major role in several signaling pathways, including Notch. The grounds of substrate recognition, however, are poorly understood. We demonstrate that a recombinant protein corresponding to the juxtamembrane region of Jagged-1, one of the Notch ligands, behaves as a structured module and is cleaved by ADAM17 catalytic domain at E1054. A short synthetic peptide is cleaved at the same site but at a much higher rate, implying that the structure of the cleavage site in the native protein is a key determinant for substrate recognition. We also show that an Alagille syndrome-associated mutation near E1054 increases the cleavage rate, which suggests that this mutation may lead to an unbalance in Notch signaling due to a higher level of Jagged-1 shedding. © 2013 Elsevier Inc.


Coglievina M.,Protein Structure and Bioinformatics Group | Guarnaccia C.,Protein Structure and Bioinformatics Group | Pintar A.,Protein Structure and Bioinformatics Group | Pongor S.,Protein Structure and Bioinformatics Group
Biochimica et Biophysica Acta - Proteins and Proteomics | Year: 2010

HES-1 is a transcriptional repressor of the basic helix-loop-helix (bHLH) family and one of the main downstream effectors in Notch signaling. Its domain architecture is composed of a bHLH region, an Orange domain, and a poorly characterized C-terminal half. We show that different degrees of structural order are present in the different regions of HES-1. The isolated bHLH domain is only marginally stable in solution, and partially folds upon dimerization. Binding to DNA promotes folding, stabilization, and protection from proteolysis of the bHLH domain. The Orange domain, on the contrary, is well folded in all conditions, forms stable dimers, and greatly increases protein resistance to thermal denaturation. The isolated proline-rich C-terminal region is mainly disordered in solution, and remains unstructured also in the full length protein. Measurements of binding constants show that HES-1 recognizes dsDNA synthetic oligonucleotides corresponding to several functional DNA targets with high affinity, but with relatively little specificity. We propose that order/disorder transitions in the different domains are associated not only with binding to DNA, but also with protein homo- and hetero-dimerization. © 2010 Elsevier B.V.

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