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Solution structure of the Legionella pneumophila Mip-rapamycin complex
Springer Science and Business Media LLC - - 2008
A. Ceymann, Martin Horstmann, Philipp Ehses, Kristian Schweimer, Anne-Katrin Paschke, Michael Steinert, Cornelius Faber
Abstract Background Legionella pneumphila is the causative agent of Legionnaires' disease. A major virulence factor of the pathogen is the homodimeric surface protein Mip. It shows peptidyl-prolyl cis/trans isomerase activty and is a receptor of FK506 and...... hiện toàn bộ
MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry
Springer Science and Business Media LLC - Tập 12 - Trang 1-11 - 2012
Janosch Hennig, Sjoerd J de Vries, Klaus DM Hennig, Leah Randles, Kylie J Walters, Maria Sunnerhagen, Alexandre MJJ Bonvin
MTMDAT is a program designed to facilitate analysis of mass spectrometry data of proteins and biomolecular complexes that are probed structurally by limited proteolysis. This approach can provide information about stable fragments of multidomain proteins, yield tertiary and quaternary structure data, and help determine the origin of stability changes at the amino acid residue level. Here, we intro...... hiện toàn bộ
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families
Springer Science and Business Media LLC - Tập 9 - Trang 1-18 - 2009
Esben M Quistgaard, Søren S Thirup
The Asp-box is a short sequence and structure motif that folds as a well-defined β-hairpin. It is present in different folds, but occurs most prominently as repeats in β-propellers. Asp-box β-propellers are known to be characteristically irregular and to occur in many medically important proteins, most of which are glycosidase enzymes, but they are otherwise not well characterized and are only rar...... hiện toàn bộ
Deciphering the shape and deformation of secondary structures through local conformation analysis
Springer Science and Business Media LLC - Tập 11 - Trang 1-17 - 2011
Julie Baussand, Anne-Claude Camproux
Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon co...... hiện toàn bộ
A lack of peptide binding and decreased thermostability suggests that the CASKIN2 scaffolding protein SH3 domain may be vestigial
Springer Science and Business Media LLC - Tập 16 - Trang 1-6 - 2016
Jamie J. Kwan, Logan W. Donaldson
CASKIN2 is a neuronal signaling scaffolding protein comprised of multiple ankyrin repeats, two SAM domains, and one SH3 domain. The CASKIN2 SH3 domain for an NMR structural determination because its peptide-binding cleft appeared to deviate from the repertoire of aromatic enriched amino acids that typically bind polyproline-rich sequences. The structure demonstrated that two non-canonical basic am...... hiện toàn bộ
Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach
Springer Science and Business Media LLC - Tập 13 - Trang 1-14 - 2013
Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy Wu, Sona Vasudevan
The post-genomic era poses several challenges. The biggest is the identification of biochemical function for protein sequences and structures resulting from genomic initiatives. Most sequences lack a characterized function and are annotated as hypothetical or uncharacterized. While homology-based methods are useful, and work well for sequences with sequence identities above 50%, they fail for sequ...... hiện toàn bộ
Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy
Springer Science and Business Media LLC - Tập 9 - Trang 1-9 - 2009
Tarmo P Roosild, Samantha Castronovo, Michael Fabbiani, Giuseppe Pizzorno
Uridine phosphorylase (UPP) is a key enzyme of pyrimidine salvage pathways, catalyzing the reversible phosphorolysis of ribosides of uracil to nucleobases and ribose 1-phosphate. It is also a critical enzyme in the activation of pyrimidine-based chemotherapeutic compounds such a 5-fluorouracil (5-FU) and its prodrug capecitabine. Additionally, an elevated level of this enzyme in certain tumours is...... hiện toàn bộ
Crystal structures of the human Dysferlin inner DysF domain
Springer Science and Business Media LLC - - 2014
Altin Sula, A.R. Cole, Corin Yeats, Christine A. Orengo, Nicholas H. Keep
Evaluation of the structural quality of modeled proteins by using globularity criteria
Springer Science and Business Media LLC - Tập 7 - Trang 1-12 - 2007
Susan Costantini, Angelo M Facchiano, Giovanni Colonna
The knowledge of the three-dimensional structure of globular proteins is fundamental for a detailed investigation of their functional properties. Experimental methods are too slow for structure investigation on a large scale, while computational prediction methods offer alternatives that are continuously being improved. The international Comparative Assessment of Structure Prediction (CASP), an "a...... hiện toàn bộ
Modeling of the OX1R–orexin-A complex suggests two alternative binding modes
Springer Science and Business Media LLC - Tập 15 - Trang 1-17 - 2015
Lasse Karhu, Ainoleena Turku, Henri Xhaard
Interactions between the orexin peptides and their cognate OX1 and OX2 receptors remain poorly characterized. Site-directed mutagenesis studies on orexin peptides and receptors have indicated amino acids important for ligand binding and receptor activation. However, a better understanding of specific pairwise interactions would benefit small molecule discovery. We constructed a set of three-dimens...... hiện toàn bộ
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