317 research outputs found

    Scalable web services for the PSIPRED Protein Analysis Workbench

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    Here, we present the new UCL Bioinformatics Group’s PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/

    N- and C-Terminal Truncations to Enhance Protein Solubility and Crystallization: Predicting Protein Domain Boundaries with Bioinformatics Tools

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    Soluble protein expression is a key requirement for biochemical and structural biology approaches to study biological systems in vitro. Production of sufficient quantities may not always be achievable if proteins are poorly soluble which is frequently determined by physico-chemical parameters such as intrinsic disorder. It is well known that discrete protein domains often have a greater likelihood of high-level soluble expression and crystallizability. Determination of such protein domain boundaries can be challenging for novel proteins. Here, we outline the application of bioinformatics tools to facilitate the prediction of potential protein domain boundaries, which can then be used in designing expression construct boundaries for parallelized screening in a range of heterologous expression systems

    The PSIPRED Protein Analysis Workbench: 20 years on

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    The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website

    The PSIPRED Protein Analysis Workbench: 20 years on

    Get PDF
    The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website

    Clathrin Adaptor Complex-interacting Protein Irc6 Functions through the Conserved C-Terminal Domain.

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    Clathrin coats drive transport vesicle formation from the plasma membrane and in pathways between the trans-Golgi network (TGN) and endosomes. Clathrin adaptors play central roles orchestrating assembly of clathrin coats. The yeast clathrin adaptor-interacting protein Irc6 is an orthologue of human p34, which is mutated in the inherited skin disorder punctate palmoplantar keratoderma type I. Irc6 and p34 bind to clathrin adaptor complexes AP-1 and AP-2 and are members of a conserved family characterized by a two-domain architecture. Irc6 is required for AP-1-dependent transport between the TGN and endosomes in yeast. Here we present evidence that the C-terminal two amino acids of Irc6 are required for AP-1 binding and transport function. Additionally, like the C-terminal domain, the N-terminal domain when overexpressed partially restores AP-1-mediated transport in cells lacking full-length Irc6. These findings support a functional role for Irc6 binding to AP-1. Negative genetic interactions with irc6∆ are enriched for genes related to membrane traffic and nuclear processes, consistent with diverse cellular roles for Irc6

    Three dimensional structure prediction and ligand-protein interaction study of expansin protein ATEXPA23 from Arabidopsis thaliana L.

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    Arabidopsis thaliana L. is a small flowering plant that is widely used as a model organism in plant biology. In the present study, we study the peripheral membrane protein ATEXPA23 from Arabidopsis thaliana L. using homology modelling and molecular docking. The microarray analysis shows expression of ATEXPA23 (AT5G39280) protein, which leads to loosening and extension of plant cell walls. This protein is differentially expressed during different stages of plant embryogenesis. It contains one expansin-like CBD domain and one expansin-like EG45 domain. ATEXPA23 belongs to the expansin family in expansin a subfamily. The 3D model after refinement is used to explore the xyloglucan binding characteristics of ATEXPA23 using AutoDock. The docking analysis shows that the surface exposed aromatic amino acid residues Phe 193 and Phe 265 interact with ligand xyloglucan through CH-л interaction. The binding energy values of docking reflect a stable conformation of the docked complex. The interaction of expansin protein with carbohydrate xyloglucan, present in hemicellulose structures of plant cell wall, is thoroughly analysed with cellotetrose and xyloglucan heptasaccharide using electrostatic potential calculation. This CH-л non-covalent interaction predominates on the cellulose-xyloglucan interaction in plant cell wall during cell growth

    Sars Cov-2 Spike Glycoprotein Mutations and Changes in Protein Structure

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    DergiPark: 774926trkjnatSevere Acute Respiratory Syndrome Corona Virus-2 (SARS CoV-2) is a single-stranded positive polarity RNA virus with a high virulence effect. Spike (S) glycoprotein is the outermost component of the SARS CoV-2 virion and is important in the entry of the virus into the cell via the angiotensin converting enzyme 2 (ACE2) receptor. ACE2 plays an important role in the regulation of human blood pressure by converting the vasoconstrictor angiotensin 2 to the vasodilator angiotensin 1-7. In this study, the changes that mutations in Asian isolates may cause in S glycoprotein structure were analyzed and modeled to contribute to drug and vaccine targeting studies. Genome, proteome and mutation analyses were done using bioinformatics tools (MAFFT, MegaX, PSIPRED, MolProbity, PyMoL). Protein modelling was performed using ProMod3. We detected 26 mutations in the S glycoprotein. The changes that these mutations reveal in the general topological and conformational structure of the S glycoprotein may affect the virulence features of SARS CoV-2. It was determined that mutations converted the receptor binding domain (RBD) from down-formation to like-up formation. It is thought that conformational change occurring after mutation in RBD may cause an increase in receptor affinity. These findings could be beneficial for disease prevention of and drug/vaccine development for SARS CoV-2.Şiddetli akut solunum yolu sendromu koronavirüsü-2 (SARS CoV-2) yüksek virülans etkiye sahip tek zincirli pozitif polariteli RNA virüsüdür. Spike (S) glikoprotein SARS CoV-2 virionunun en dıştaki bileşenidir ve anjiyotensin dönüştürücü enzim 2 (ACE2) reseptörü aracılığı ile virüsün hücreye girişinde önemlidir. ACE2, vazokonstriktör anjiyotensin 2'yi vazodilatör anjiyotensin 1-7'ye dönüştürerek insanda kan basıncının düzenlenmesinde önemli roller üstlenir. Bu çalışmada, Asya izolatlarındaki mutasyonların S glikoprotein yapısında neden olabileceği değişiklikler analiz edilmiş ve ilaç ve aşı hedefleme çalışmalarına katkıda bulunmak üzere modellenmiştir. Genom, proteom ve mutasyon analizleri biyoinformatik araçları (MAFFT, MegaX, PSIPRED, MolProbity, PyMoL) kullanılarak yapıldı. Protein modellemesi ProMod3 kullanılarak yapıldı. S glikoproteinde 26 mutasyon tespit edilmiştir. Bu mutasyonların S glikoproteininin genel topolojik ve konformasyonel yapısında ortaya çıkardığı değişiklikler, SARS CoV-2’nin virülans özelliklerini etkileyebilir. Mutasyonların reseptör bağlanma bölgesini (RBB) kapalı formasyondan açık formasyon benzeri bir yapıya dönüştürdüğü belirlenmiştir. RBB'de mutasyondan sonra meydana gelen konformasyonel değişimin reseptör afinitesinde bir artışa neden olabileceği düşünülmektedir. Bu bulgular hastalığın önlenmesi ve SARS CoV-2 ilaç ve aşı geliştirme çalışmaları için faydalı olabilir

    Selection of T cell epitopes from S. mansoni Sm23 protein as a vaccine construct, using Immunoinformatics approach

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    Schistosomiasis, a neglected and most prevalenttropical diseases after malaria, have been a threat to people living in endemic areas. With regards to possible resistance to the popular drug (praziquantel) use for treatment of schistosomiasis, the need for a permanent vaccinating approach has been justified. This study uses an in silico approach to identify potential target vaccine candidate or T cell epitopes (T cell response activating epitope) for the treatment of schistosomiasis. This research therefore identified some candidate T cell epitopes from Sm23 protein of Schistosma mansoni using immunoinformatics tools. Nonameric epitopes like 85YMYAFFLVV93 , 83MLYMYAFFL91 , 8MRCLKSCVF16 , 41SQYGDNLHK49 and 104VAVVYKDRI112 was found to exhibit strong binding affinity with some human leukocyte antigen (HLA). The predicted epitope was found to have no similarity with human proteome, a good attribute that is conferred on any good vaccine candidate. The predicted epitopes provide promising drug candidates and could be tested by wet laboratory as targeted vaccine against S. mansoni infection

    The Major Soybean Allergen Gly m Bd 28K Induces Hypersensitivity Reactions in Mice Sensitized to Cow's Milk Proteins

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    Reactions to soy have been reported in a proportion of patients with IgE-mediated cow’s milk allergy (CMA). In this work, we analyzed if Gly m Bd 28K/P28, one of the major soybean allergens, is a cross-reactive allergen with cow milk proteins (CMP). We showed that P28 was recognized by IgE sera from CMA patients and activated human peripheral basophils degranulation. Moreover, IgE sera of mice exclusively sensitized to CMP recognized P28. Splenocytes from sensitized animals secreted IL-5 and IL-13 when incubated with CMP or soy proteins, but only IL-13 when treated with P28. In addition, a skin test was strongly positive for CMP and weakly positive for P28. Remarkably, milk-sensitized mice showed hypersensitivity symptoms following sublingual challenge with P28 or CMP. With the use of bioinformatics’ tools seven putative cross-reactive epitopes were identified. In conclusion, using in vitro and in vivo tests we demonstrated that P28 is a novel cross-reactive allergen with CMP.Fil: Candreva, Ángela María. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Estudios Inmunológicos y Fisiopatológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Estudios Inmunológicos y Fisiopatológicos; ArgentinaFil: Smaldini, Paola Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Estudios Inmunológicos y Fisiopatológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Estudios Inmunológicos y Fisiopatológicos; ArgentinaFil: Curciarello, Renata. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Estudios Inmunológicos y Fisiopatológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Estudios Inmunológicos y Fisiopatológicos; ArgentinaFil: Fossati, Carlos Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Estudios Inmunológicos y Fisiopatológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Estudios Inmunológicos y Fisiopatológicos; ArgentinaFil: Docena, Guillermo H.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Estudios Inmunológicos y Fisiopatológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Estudios Inmunológicos y Fisiopatológicos; ArgentinaFil: Petruccelli, Silvana. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentin
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