scholarly journals Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Morgane Boone ◽  
Pathmanaban Ramasamy ◽  
Jasper Zuallaert ◽  
Robbin Bouwmeester ◽  
Berre Van Moer ◽  
...  
Keyword(s):  
Surface Display ◽  
Solid Base ◽  
Ribosomal Biogenesis ◽  
Protein Fragment ◽  
Chain Flexibility ◽  
Protein Fragments ◽  
Machine Learning Methods ◽  
Protein Biogenesis ◽  
Secretory System ◽  
Fragment Libraries

AbstractWhile transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50–100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.

scholarly journals Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

2018 ◽  
Author(s):  
M. Boone ◽  
P. Ramasamy ◽  
J. Zuallaert ◽  
R. Bouwmeester ◽  
B. Van Moer ◽  
...  
Keyword(s):  
Protein Design ◽  
De Novo ◽  
Recombinant Protein Expression ◽  
Surface Display ◽  
Protein Fragment ◽  
Chain Flexibility ◽  
Protein Fragments ◽  
Protein Biogenesis ◽  
Secretory System ◽  
Fragment Libraries

AbstractWhile transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here developed a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50 - 100 amino acids, we generated datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. SECRiFY is the first methodology that generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability predictors. The finding that secretability is indeed a learnable feature of protein sequences is of significant impact in the broad area of recombinant protein expression and de novo protein design.

DETECTION OF BAT CORONAVIRUS AND SPECIFIC ANTIBODIES IN CHESTNUT BAT (SCOTOPHILUS KUHLII) POPULATION IN CENTRAL TAIWAN

2016 ◽  
Vol 42 (01) ◽  
pp. 19-26 ◽  
Author(s):  
Bo-Gang Su ◽  
Hong Chang Chen ◽  
Hsi-Chi Cheng ◽  
Yi-Ning Chen
Keyword(s):  
Cross Reactivity ◽  
Rdrp Gene ◽  
Rt Pcr ◽  
Protein Fragment ◽  
Serum Samples ◽  
Protein Fragments ◽  
N Protein ◽  
Polymerase Chain ◽  
Central Taiwan ◽  
Bat Coronavirus

Bats can serve as natural reservoirs for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome coronavirus (MERS-CoV). Investigating the prevalence of bat CoV is critical for assessing the risks of the outbreaks of emerging CoV. Chestnut bats (Scotophilus kuhlii) were captured in this study for detecting the partial RNA-dependent RNA polymerase (RdRp) gene in their feces through reverse transcription polymerase chain reaction (RT-PCR) and antibodies to the nucleocapsid (N) protein of bat CoV through western blotting (WB) analysis. Three recombinant N protein fragments (N1, N2, N3) of the isolated Scotophilus bat CoV/CYCU-S1/TW/2013 were expressed by Escherichia coli. WB analyses were performed with bat serum samples and the sera of a patient who recovered from a SARS-CoV infection. Fragment N2 contained a highly conserved motif among CoVs whereas N1 and N3 protein fragments were specific to the S. kuhlii bat CoV. A total of 32 fecal and 19 serum samples were collected in Changhua County and Yunlin County during 2013 and 2014. About 17 fecal samples tested positive for the RdRp gene with an overall prevalence of 53%. Sequences comparison showed that the Scotophilus bat CoV isolates in Taiwan belonged to the genus Alphacoronavirus and were closest to Scotophilus bat CoV/Hainan/China/2005 and Diliman1552G1/Philippines/2008, followed by porcine epidemic diarrhea coronavirus. Only one bat serum sample reacted positively to all 3[Formula: see text]N protein fragments. Cross-reactivity was observed between N2 protein fragment and the sera of a patient recovered from a SARS-CoV infection. The results indicated that Scotophilus bat CoV was circulating endemically in chestnut bat population in Taiwan.

The peptide-loading complex – antigen translocation and MHC class I loading

2009 ◽  
Vol 390 (8) ◽  
Author(s):  
Christian Schölz ◽  
Robert Tampé
Keyword(s):  
Mhc Class I ◽  
Antigen Processing ◽  
Surface Display ◽  
Class I ◽  
Antigenic Peptides ◽  
Mhc I ◽  
Protein Fragments ◽  
Long Term Stability ◽  
Peptide Loading ◽  
Mhc Class I Molecules

Abstract A large and dynamic membrane-associated machinery orchestrates the translocation of antigenic peptides into the endoplasmic reticulum (ER) lumen for subsequent loading onto major histocompatibility complex (MHC) class I molecules. The peptide-loading complex ensures that only high-affinity peptides, which guarantee long-term stability of MHC I complexes, are presented to T-lymphocytes. Adaptive immunity is dependent on surface display of the cellular proteome in the form of protein fragments, thus allowing efficient recognition of infected or malignant transformed cells. In this review, we summarize recent findings of antigen translocation by the transporter associated with antigen processing and loading of MHC class I molecules in the ER, focusing on the mechanisms involved in this process.

scholarly journals Fragger: a protein fragment picker for structural queries

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1722 ◽  
Author(s):  
Francois Berenger ◽  
David Simoncini ◽  
Arnout Voet ◽  
Rojan Shrestha ◽  
Kam Y.J. Zhang
Keyword(s):  
Amino Acid ◽  
Protein Design ◽  
Data Bank ◽  
Amino Acid Sequences ◽  
Structural Fragment ◽  
Protein Fragment ◽  
Distance Threshold ◽  
Protein Fragments ◽  
Specific Subset ◽  
Design Activities

Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

scholarly journals Most Japanese individuals are genetically predisposed to recognize an immunogenic protein fragment shared between COVID-19 and common cold coronaviruses

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 196
Author(s):  
Johannes M. Dijkstra ◽  
Aaron P. Frenette ◽  
Brian Dixon
Keyword(s):  
T Cell ◽  
Common Cold ◽  
Cell Epitope ◽  
Indigenous Populations ◽  
Immune Memory ◽  
T Cell Epitope ◽  
Immunogenic Protein ◽  
Protein Fragment ◽  
Protein Fragments ◽  
The Common

In the spring of 2020, we and others hypothesized that T cells in COVID-19 patients may recognize identical protein fragments shared between the coronaviruses of the common cold and COVID-19 and thereby confer cross-virus immune memory. Here, we look at this issue by screening studies that, since that time, have experimentally addressed COVID-19 associated T cell specificities. Currently, the identical T cell epitope shared between COVID-19 and common cold coronaviruses most convincingly identified as immunogenic is the CD8+ T cell epitope VYIGDPAQL if presented by the MHC class I allele HLA-A*24:02. The HLA-A*24:02 allele is found in the majority of Japanese individuals and several indigenous populations in Asia, Oceania, and the Americas. In combination with histories of common cold infections, HLA-A*24:02 may affect their protection from COVID-19.

scholarly journals Differences in tomato seed protein profiles obtained by SDS-PAGE analysis

2008 ◽  
Vol 53 (1) ◽  
pp. 13-23
Author(s):  
Elizabeta Miskoska-Milevska ◽  
Blagica Dimitrievska ◽  
Koo Poru ◽  
Zoran Popovski
Keyword(s):  
Seed Protein ◽  
Seed Proteins ◽  
Protein Profiles ◽  
Protein Fragment ◽  
Tomato Seed ◽  
Protein Fragments ◽  
Molecular Weights ◽  
Tomato Seeds ◽  
Sds Page ◽  
Total Seed

The protein profiles of tomato seeds from sub-species ( subsp. cultum Brezh., subsp. subspontaneum Brezh. and subsp. spontaneum Brezh.) were analyzed using SDS-PAGE technique. Electrophoreograms and denzitograms of total, soluble and non-soluble proteins of 31 different samples have showed quantitative and qualitative differences. Qualitative differences in electrophoregrams of total seed proteins refer to protein fragments in zone A (114 kDa, 83 kDa and 65 kDa) and protein fragment in zone C (17 kDa). Qualitative differences in electrophoregrams of soluble seed proteins refer to protein fragment in zone A (94 kDa). Qualitative differences in electrophoregrams of nonsoluble seed proteins refer to protein fragments with molecular weights of: 210 kDa, 85 kDa, 67 kDa and 26 kDa.

scholarly journals Fragger: a protein fragment picker for structural queries

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1722
Author(s):  
Francois Berenger ◽  
David Simoncini ◽  
Arnout Voet ◽  
Rojan Shrestha ◽  
Kam Y.J. Zhang
Keyword(s):  
Amino Acid ◽  
Protein Design ◽  
Data Bank ◽  
Amino Acid Sequences ◽  
Structural Fragment ◽  
Protein Fragment ◽  
Distance Threshold ◽  
Protein Fragments ◽  
Specific Subset ◽  
Design Activities

Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

scholarly journals Escherichia coli recombinant expression of SARS-CoV-2 protein fragments.

2021 ◽  
Author(s):  
Bailey E McGuire ◽  
Julia E Mela ◽  
Vanessa C Thompson ◽  
Logan R Cucsksey ◽  
Claire E Stevens ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Fusion Protein ◽  
Fusion Proteins ◽  
Recombinant Expression ◽  
Binding Domain ◽  
Spike Protein ◽  
Carbohydrate Binding ◽  
Protein Fragment ◽  
Protein Fragments ◽  
E Coli

We have developed a method for the inexpensive, high-level expression of antigenic protein fragments of SARS-CoV-2 proteins in Escherichia coli. Our approach used the thermophilic carbohydrate binding domain 9 (CBM9) module as an N-terminal carrier protein and affinity tag.  The CBM9 module was joined to SARS-CoV-2 protein fragments via a flexible proline-threonine rich linker, which proved to be resistant to E. coli proteases. Two CBM9-spike protein fragment fusion proteins and one CBM9-nucleocapsid fragment fusion protein largely resisted protease degradation, while most of the CBM9-fusion proteins were degraded at some site in the SARS-CoV-2 protein fragment. All fusion proteins were expressed in E. coli at about 0.1 g/L, and could be purified with a single affinity binding step using inexpensive cellulose powder. Three purified CBM9-SARS-CoV-2 fusion proteins were tested and found to bind antibody directed to the appropriate SARS-CoV-2 antigenic region. The largest CBM9 fusion protein incorporates a spike protein self-folding domain, and includes amino acids 540-588 of the spike protein. This conserved region is immediately C-terminal to the receptor binding domain, is widely recognized by human convalescent sera, and contains a putative protective epitope.

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