peptide complexes
Recently Published Documents


TOTAL DOCUMENTS

650
(FIVE YEARS 58)

H-INDEX

64
(FIVE YEARS 6)

Author(s):  
E.I. Fatullaev ◽  
V.V. Bezrodnyi ◽  
I.M. Neelov

Biocompatible peptide dendrimers and dendrigrafts have useful properties for application in biomedicine. In previous papers the computational approach for study lysine dendrimers and dendrigrafts as well as their complexes with various medical peptides was used. In this paper the comparison of complex formation between molecules of therapeutic AEDG tetrapeptide and novel K2R peptide dendrimer or DG2 dendrigraft of near the same size and charge was fulfilled. The systems consisting of 16 therapeutic AEDG tetrapeptide molecules and one dendrimer or one dendrigraft were studied by molecular dynamics simulation. Full atomic models of these molecules in water with explicit counterions were used for this goal. First of all, the process of complex formation was studied. It was obtained that peptide molecules were attracted by both branched molecules and were quickly adsorbed by them. Times of complexes formation as well as size, anisotropy and structure of each complex were calculated. It was demonstrated that both K2R dendrimer and DG2 dendrigraft are effective for complexation of these peptide molecules but new dendrimer complex is more stable than dendrigraft complex because it has almost twice more hydrogen bonds with peptide molecules and 33% more ion pairs with their charged groups.


2021 ◽  
Author(s):  
Jindrich Kynicky ◽  
Vedran Milosavljevic ◽  
Pavlina Jelinkova ◽  
Yazan Haddad ◽  
Miguel Angel Merlos Rodrigo ◽  
...  

Author(s):  
Julian Heinrich ◽  
Karolina Bossad-Ahmad ◽  
Mie Riisom ◽  
Haleh H. Haeri ◽  
Tasha R. Steel ◽  
...  

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alessandro Montemurro ◽  
Viktoria Schuster ◽  
Helle Rus Povlsen ◽  
Amalie Kai Bentzen ◽  
Vanessa Jurtz ◽  
...  

AbstractPrediction of T-cell receptor (TCR) interactions with MHC-peptide complexes remains highly challenging. This challenge is primarily due to three dominant factors: data accuracy, data scarceness, and problem complexity. Here, we showcase that “shallow” convolutional neural network (CNN) architectures are adequate to deal with the problem complexity imposed by the length variations of TCRs. We demonstrate that current public bulk CDR3β-pMHC binding data overall is of low quality and that the development of accurate prediction models is contingent on paired α/β TCR sequence data corresponding to at least 150 distinct pairs for each investigated pMHC. In comparison, models trained on CDR3α or CDR3β data alone demonstrated a variable and pMHC specific relative performance drop. Together these findings support that T-cell specificity is predictable given the availability of accurate and sufficient paired TCR sequence data. NetTCR-2.0 is publicly available at https://services.healthtech.dtu.dk/service.php?NetTCR-2.0.


Author(s):  
Min Xu ◽  
Baomei Zhou ◽  
Yan Ding ◽  
Shanshan Du ◽  
Mengke Su ◽  
...  
Keyword(s):  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juliette Vaurs ◽  
Gaël Douchin ◽  
Klara Echasserieau ◽  
Romain Oger ◽  
Nicolas Jouand ◽  
...  

AbstractOver the past two decades, there has been a great interest in the study of HLA-E-restricted αβ T cells during bacterial and viral infections, including recently SARS-CoV-2 infection. Phenotyping of these specific HLA-E-restricted T cells requires new tools such as tetramers for rapid cell staining or sorting, as well as for the identification of new peptides capable to bind to the HLA-E pocket. To this aim, we have developed an optimal photosensitive peptide to generate stable HLA-E/pUV complexes allowing high-throughput production of new HLA-E/peptide complexes by peptide exchange. We characterized the UV exchange by ELISA and improved the peptide exchange readout using size exclusion chromatography. This novel approach for complex quantification is indeed very important to perform tetramerization of MHC/peptide complexes with the high quality required for detection of specific T cells. Our approach allows the rapid screening of peptides capable of binding to the non-classical human HLA-E allele, paving the way for the development of new therapeutic approaches based on the detection of HLA-E-restricted T cells.


2021 ◽  
Author(s):  
Junsu Ko ◽  
Juyong Lee

In this preprint, we investigated whether AlphaFold2, AF2, can predict protein-peptide complex structures only with sequence information. We modeled the structures of 203 protein-peptide complexes from the PepBDB DB and 183 from the PepSet. The structures were modeling with concatenated sequences of receptors and peptides via poly-glycine linker. We found that for more than half of the test cases, AF2 predicted the bound structures of peptides with good accuracy, C_alpha-RMSD of a peptide < 3.0 angstrom. For about 40% of cases, the peptide structures were modeled with an accuracy of C_alpha-RMSD < 2.0 angstrom. Our benchmark results clearly show that AF2 has a great potential to be applied to various higher-order structure prediction tasks.


Sign in / Sign up

Export Citation Format

Share Document