Biology subjects

Titov, A.

Publications and source records attributed to Titov, A..

2 recordsLinked to original sources

bioRxiv2023

Determination of hydrogen bonds in Gromacs: new implementation to overcome the limitation

This work describes a new software algorithm associated with determination of hydrogen bonds in biomacromolecules and their environment. The already existing algorithm for determining hydrogen bond networks in Gromacs has a number of impenetrable limitations in the analysis of structures and trajectories. The new implementation of the algorithm for determining hydrogen bond networks in the form of a native Gromacs trajectory analysis module allows to quickly analyze molecular dynamics trajectories without restrictions, thereby overcoming the limitation of original algorithm. The application of the developed algorithm made it possible to obtain and analyze the networks of hydrogen bonds of the studied defensin-like protein Pentadiplandra brazzeana, as well as to study the lifetime of hydrogen bonds between the residues of this protein and water molecules. The data obtained using the new implementation coincided with the experimental one. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/555860v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@81727aorg.highwire.dtl.DTLVardef@82de36org.highwire.dtl.DTLVardef@1cad89forg.highwire.dtl.DTLVardef@53ec2a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2020

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection

COVID-19 is a global pandemic caused by the SARS-CoV-2 coronavirus. T cells play a key role in the adaptive antiviral immune response by killing infected cells and facilitating the selection of virus-specific antibodies. However neither the dynamics and cross-reactivity of the SARS-CoV-2-specific T cell response nor the diversity of resulting immune memory are well understood. In this study we use longitudinal high-throughput T cell receptor (TCR) sequencing to track changes in the T cell repertoire following two mild cases of COVID-19. In both donors we identified CD4+ and CD8+ T cell clones with transient clonal expansion after infection. The antigen specificity of CD8+ TCR sequences to SARS-CoV-2 epitopes was confirmed by both MHC tetramer binding and presence in large database of SARS-CoV-2 epitope-specific TCRs. We describe characteristic motifs in TCR sequences of COVID-19-reactive clones and show preferential occurence of these motifs in publicly available large dataset of repertoires from COVID-19 patients. We show that in both donors the majority of infection-reactive clonotypes acquire memory phenotypes. Certain T cell clones were detected in the memory fraction at the pre-infection timepoint, suggesting participation of pre-existing cross-reactive memory T cells in the immune response to SARS-CoV-2.

immunology↗