puplications of the research group drug bioinformatics([HIPS]WIBI)http://hdl.handle.net/10033/6215202024-02-02T18:20:40Z2024-02-02T18:20:40ZEpistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability.Dultz, GeorgSrikakulam, Sanjay KKonetschnik, MichaelShimakami, TetsuroDoncheva, Nadezhda TDietz, JuliaSarrazin, ChristophBiondi, Ricardo MZeuzem, StefanTampé, RobertKalinina, Olga VWelsch, Christophhttp://hdl.handle.net/10033/6230872021-10-30T01:52:32Z2021-07-31T00:00:00ZEpistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability.
Dultz, Georg; Srikakulam, Sanjay K; Konetschnik, Michael; Shimakami, Tetsuro; Doncheva, Nadezhda T; Dietz, Julia; Sarrazin, Christoph; Biondi, Ricardo M; Zeuzem, Stefan; Tampé, Robert; Kalinina, Olga V; Welsch, Christoph
The Q80K polymorphism in the NS3-4A protease of the hepatitis C virus is associated with treatment failure of direct-acting antiviral agents. This polymorphism is highly prevalent in genotype 1a infections and stably transmitted between hosts. Here, we investigated the underlying molecular mechanisms of evolutionarily conserved coevolving amino acids in NS3-Q80K and revealed potential implications of epistatic interactions in immune escape and variants persistence. Using purified protein, we characterized the impact of epistatic amino acid substitutions on the physicochemical properties and peptide cleavage kinetics of the NS3-Q80K protease. We found that Q80K destabilized the protease protein fold (p < 0.0001). Although NS3-Q80K showed reduced peptide substrate turnover (p < 0.0002), replicative fitness in an H77S.3 cell culture model of infection was not significantly inferior to the WT virus. Epistatic substitutions at residues 91 and 174 in NS3-Q80K stabilized the protein fold (p < 0.0001) and leveraged the WT protease stability. However, changes in protease stability inversely correlated with enzymatic activity. In infectious cell culture, these secondary substitutions were not associated with a gain of replicative fitness in NS3-Q80K variants. Using molecular dynamics, we observed that the total number of residue contacts in NS3-Q80K mutants correlated with protein folding stability. Changes in the number of contacts reflected the compensatory effect on protein folding instability by epistatic substitutions. In summary, epistatic substitutions in NS3-Q80K contribute to viral fitness by mechanisms not directly related to RNA replication. By compensating for protein-folding instability, epistatic interactions likely protect NS3-Q80K variants from immune cell recognition.
2021-07-31T00:00:00ZAn extended catalogue of tandem alternative splice sites in human tissue transcriptomes.Mironov, AlekseiDenisov, StepanGress, AlexanderKalinina, Olga VPervouchine, Dmitri Dhttp://hdl.handle.net/10033/6229052021-06-15T01:40:32Z2021-04-07T00:00:00ZAn extended catalogue of tandem alternative splice sites in human tissue transcriptomes.
Mironov, Aleksei; Denisov, Stepan; Gress, Alexander; Kalinina, Olga V; Pervouchine, Dmitri D
Tandem alternative splice sites (TASS) is a special class of alternative splicing events that are characterized by a close tandem arrangement of splice sites. Most TASS lack functional characterization and are believed to arise from splicing noise. Based on the RNA-seq data from the Genotype Tissue Expression project, we present an extended catalogue of TASS in healthy human tissues and analyze their tissue-specific expression. The expression of TASS is usually dominated by one major splice site (maSS), while the expression of minor splice sites (miSS) is at least an order of magnitude lower. Among 46k miSS with sufficient read support, 9k (20%) are significantly expressed above the expected noise level, and among them 2.5k are expressed tissue-specifically. We found significant correlations between tissue-specific expression of RNA-binding proteins (RBP), tissue-specific expression of miSS, and miSS response to RBP inactivation by shRNA. In combination with RBP profiling by eCLIP, this allowed prediction of novel cases of tissue-specific splicing regulation including a miSS in QKI mRNA that is likely regulated by PTBP1. The analysis of human primary cell transcriptomes suggested that both tissue-specific and cell-type-specific factors contribute to the regulation of miSS expression. More than 20% of tissue-specific miSS affect structured protein regions and may adjust protein-protein interactions or modify the stability of the protein core. The significantly expressed miSS evolve under the same selection pressure as maSS, while other miSS lack signatures of evolutionary selection and conservation. Using mixture models, we estimated that not more than 15% of maSS and not more than 54% of tissue-specific miSS are noisy, while the proportion of noisy splice sites among non-significantly expressed miSS is above 63%.
2021-04-07T00:00:00ZDIGGER: exploring the functional role of alternative splicing in protein interactions.Louadi, ZakariaYuan, KevinGress, AlexanderTsoy, OlgaKalinina, Olga VBaumbach, JanKacprowski, TimList, Markushttp://hdl.handle.net/10033/6225222020-10-21T01:32:58Z2020-09-25T00:00:00ZDIGGER: exploring the functional role of alternative splicing in protein interactions.
Louadi, Zakaria; Yuan, Kevin; Gress, Alexander; Tsoy, Olga; Kalinina, Olga V; Baumbach, Jan; Kacprowski, Tim; List, Markus
Alternative splicing plays a major role in regulating the functional repertoire of the proteome. However, isoform-specific effects to protein-protein interactions (PPIs) are usually overlooked, making it impossible to judge the functional role of individual exons on a systems biology level. We overcome this barrier by integrating protein-protein interactions, domain-domain interactions and residue-level interactions information to lift exon expression analysis to a network level. Our user-friendly database DIGGER is available at https://exbio.wzw.tum.de/digger and allows users to seamlessly switch between isoform and exon-centric views of the interactome and to extract sub-networks of relevant isoforms, making it an essential resource for studying mechanistic consequences of alternative splicing.
2020-09-25T00:00:00ZThe bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes.Sikandar, AsfandyarFranz, LauraAdam, SebastianSantos-Aberturas, JavierHorbal, LiliyaLuzhetskyy, AndriyTruman, Andrew WKalinina, Olga VKoehnke, Jeskohttp://hdl.handle.net/10033/6224212020-09-08T01:34:12Z2020-06-29T00:00:00ZThe bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes.
Sikandar, Asfandyar; Franz, Laura; Adam, Sebastian; Santos-Aberturas, Javier; Horbal, Liliya; Luzhetskyy, Andriy; Truman, Andrew W; Kalinina, Olga V; Koehnke, Jesko
d-amino acids endow peptides with diverse, desirable properties, but the post-translational and site-specific epimerization of l-amino acids into their d-counterparts is rare and chemically challenging. Bottromycins are ribosomally synthesized and post-translationally modified peptides that have overcome this challenge and feature a d-aspartate (d-Asp), which was proposed to arise spontaneously during biosynthesis. We have identified the highly unusual α/β-hydrolase (ABH) fold enzyme BotH as a peptide epimerase responsible for the post-translational epimerization of l-Asp to d-Asp during bottromycin biosynthesis. The biochemical characterization of BotH combined with the structures of BotH and the BotH–substrate complex allowed us to propose a mechanism for this reaction. Bioinformatic analyses of BotH homologs show that similar ABH enzymes are found in diverse biosynthetic gene clusters. This places BotH as the founding member of a group of atypical ABH enzymes that may be able to epimerize non-Asp stereocenters across different families of secondary metabolites.
2020-06-29T00:00:00Z