• The tertiary structure of CBDN1 is strikingly similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other sugar-binding proteins with jelly-roll folds. (wikipedia.org)
  • Carbohydrate-binding module family 10 (CBM10) is found in two distinct sets of proteins with different functions. (wikipedia.org)
  • RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)
  • Known as "destabilising motifs", these sequences attract the attention of a group of proteins called Ccr4-Not. (elifesciences.org)
  • Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
  • At least four phylogenetically distinct groups of bacteria encode repeat proteins with the common ability to bind specific DNA sequences with a unique but conserved code. (uni-muenchen.de)
  • RipTALs are effector proteins delivered during bacterial wilt disease caused by R. solanacearum strains. (uni-muenchen.de)
  • In the case of the RipTALs this work should begin to unravel the role these proteins play in bacterial wilt disease, as a means to fight this devastating pathogen. (uni-muenchen.de)
  • In addition the TALEs and RipTALs may simply represent one face of the TALE-likes, a protein family mediating as yet unknown biological roles as bacterial DNA binding proteins. (uni-muenchen.de)
  • Erythromycin targets bacterial ribosomes - the nanomachine responsible for the translation of messenger RNA (mRNA) sequences into protein - thus preventing synthesis of the proteins required for continued growth and survival. (uni-muenchen.de)
  • For example, aph promoter combined with different RBS sequences were used for expression of reporter proteins in C. glutamicum (Zhang et al. (springeropen.com)
  • The anaerobic bacterial dockerins are homologous to EF hands (calcium-binding motifs) and require calcium for activity whereas the fungal dockerin does not require calcium. (wikipedia.org)
  • Unlike in B. subtilis, SpoIIQ of Clostridium difficile has intact LytM zinc-binding motifs. (nih.gov)
  • Currents tools are based on conserved motifs and are applied to peptides with many known binding TCRs. (frontiersin.org)
  • Finally, the interaction between cohesin and dockerin appears to be species specific in bacteria, there is almost no species specificity of binding within fungal species and no identified sites that distinguish different species. (wikipedia.org)
  • Each repeat binds a single DNA base, and specificity is determined by the amino acid residue at position 13 of each repeat. (uni-muenchen.de)
  • The affinity of a TCR for a given peptide epitope and the specificity of the binding are governed by the heterodimeric αβ T-cell receptors ( 2 ). (frontiersin.org)
  • In both TCRα and TCRβ chains, CDR3 loops have the highest sequence diversity and are the principal determinants of receptor binding specificity. (frontiersin.org)
  • CBMs are classified into numerous families, based on amino acid sequence similarity. (wikipedia.org)
  • This gene encodes a taxon-specific crystallin protein that binds NADPH and has sequence similarity to bacterial ornithine cyclodeaminases. (thermofisher.com)
  • It has been shown to be a bacterial homolog of eukaryotic tubulin, based both on a low sequence identity and a striking structural similarity (2). (cytoskeleton.com)
  • The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. (nature.com)
  • The QuickLyse Miniprep Kit provides a rapid spin-column-based method for isolating sequencing-grade plasmid DNA. (qiagen.com)
  • The QuickLyse Miniprep Kit yields sufficient plasmid DNA for any downstream application, including automated sequencing. (qiagen.com)
  • F-plasmid partition complexes containing ParB F and parS F move by generating and following a local concentration gradient of nucleoid-bound ParA F . However, the process through which ParB F activates ParA F -ATPase has not been defined. (biorxiv.org)
  • F-plasmid has a parS sequence cluster ( parS F , also called sopC ) composed of twelve repeats of a 16 bp consensus sequence, each separated by 27 base-pair spacer sequences ( Helsberg and Eichenlaub, 1986 ). (biorxiv.org)
  • Recently, high-throughput DNA sequencing has enabled large-scale characterization of TCR sequences, producing detailed T cell repertoire (Rep-Seq) ( 11 ). (frontiersin.org)
  • Because Protein G has greater affinity than Protein A for most mammalian IgGs, it may be used for the purification of mammalian IgGs that do not bind well to Protein A. Protein G binds with significantly greater capacity than Protein A to several IgG subclasses such as human IgG3, mouse IgG1 and rat IgG2a. (thermofisher.com)
  • The drug-induced stalling allows for a change in the structural conformation of the mRNA, which in turn, unmasks a ribosome-binding site downstream, enabling the nucleotide sequence that encodes the resistance factor itself to be translated. (uni-muenchen.de)
  • Finally, gadB2 and mutant gadB1 were co-expressed under the optimal promoter and RBS combination, thus converted Glu into GABA completely and improved GABA production to more than 25 g/L. This study provides useful promoters and RBS sequences for gene expression in C. glutamicum . (springeropen.com)
  • Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. (nature.com)
  • First, one of the modifications allows it to bind just outside of the rifampicin binding pocket, increasing the strength of its affinity to the RNA polymerase in rifampicin-resistant bacteria. (scienceblog.com)
  • Bacterial cell resuspension, lysis, and DNA binding are achieved in a single buffer, enabling fast DNA purification with minimal hands-on time. (qiagen.com)
  • Bacterial cells are resuspended and lysed and DNA is bound in a single buffer, enabling fast DNA purification with minimal hands-on time. (qiagen.com)
  • Carbohydrate-binding module family 1 (CBM1) consists of 36 amino acids. (wikipedia.org)
  • The encoded protein does not perform a structural role in lens tissue, and instead it binds thyroid hormone for possible regulatory or developmental roles. (thermofisher.com)
  • CBMs of microbial glycoside hydrolases play a central role in the recycling of photosynthetically fixed carbon through their binding to specific plant structural polysaccharides. (wikipedia.org)
  • High-resolution cryo-electron microscopy has now revealed in unprecedented detail the structural changes in the bacterial ribosome which results in resistance to the antibiotic erythromycin. (uni-muenchen.de)
  • Following specific binding of T cell receptors to viral and bacterial-derived peptides bound to MHC ( 5 ), or from neo-antigens ( 8 - 10 ), the appropriate T cells expand, resulting in the increased frequency of T cells carrying such receptors. (frontiersin.org)
  • Together these data confirm the maintenance of host-specific minority variants in arbovirus mutant swarms, suggest a unique role for NS3 in viral fitness, and demonstrate that intrahost sequence data can inform mechanisms of host-specific adaptation. (bvsalud.org)
  • There are inconsistencies in reported binding properties of IgG to Protein G. Variations in isolation and manufacturing methods for Protein G may affect IgG binding, partially because there are differing numbers of IgG-binding sites on various sources of Protein G. Binding studies have been performed using native Protein G and several different recombinant forms. (thermofisher.com)
  • Current sequencing methods allow for detailed samples of T cell receptors (TCR) repertoires. (frontiersin.org)
  • We employ new Natural Language Processing (NLP) based methods to predict whether any TCR and peptide bind. (frontiersin.org)
  • We combined large-scale TCR-peptide dictionaries with deep learning methods to produce ERGO (pEptide tcR matchinG predictiOn), a highly specific and generic TCR-peptide binding predictor. (frontiersin.org)
  • Kanglemycin A is related to rifampicin, an antibiotic that functions by binding to bacterial RNA polymerase, the enzyme responsible for RNA production, and preventing it from making more RNA," said Murakami. (scienceblog.com)
  • The majority of these domains have carbohydrate-binding activity. (wikipedia.org)
  • CBMs were previously known as cellulose-binding domains. (wikipedia.org)
  • Carbohydrate-binding module family 4 (CBM4) includes the two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at the N terminus of the 1,4-beta-glucanase, CenC, from Cellulomonas fimi. (wikipedia.org)
  • Carbohydrate-binding module family 6 (CBM6) is unusual in that it contains two substrate-binding sites, cleft A and cleft B. Cellvibrio mixtus endoglucanase 5A contains two CBM6 domains, the CBM6 domain at the C-terminus displays distinct ligand binding specificities in each of the substrate-binding clefts. (wikipedia.org)
  • but in anaerobic fungi they are protein binding domains, referred to as dockerin domains. (wikipedia.org)
  • In anaerobic bacteria that degrade plant cell walls, exemplified by Clostridium thermocellum, the dockerin domains of the catalytic polypeptides can bind equally well to any cohesin from the same organism. (wikipedia.org)
  • DNA sequencing of native Protein G identifies two IgG-binding domains and sites for albumin and cell surface binding. (thermofisher.com)
  • The albumin and cell surface binding domains have been eliminated from Recombinant Protein G to reduce nonspecific binding and, therefore, can be used to separate IgG from crude samples. (thermofisher.com)
  • We studied CTP- and parS F -modulated ParA F -ParB F complex assembly, in which DNA-bound ParA F -ATP dimers are activated for ATP hydrolysis by interacting with two ParB F N-terminal domains. (biorxiv.org)
  • The eukaryotic transactivation domain, which lends this group their name, allows them to activate specifically targeted host genes for the benefit of the bacterial invader. (uni-muenchen.de)
  • Just like eukaryotic tubulin, FtsZ polymerizes as well as binds and hydrolyzes GTP in a polymerization dependent manner. (cytoskeleton.com)
  • To enhance GABA production in C. glutamicum , ribosomal binding site (RBS) sequence and promoter were searched and optimized for increasing the expression efficiency of gadB2 . (springeropen.com)
  • This combination of RBS sequence and AS contributed to gadB2 expression, increased GAD activity by 156% and GABA production by 82% compared to normal strong RBS and AS combination. (springeropen.com)
  • Therefore, optimization of promoters and RBS sequences has been applied for protein expression in C. glutamicum . (springeropen.com)
  • In addition, there are significant binding differences when different buffers are used. (thermofisher.com)
  • Analysis of binding kinetics reveals that this is primarily due to differences in dissociation rate constants. (elifesciences.org)
  • Differences in binding characteristics between Protein A and Protein G may be explained by the differing compositions in the IgG-binding sites of each protein. (thermofisher.com)
  • Together with the FH polymorphisms between vertebrate hosts, these findings suggest that minor sequence variation in this bacterial outer surface protein may confer dramatic differences in host-specific, FH-binding-mediated infectivity. (bvsalud.org)
  • SpoIIQ, but not SpoIIQ(H120S) , binds Zn(2+) , and metal absence alters the SpoIIQ-SpoIIIAH complex in vitro. (nih.gov)
  • Swapping the divergent region in the FH-binding interface between rodent- and bird-associated CspZ variants alters the ability to promote rodent- and bird-specific early-onset dissemination. (bvsalud.org)
  • Comparing repeat sequences across all groups reveals that only three positions are hyper-conserved. (uni-muenchen.de)
  • Optimal binding occurs at pH 5, although binding is also effective at pH 7.0 to 7.2. (thermofisher.com)
  • R4 exhibited the highest strength among RBS sequences tested, with 6 nt the optimal aligned spacing (AS) between RBS and start codon. (springeropen.com)
  • For example, the fungal enzymes contain one, two or three copies of the dockerin sequence in tandem within the catalytic polypeptide. (wikipedia.org)
  • The Bats and MOrTLs are primarily of interest as comparison groups to the TALEs and RipTALs and as sources of sequence diversity for future efforts into TALE repeat engineering. (uni-muenchen.de)
  • We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). (nature.com)
  • In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes (for example glycoside hydrolases). (wikipedia.org)
  • Carbohydrate-binding module family 2 (CBM2) contains two conserved cysteines - one at each extremity of the domain - which have been shown to be involved in a disulfide bond. (wikipedia.org)
  • Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from C. fimi 1,4-beta-glucanase CenC (CBDN1). (wikipedia.org)
  • Unlike most protocols that use a 3-step lysis procedure, the QuickLyse Miniprep Kit combines enzymatic and osmotic processes to lyse bacterial cells in a single, 3-minute step. (qiagen.com)
  • In contrast, many TCR responses are characterized by a high level of cross-reactivity with single TCRs binding a large number of MHC-bound peptides, and single peptides binding a large number of TCRs ( 16 , 17 ). (frontiersin.org)
  • Working together with others I was able to show that repeats from each group of TALE-likes mediate sequence specific DNA binding, revealing a conserved code in each case. (uni-muenchen.de)
  • The researchers screened a library of naturally occurring compounds from U.K. biotech company Demuris Ltd. for their ability to inhibit bacterial cell growth or prevent the production of RNA - an essential process in all living organisms - in bacteria. (scienceblog.com)
  • The isolated DNA can be used directly in standard applications, including automated sequencing, PCR, restriction analysis, and cloning. (qiagen.com)
  • The mRNAs can carry short sequences of genetic letters that can trigger their own destruction. (elifesciences.org)
  • We find that the fission yeast homologues of Tristetraprolin/TTP and Pumilio/Puf (Zfs1 and Puf3) interact with Ccr4-Not via multiple regions within low-complexity sequences, suggestive of a multipartite interface that extends beyond previously defined interactions. (elifesciences.org)
  • Utilizing WNV deep-sequencing data, we previously identified a naturally occurring, mosquito-biased substitution, NS3 P319L. (bvsalud.org)
  • Successful recognition of antigenic peptides bound to Major Histocompatibility Complexes (pMHCs) requires specific binding of the TCR to these complexes ( 5 - 7 ), which in turn modulates the cell's fitness, clonal expansion, and acquisition of effector properties ( 7 ). (frontiersin.org)
  • We tested this hypothesis by determining the crystal structure of the CspZ-human FH complex, and identifying minor variation localized in the FH-binding interface yielding bird and rodent FH-specific binding activity that impacts infectivity. (bvsalud.org)
  • Despite high sequence conservation, CspZ variants differ in human FH-binding ability. (bvsalud.org)
  • To determine the mechanism of kanglemycin A action against rifampicin-resistant RNA polymerase, the Murakami group used X-ray crystallography to determine the three-dimensional structure of the complex of kanglemycin A bound to bacterial RNA polymerase. (scienceblog.com)
  • However, as many experimental settings provide, only beta chains, a binding prediction tool based on these chains is of importance. (frontiersin.org)
  • While both chains have been reported to be important to affect binding, we show here that for many TCR-peptide pairs the TCR's binding to target MHC-peptide can be determined with high accuracy using the β-chain only. (frontiersin.org)
  • Protein G is a bacterial cell wall protein isolated from group G Streptococci. (thermofisher.com)
  • Kanglemycin A binds to the same groove, but its structure revealed extensions that also bind just outside the groove allowing it to inhibit activity of rifampicin-resistant RNA polymerase. (scienceblog.com)
  • In the introduction of this dissertation, which explores TALE biology, a particular focus will be placed on the DNA binding properties of TALEs and how this can be put to use in TALE technology. (uni-muenchen.de)
  • The galectin lattice is a multi-valent interaction of galectins with glycoproteins at the cell surface that displays rapid exchange of binding partners with properties of liquid-liquid phase transitions, thereby acting as an intermediary between freely diffusing glycoproteins and stable complexes in the membrane. (gr.jp)
  • The initiation of transcription is fundamentally controlled by the promoter elements, while the initiation of translation is mainly affected by the strength of ribosomal binding site (RBS). (springeropen.com)
  • Many putative CBMs have been identified by amino acid sequence alignments but only a few representatives have been shown experimentally to have a carbohydrate-binding function. (wikipedia.org)
  • To survive in hosts and escape complement-mediated immune clearance, Bb produces the outer surface protein CspZ that binds the complement inhibitor factor H (FH) to facilitate bacterial dissemination in vertebrates. (bvsalud.org)
  • Figure 1: DNA curtains assay for target binding by Cas9-RNA. (nature.com)
  • Figure 2: Cas9-RNA remains bound to cleaved products and localizes to PAM-rich regions during the target search. (nature.com)
  • I will argue that the TALE-likes represent a fascinating case of conserved structure and function in a diverse sequence space. (uni-muenchen.de)
  • Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. (nature.com)
  • To determine from a repertoire whether its host had been exposed to a target, computational tools that predict TCR-epitope binding are required. (frontiersin.org)
  • FtsZ is a bacterial cytoskeletal protein that is essential for cell division many prokaryotes (1). (cytoskeleton.com)