Variable Loop Research Articles

Stress-induced modification of Escherichia coli tRNA generates 5-methylcytidine in the variable loop

There has been recent interest in trying to understand the connection between transfer RNA (tRNA) posttranscriptional modifications and changes in-cellular environmental conditions. Here, we report on the identification of the modified nucleoside 5-methylcytidine (m5C) in Escherichia coli tRNAs. This modification was determined to be present at position 49 of tRNA Tyr-QUA-II. Moreover, m5C levels in this tRNA are significantly elevated under high reactive oxygen specieis (ROS) conditions in E. coli cells. We identified the known ribosomal RNA methyltransferase rsmF as the enzyme responsible for m5C synthesis in tRNA and enzyme transcript levels are responsive to elevated levels of ROS in the cell. We further find that changes in m5C levels in this tRNA are not specific to Fenton-like reaction conditions elevating ROS, but heat shock can also induce increased modification of tRNA Tyr-QUA-II. Altogether, this work illustrates how cells adapt to changing environmental conditions through variations in tRNA modification profiles.

FIRST-IN-HUMAN EXPERIENCE OF HIGH ENERGY ELECTROPULSE PULSED FIELD ABLATION: ACUTE RESULTS FOR PULMONARY VEINS AND POSTERIOR WALL ISOLATION

Different iterations of catheter and energy delivery system configurations are evolving for pulsed field ablation (PFA); however, some have used large and complex catheters, required large sheaths and had a recognised risk of haemolysis. To evaluate the acute safety and efficacy of a custom designed 8F variable loop multielectrode mapping and PFA catheter with contact sensing. This acute feasibility study recruited 30 patients undergoing de novo ablation of paroxysmal or persistent atrial fibrillation (AF). The ElectroPulse Study is a first-in-human, non-randomised, prospective study of a novel PFA system that utilizes an 8F 10-electrode variable loop steerable mapping and ablation catheter with 2800V biphasic bipolar waveform. All patients had pulmonary vein (PV) and posterior wall isolation (PWI) using the PFA system. The main outcomes were the acute success of PV/PWI and peri-procedural serious adverse events. Complete PV/PWI was successfully achieved in all 30 patients with 59.7±7.2 applications. Total procedural time was 113.6±26.3 mins with fluoroscopy time of 8.0±5.5 mins and LA dwell time of 78.7±18.6 mins. There was no esophageal injury, phrenic nerve palsy, clinical stroke or death. Brain MRI detected 2 new but transient silent cerebral lesions. Two patients (6.7%) had vascular access complications. Although there were changes in the biomarkers for hemolysis, none of the patient experienced clinical hemolysis or related acute kidney injury. This first-in-human study demonstrated that PFA using a novel variable loop catheter with a contact sensing system safely achieved 100% acute PVI/PWI with safety profile comparable to existing PFA systems.

Long-term patient clinical benefits and healthcare utilization after pulsed field ablation in paroxysmal atrial fibrillation: sub-analyses from the multicenter inspIRE trial

Abstract Background/Introduction The treatment of atrial fibrillation (AF) with pulsed field ablation (PFA) aims to prevent AF recurrence while reducing complications from the ablation modality. Similar to thermal ablation, PFA has proven to be safe and effective for treatment of paroxysmal AF (PAF); however, there is scarce evidence on patient-related clinical benefits, including healthcare utilization, using this new energy modality. Purpose The objective of this study is to assess long-term clinical improvements in patient care, symptoms, and quality-of-life (QOL) after PFA ablation in PAF. Methods InspIRE was a multicentre study evaluating the safety and efficacy of variable loop PFA catheters integrated with a 3D mapping system for treatment of symptomatic PAF. Patients were followed for up to 12 months for the following QOL and healthcare utilization endpoints: Atrial Fibrillation Effect on Quality-of-Life (AFEQT) score, Class I/III AAD utilization, repeat ablation, incidence of direct current cardioversion (DCCV), and cardiovascular (CV) hospitalization. Post-hoc Kaplan-Meier estimates for clinical benefit success at 12 months were provided. Success was defined as composite freedom from occurrence of the following events post-blanking: repeat ablation, CV hospitalization, AAD utilization, and DCCV post-blanking. Predictors of clinical benefit success were explored via multivariate logistic regression analysis. Results A total of 186 enrolled patients (59±10 years; 70.0% male; CHA2DS2-VASC score 1.3±1.2) underwent PVI. Compared to baseline: 1) improvements in the AFEQT composite score were seen at 12 months (P<0.001); 2) Class I/III AAD use was reduced from 81.7% to 20.1% at 6-12 months (P<0.05); and 3) the proportion of subjects with DCCV decreased from 13.7% up to 12 months before the index procedure to 3.3% up to 12 months after the index procedure (P<0.001, Figure 1). Minimal clinically important difference in QoL (≥5 points improvement in AFEQT) was achieved in 85.2% of patients. Patients free from 12-month AF/AT/AFL recurrence (asymptomatic and symptomatic) had significantly greater improvements in AFEQT scores from baseline to 12 months versus those with recurrence (P=0.01). The clinical benefit success rate at 12 months was 87.5% (Figure 2). Patients who failed the clinical benefit endpoint were counted, including those with repeat ablation (7.5%), those on new or higher dose of AAD (6.5%), those hospitalized for CV (4.8%), and those who had DCCV post-blanking (1.6%). Multivariate logistic regression analysis showed that left ventricle ejection fraction <60% (OR: 0.22; 95% CI: 0.08-0.62; P<0.05) and incidence of diabetes (OR: 7.25; 95% CI: 2.00, 26.3; p<0.05) were associated with a higher risk of clinical benefit failure. Conclusions PFA ablation of PAF patients led to a clinical benefit success rate of 87.5%, with clinically meaningful improvement in QOL, as well as a reductions in AAD use, cardioversion, and hospitalization.Figure 1.Improvements in QoL and HealthFigure 2.Kaplan-Meier Analysis of Time

Campycins are novel broad-spectrum antibacterials killing Campylobacter jejuni

Pyocins are high molecular weight bacteriocins produced by Pseudomonas aeruginosa that can be retargeted to new bacterial species by exchanging the pyocin tail fibers with bacteriophage receptor binding proteins (RBPs). Here, we develop retargeted pyocins called campycins as new antibacterials to precisely and effectively kill the major foodborne pathogen Campylobacter jejuni. We used two diverse RBPs (H-fibers) encoded by CJIE1 prophages found in the genomes of C. jejuni strains CAMSA2147 and RM1221 to construct campycin 1 and campycin 2, respectively. Campycins 1 and 2 could target all C. jejuni strains tested due to complementary antibacterial spectra. In addition, both campycins led to more than 3 log reductions in C. jejuni counts under microaerobic conditions at 42 °C, whereas the killing efficiency was less efficient under anaerobic conditions at 5 °C. Furthermore, we discovered that both H-fibers used to construct the campycins bind to the essential major outer membrane protein (MOMP) present in all C. jejuni in a strain-specific manner. Protein sequence alignment and structural modeling suggest that the highly variable extracellular loops of MOMP form the binding sites of the diverse H-fibers. Further in silico analyses of 5000 MOMP sequences indicated that the protein falls into three major clades predicted to be targeted by either campycin 1 or campycin 2. Thus, campycins are promising antibacterials against C. jejuni and are expected to broadly target numerous strains of this human pathogen in nature and agriculture.Key points• Campycins are engineered R-type pyocins containing H-fibers from C. jejuni prophages• Campycins reduce C. jejuni counts by >3 logs at conditions promoting growth• Campycins bind to the essential outer membrane protein MOMP in a strain-dependent way

Mettl1-dependent m7G tRNA modification is essential for maintaining spermatogenesis and fertility in Drosophila melanogaster

Modification of guanosine to N7-methylguanosine (m7G) in the variable loop region of tRNA is catalyzed by the METTL1/WDR4 heterodimer and stabilizes target tRNA. Here, we reveal essential functions of Mettl1 in Drosophila fertility. Knockout of Mettl1 (Mettl1-KO) causes no major effect on the development of non-gonadal tissues, but abolishes the production of elongated spermatids and mature sperm, which is fully rescued by expression of a Mettl1-transgene, but not a catalytic-dead Mettl1 transgene. This demonstrates that Mettl1-dependent m7G is required for spermatogenesis. Mettl1-KO results in a loss of m7G modification on a subset of tRNAs and decreased tRNA abundance. Ribosome profiling shows that Mettl1-KO led to ribosomes stalling at codons decoded by tRNAs that were reduced in abundance. Mettl1-KO also significantly reduces the translation efficiency of genes involved in elongated spermatid formation and sperm stability. Germ cell-specific expression of Mettl1 rescues disrupted m7G tRNA modification and tRNA abundance in Mettl1-KO testes but not in non-gonadal tissues. Ribosome stalling is much less detectable in non-gonadal tissues than in Mettl1-KO testes. These findings reveal a developmental role for m7G tRNA modification and indicate that m7G modification-dependent tRNA abundance differs among tissues.

Docking interactions determine substrate specificity of members of a widespread family of protein phosphatases

How protein phosphatases achieve specificity for their substrates is a major outstanding question. PPM family serine/threonine phosphatases are widespread in bacteria and eukaryotes, where they dephosphorylate target proteins with a high degree of specificity. In bacteria, PPM phosphatases control diverse transcriptional responses by dephosphorylating anti-anti-sigma factors of the STAS domain family, exemplified by B. subtilis phosphatases SpoIIE, which controls cell-fate during endospore formation, and RsbU, which initiates the General Stress Response. Using a combination of forward genetics, biochemical reconstitution, and AlphaFold2 structure prediction, we identified a conserved, tripartite substrate docking interface comprised of three variable loops on the surface of the PPM phosphatase domains of SpoIIE and RsbU that recognize the three-dimensional structure of the substrate protein. Non-conserved amino acids in these loops facilitate the accommodation of the cognate substrate and prevent dephosphorylation of the non-cognate substrate. Together, single-amino acid substitutions in these three elements cause an over five-hundred fold change in specificity. Our data additionally suggest that substrate-docking interactions regulate phosphatase specificity through a conserved allosteric switch element that controls the catalytic efficiency of the phosphatase by positioning the metal cofactor and substrate. We hypothesize that this is a generalizable mechanistic model for PPM family phosphatase substrate specificity. Importantly, the substrate docking interface with the phosphatase is only partially overlapping with the much more extensive interface with the upstream kinase, suggesting the possibility that kinase and phosphatase specificity evolved independently.

Computed tomographic characteristics of anatomical variations of external and internal jugular veins in dogs.

The external jugular vein (EJV) has been commonly used for clinical procedures in veterinary medicine, while the internal jugular vein (IJV) has been used mainly for research. Limited literature regarding anatomical variants in both EJV and IJV is available. The objectives of this descriptive retrospective study were to identify the number of dogs with variations of the jugular veins in canine patients undergoing CT of the head and neck and characterize these variations. Of 1000 dogs, 193 dogs (19.3%) had anatomical variations. Six types of anatomical variations were identified. The most common Type I was the absence of the linguofacial vein (72.0%, n=139), with the lingual, facial, and maxillary veins entering the EJV at a common branching point. Type II described a variable course of the EJV and IJV, which in some dogs resulted in the absence of the EJV (14.0%, n=27). Type III was a variable anastomotic loop formed by the linguofacial or maxillary vein cranial or at the junction of the EJV (4.2%, n=8). In Type IV, the EJV was either suspected to be aplastic or markedly reduced in diameter compared with the contralateral side just distal to its formation (3.6%, n=7). Type V was found in only six dogs (3.1%) with unilateral differences in the diameter of the IJV. Six of 193 dogs had a combination of more than one variation (Type VI, 3.1%). Type I was significantly observed more frequently in meso- and dolichocephalic breeds. Type II was significantly observed more frequently in brachycephalic breeds.

Application repetition and electrode-tissue contact result in deeper lesions using a pulsed-field ablation circular variable loop catheter.

Pulsed-field ablation (PFA) is a novel, myocardial-selective, non-thermal ablation modality used to target cardiac arrhythmias. Although prompt electrogram (EGM) signal disappearance is observed immediately after PFA application in the pulmonary veins, whether this finding results in adequate transmural lesions is unknown. The aim of this study is to check whether application repetition and catheter-tissue contact impact lesion formation during PFA. A circular loop PFA catheter was used to deliver repeated energy applications with various levels of contact force. A benchtop vegetal potato model and a beating heart ventricular myocardial model were utilized to evaluate the impact of application repetition, contact force, and catheter repositioning on contiguity and lesion depth. Lesion development occurred over 18 h in the vegetal model and over 6 h in the porcine model. Lesion formation was found to be dependent on application repetition and contact. In porcine ventricles, single and multiple stacked applications led to a lesion depth of 3.5 ± 0.7 and 4.4 ± 1.3 mm, respectively (P = 0.002). Furthermore, the greater the catheter-tissue contact, the more contiguous and deeper the lesions in the vegetal model (1.0 ± 0.9 mm with no contact vs. 5.4 ± 1.4 mm with 30 g of force; P = 0.0001). Pulsed-field ablation delivered via a circular catheter showed that both repetition and catheter contact led independently to deeper lesion formation. These findings indicate that endpoints for effective PFA are related more to PFA biophysics than to mere EGM attenuation.

Origin of Type II tRNA Variable Loops, Aminoacyl-tRNA Synthetase Allostery from Distal Determinants, and Diversification of Life

The three 31 nucleotide minihelix tRNA evolution theorem describes the evolution of type I and type II tRNAs to the last nucleotide. In databases, type I and type II tRNA V loops (V for variable) were improperly aligned, but alignment based on the theorem is accurate. Type II tRNA V arms were a 3′-acceptor stem (initially CCGCCGC) ligated to a 5′-acceptor stem (initially GCGGCGG). The type II V arm evolved to form a stem–loop–stem. In Archaea, tRNALeu and tRNASer are type II. In Bacteria, tRNALeu, tRNASer, and tRNATyr are type II. The trajectory of the type II V arm is determined by the number of unpaired bases just 5′ of the Levitt base (Vmax). For Archaea, tRNALeu has two unpaired bases, and tRNASer has one unpaired base. For Bacteria, tRNATyr has two unpaired bases, tRNALeu has one unpaired base, and tRNASer has zero unpaired bases. Thus, the number of synonymous type II tRNA sets is limited by the possible trajectory set points of the arm. From the analysis of aminoacyl-tRNA synthetase structures, contacts to type II V arms appear to adjust allosteric tension communicated primarily via tRNA to aminoacylating and editing active sites. To enhance allostery, it appears that type II V arm end loop contacts may tend to evolve to V arm stem contacts.

HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state.

HIV-1 infection is initiated by the interaction between the gp120 subunit in the envelope (Env) trimer and the cellular receptor CD4 on host cells. This interaction induces substantial structural rearrangement of the Env trimer. Currently, static structural information for prefusion-closed trimers, CD4-bound prefusion-open trimers, and various antibody-bound trimers is available. However, dynamic features between these static states (e.g., transition structures) are not well understood. Here, we investigate the full transition pathway of a site specifically glycosylated Env trimer between prefusion-closed and CD4-bound-open conformations by collective molecular dynamics and single-molecule Förster resonance energy transfer (smFRET). Our investigations reveal and confirm important features of the transition pathway, including movement of variable loops to generate a glycan hole at the trimer apex and formation or rearrangements of α-helices and β-strands. Notably, by comparing the transition pathway to known Env-structures, we uncover evidence for a transition intermediate, with four antibodies, Ab1303, Ab1573, b12, and DH851.3, recognizing this intermediate. Each of these four antibodies induce population shifts of Env to occupy a newly observed smFRET state: the "occluded-intermediate" state. We propose this occluded-intermediate state to be both a prevalent state of Env and an on-path conformation between prefusion-closed and CD4-bound-open states, previously overlooked in smFRET analyses.

Differences in neutralizing antibody sensitivities and envelope characteristics indicate distinct antigenic properties of Nigerian HIV-1 subtype G and CRF02_AG

The magnitude of the HIV-1 epidemic in Nigeria is second only to the subtype C epidemic in South Africa, yet the subtypes prevalent in Nigeria require further characterization. A panel of 50 subtype G and 18 CRF02_AG Nigerian HIV-1 pseudoviruses (PSV) was developed and envelope coreceptor usage, neutralization sensitivity and cross-clade reactivity were characterized. These PSV were neutralized by some antibodies targeting major neutralizing determinants, but potentially important differences were observed in specific sensitivities (eg. to sCD4, MPER and V2/V3 monoclonal antibodies), as well as in properties such as variable loop lengths, number of potential N-linked glycans and charge, demonstrating distinct antigenic characteristics of CRF02_AG and subtype G. There was preferential neutralization of the matched CRF/subtype when PSV from subtype G or CRF02_AG were tested using pooled plasma. These novel Nigerian PSV will be useful to study HIV-1 CRF- or subtype-specific humoral immune responses for subtype G and CRF02_AG.

Acoustic Effects of Uneven Polymeric Layers on Tunable SAW Oscillators

Surface acoustic wave (SAW) sensors in tunable oscillator configuration, with a deposited polymeric layer, were used to investigate the layer’s impact on the oscillator’s resonant frequency. The SAW oscillators were tuned by means of variable loop amplification. Full-range amplification variation led to a resonant frequency increase of ~1.7 MHz due to the layer’s nonlinear reaction. The layer’s morphology and location resulted in a specific resonant frequency–amplitude dependence. Five types of layers were used to test the causal linkage between the layers’ morphological parameters or positioning and the SAW oscillator’s resonant frequency. The frequency variation trend is almost linear, with a complex minute variation. Small amplitude sigmoids occur at certain attenuation values, due to layer acoustic resonances. Multiple sigmoids were linked with layer resonances of different orders. A good correlation between the layer’s thickness and resonance position was found.

Abstract 5697: MILIP drives triple-negative breast cancer through complexing with transfer RNAs to promote protein production

Abstract Despite the progress in endocrine therapy, targeted therapy and immunotherapy, the treatment of triple-negative breast cancer (TNBC), one of the most aggressive types of breast cancer, is challenging. This is closely associated with the lack of effective molecular targets in TNBC cells for therapeutic intervention. Here we report that the long noncoding RNA (lncRNA) MILIP drives TNBC cell survival, proliferation and tumorigenicity through complexing with transfer RNAs (tRNAs) to promote protein production, and thus represents a potential therapeutic target in TNBC. MILIP was expressed at high levels in TNBC cells that commonly harbor loss-of-function mutations of the tumor suppressor p53, yet MILIP silencing diminished TNBC cell viability and retarded TNBC xenograft growth, indicating that MILIP functions distinctively in TNBC beyond its well-established role in repressing p53 in other types of cancers. Mechanistical investigations revealed that MILIP interacted with eukaryotic translation elongation factor 1 alpha 1 (eEF1α1) and formed an RNA-RNA duplex with tRNALeu and tRNASer, type II tRNAs, through their variable loops, thus facilitating the binding of eEF1α1 to these tRNAs. Disrupting the interaction between MILIP and eEF1α1 or tRNAs diminished protein production and cell viability, with therapeutic potential revealed where targeting MILIP using Gapmers inhibited TNBC growth and cooperated with the clinically available protein synthesis inhibitor omacetaxine mepesuccinate in vivo. Collectively, these results identified MILIP as an RNA translation elongation factor to promote protein production in TNBC cells and demonstrated that experimental therapy with MILIP Gapmers inhibits TNBC growth, indicating MILIP targeting is a potential avenue for developing improved TNBC treatment through blocking protein synthesis. Citation Format: Yuchen Feng, Simin Zheng, Xiaohong Zhao, Yuanyuan Zhang, Ran Xu, Liang Xu, Thomas Preiss, Lei Jin, Jinnan Gao, Xu Dong Zhang. MILIP drives triple-negative breast cancer through complexing with transfer RNAs to promote protein production [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5697.

Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT3.

Mycobacterium tuberculosistransfer RNA (tRNA) terminal nucleotidyltransferase toxin, MenT3, incorporates nucleotides at the 3'-CCA end of tRNAs, blocking their aminoacylation and inhibiting protein synthesis. Here, we show that MenT3 most effectively adds CMPs to the 3'-CCA end of tRNA. The crystal structure of MenT3 in complex with CTP reveals a CTP-specific nucleotide-binding pocket. The 4-NH2 and the N3 and O2 atoms of cytosine in CTP form hydrogen bonds with the main-chain carbonyl oxygen of P120 and the side chain of R238, respectively. MenT3 expression in Escherichiacoli selectively reduces the levels of seryl-tRNASers, indicating specific inactivation of tRNASers by MenT3. Consistently, MenT3 incorporates CMPs into tRNASer most efficiently, among the tested E. coli tRNA species. The longer variable loop unique to class II tRNASers is crucial for efficient CMP incorporation into tRNASer by MenT3. Replacing the variable loop of E. coli tRNAAla with the longer variable loop of M.tuberculosis tRNASer enables MenT3 to incorporate CMPs into the chimeric tRNAAla. The N-terminal positively charged region of MenT3 is required for CMP incorporation into tRNASer. A docking model of tRNA onto MenT3 suggests that an interaction between the N-terminal region and the longer variable loop of tRNASer facilitates tRNA substrate selection.

Magic-angle spinning NMR structure of Opa60 in lipid bilayers

Here we report the structure of Opa60 in lipid bilayers using proton-detected magic-angle spinning nuclear magnetic resonance (MAS NMR). Preparations including near-native oligosaccharide lipids reveal a consistent picture of a stable transmembrane beta barrel with a minor increase in the structured region as compared with the previously reported detergent structure. The large variable loops known to interact with host proteins could not be detected, confirming their dynamic nature even in a lipid bilayer environment. The structure provides a starting point for investigation of the functional role of Opa60 in gonococcal infection, which is understood to involve interaction with host proteins. At the same time, it demonstrates the recent advances in proton-detected methodology for membrane protein structure determination at atomic resolution by MAS NMR.

Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape

Immunotherapy, including immune checkpoint inhibitors and adoptive cell transfer, has obtained great progress, but their efficiencies vary among patients due to the genetic and epigenetic differences. Human MEX3B (hMEX3B) protein is an RNA-binding protein that contains two KH domains at the N-terminus and a RING domain at its C-terminus, which has the activity of E3 ubiquitin ligase and is essential for RNA degradation. Current evidence suggests that hMEX3B is involved in many important biological processes, including tumor immune evasion and HLA-A regulation, but the sequence of substrate RNA recognized by hMEX3B and the functional molecular mechanisms are unclear. Here, we first screened the optimized hMEX3B binding sequence on the HLA-A mRNA and reported that the two tandem KH domains can bind with their substrate one hundred times more than the individual KH domains. We systematically investigated the binding characteristics between the two KH domains and their RNA substrates by nuclear magnetic resonance (NMR). Based on this information and the small-angle X-ray scattering (SAXS) data, we used molecular dynamics simulations to obtain structural models of KH domains in complex with their corresponding RNAs. By analyzing the models, we noticed that on the KH domains’ variable loops, there were two pairs of threonines and arginines that can disrupt the recognition of the RNA completely, and this influence had also been verified both in vitro and in vivo. Finally, we presented a functional model of the hMEX3B protein, which indicated that hMEX3B regulated the degradation of its substrate mRNAs in many biological processes. Taken together, our research illustrated how the hMEX3B protein played a key role in translation inhibition during the immune response to tumor cells and provided an idea and a lead for the study of the molecular mechanism and function of other MEX3 family proteins.

Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2

SARS-CoV-2 can infect human cells through the recognition of the human angiotensin-converting enzyme 2 receptor. This affinity is given by six amino acid residues located in the variable loop of the receptor binding domain (RBD) within the Spike protein. Genetic recombination involving bat and pangolin Sarbecoviruses, and natural selection have been proposed as possible explanations for the acquisition of the variable loop and these amino acid residues. In this study we employed Bayesian phylogenetics to jointly reconstruct the phylogeny of the RBD among human, bat and pangolin Sarbecoviruses and detect recombination events affecting this region of the genome. A recombination event involving RaTG13, the closest relative of SARS-CoV-2 that lacks five of the six residues, and an unsampled Sarbecovirus lineage was detected. This result suggests that the variable loop of the RBD didn’t have a recombinant origin and the key amino acid residues were likely present in the common ancestor of SARS-CoV-2 and RaTG13, with the latter losing five of them probably as the result of recombination.

Towards a structural and functional analysis of the immunoglobulin-fold proteome.

The immunoglobulinfold (Igfold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Igfold proteome. The central role of this Igfold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Igfold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Igfold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Igfold proteome. This overview also highlights how this Igfold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.

Characterization and biodistribution of under-employed gene therapy vector AAV7.

The use of adeno-associated viruses (AAVs) as gene delivery vectors has vast potential for the treatment of many severe human diseases. Over one hundred naturally existing AAV capsid variants have been described and classified into phylogenetic clades based on their sequences. AAV8, AAV9, AAVrh.10, and other intensively studied capsids have been propelled into pre-clinical and clinical use, and more recently, marketed products; however, less-studied capsids may also have desirable properties (e.g., potency differences, tissue tropism, reduced immunogenicity, etc.) that have yet to be thoroughly described. These data will help build a broader structure-function knowledge base in the field, present capsid engineering opportunities, and enable the use of novel capsids with unique properties.

Abstract 17158: Effects of Human Monoclonal Antibodies on ADAMTS13 in Immune Thrombotic Thrombocytopenic Purpura

Introduction: Immune thrombotic thrombocytopenic purpura (iTTP) is caused by antibody-mediated deficiency of the metalloprotease ADAMTS13, which cleaves VWF. Myocardial infarction and ischemic strokes are common and often fatal sequelae of iTTP. Inhibitory anti-ADAMTS13 antibodies appear to affect catalytic turnover more than apparent substrate binding affinity (PMID 37023370). Exploring how antibodies affect VWF cleavage by ADAMTS13 in physiologic conditions is needed to better understand the pathophysiology of iTTP. Hypothesis: Anti-ADAMTS13 antibodies may influence ADAMTS13 function by affecting catalytic turnover and/or apparent substrate binding affinity differently in physiologic conditions than in standard assay conditions. Aims: Characterize how single chain fragments of the variable loop (scFv’s) previously identified from a phage display library derived from several iTTP patients’ antibodies affect ADAMTS13-mediated VWF cleavage in conditions that more closely represent plasma and see if/how they differ from scFv-mediated effects in standard conditions. Methods: ADAMTS13 in normal human plasma was titrated with increasing concentrations of the substrate FRETS-VWF73 to derive maximum velocity ( V max ) and apparent Michaelis constant ( K M,app ) in standard assay conditions (pH 6.0) and conditions closer to physiologic (pH 7.0). The same parameters were derived in the presence of saturating concentrations of scFv’s. Results: Compared to VWF cleavage by ADAMTS13 in the absence of scFv, the inhibitory scFv4-20 decreased V max at both pH 6.0 and pH 7.0; K M,app decreased at pH 6.0 and increased at pH 7.0. The stimulatory scFv3-3 and scFv4-41 increased V max at each pH, while K M,app in the presence of each scFv decreased only at pH 7.0. Conclusions: Anti-ADAMTS13 antibody-mediated effects on VWF cleavage differ when comparing standard and more physiologic pH conditions, guiding future investigative directions into iTTP pathophysiology.