Biology subjects

Martemyanov, K.

Publications and source records attributed to Martemyanov, K..

6 recordsLinked to original sources

bioRxiv2026

Auto-SMART: a web-based platform for repair-template design for CRISPR/Cas9 homology-directed editing

Genome engineering via CRISPR/Cas9 has been widely applied in biological research and developing gene therapies. However, genome editing flexibility is strongly constrained by the position and quality of guide RNAs relative to the intended edit: desired edit sites are frequently positioned far from efficient protospacer adjacent motifs (PAM). SMART (Silently Mutate And Repair Template) technique relaxes this constraint by silently mutating the gap between the Cas9 cut and the edit in the repair donor, preserving the encoded protein while expanding the usable guide-RNA design space. Designing such donors manually requires coordinated reasoning over transcript structure, reading frame, candidate protospacers, codon usage, homology arms and the expected edited allele. Auto-SMART is a web platform that automates this process for CRISPR/Cas9-mediated insertion, deletion, point mutation and sequence replacement in coding exons and in introns. Users choose a genome assembly, search a gene symbol or transcript, select a modification site and select an editing operation. Auto-SMART finds nearby Streptococcus pyogenes Cas9 (SpCas9) guides, ranks them by predicted on-target activity and cut-to-edit geometry, builds repair templates with synonymous substitutions, automatically recodes residual on-target sites to prevent re-cutting and renders interpretable panels for the target locus, donor template and locus after HDR, together with a downloadable report and a Primer3 genotyping handoff. The web application for Auto-SMART is freely available at https://auto-smart.chuanping.org/.

genetics↗

bioRxiv2026

Optoretinography in R9AP-bradyopsia reveals the essential role of G-protein signaling in the human cone elongation response

Human cone and rod outer segments exhibit a rapid shrinkage followed by a slower elongation in response to light, forming the basis of the optoretinogram. The molecular basis of this optical assay of photoreceptor function remains incompletely understood. In mouse rods, the elongation response requires transducin, the G-protein -subunit activated in the initial amplifying step of the phototransduction cascade. Here, we measured human cone outer segment responses in subjects with bradyopsia arising from a triple-deletion mutation in R9AP, the anchor and transport protein for the GTPase-activating protein (GAP) RGS9. Immunoprecipitation showed that the mutant R9AP has greatly reduced affinity for RGS9, predictably reducing the level of RGS9 in the outer segment. The bradyopsia subjects elongation responses had normal activation kinetics, amplitude and photosensitivity, but markedly slowed recovery. These results indicate that normal levels of RGS9 are required for deactivation of the cone elongation response, situating the underlying molecular mechanism within the G-protein cascade at or prior to formation of the GAP complex. The recovery of the cone elongation response, measured in a paired-flash paradigm for stimuli isomerizing up to 75% of opsin, revealed that elongation requires a substrate that is depleted and recovers in a bleach-dependent manner. In particular, recovery from the highest bleaching exposure (75%) tracked the time course of cone opsin regeneration, implying that unregenerated cone opsin produces "dark light", known in rods to arise from constitutive activation of G-protein. Taken together, the results from controls and bradyopsia identify the inactive (GDP-bound) transducin complex as the essential substrate for the human cone elongation response. Suppression of the elongation response in the paired-flash paradigm further revealed the complete profile of the initial fast cone outer segment shrinkage response and reinforced its origin in opsin structural changes. Overall, these results identify key mechanistic elements of the optoretinogram and enable its use as a molecularly interpretable, non- invasive assay of cone function in disease and therapeutic response.

neuroscience↗

bioRxiv2026

Unique pore architecture underlies constitutive gating of human retinalTRPM1

Transient receptor potential melastatin 1 (TRPM1), a Ca{superscript 2}-permeable nonselective cation channel essential for retinal ON bipolar cell signaling and night vision, and implicated in congenital night blindness, has remained structurally and functionally poorly characterized. Here we report the first cryo-electron microscopy structure of human TRPM1 in conducting state. Although the channel assembles as a tetramer, it adopts an unexpected clockwise domain-swapped pore module with rotational geometry inverse to that observed in previously characterized 6-TM tetrameric channels. This inverted topology is accompanied by extensive remodeling of the S5-P-S6 module, dilation of the selectivity filter, expansion of the central cavity, and splaying of S6 to form a wide intracellular gate. Single-channel recordings reveal constitutive activity consistent with the conductive state captured. Together, these findings uncover a new 6-TM fold in tetrameric channel and provide a framework for understanding TRPM1 gating and disease-associated dysfunction.

biochemistry↗

bioRxiv2024

DeFrND: detergent-free reconstitution into native nanodiscs with designer membrane scaffold peptides

Membrane scaffold proteins-based nanodiscs (NDs) have facilitated unprecedented structural and biophysical analysis of membrane proteins in a near-native lipid environment. However, successful reconstitution of membrane proteins in NDs requires prior solubilization and purification in detergents, which may impact their physiological structure and function. Furthermore, the detergent-mediated reconstitution of NDs is unlikely to recapitulate the precise composition or asymmetry of native membranes. To circumvent this fundamental limitation of traditional ND technology, we herein describe the development of membrane-solubilizing peptides to directly extract membrane proteins from native cell membranes into nanoscale discoids. By systematically protein engineering and screening, we created a new class of chemically modified Apolipoprotein-A1 mimetic peptides to enable the formation of detergent-free NDs (DeFrNDs) with high efficiency. NDs generated with these engineered membrane scaffold peptides are suitable for obtaining high-resolution structures using single-particle cryo-EM with native lipids. To further highlight the versatility of DeFrNDs, we directly extract a sampling of membrane signaling proteins with their surrounding native membranes for biochemical and biophysical interrogations.

biophysics↗

bioRxiv2023

Fine-tuning GPCR-mediated neuromodulation by biasing signaling through different G-protein subunits

GPCRs mediate neuromodulation through activation of heterotrimeric G-proteins (G{beta}{gamma}). Classical models depict that G-protein activation leads to a one-to-one formation of G-GTP and G{beta}{gamma} species. Each of these species propagates signaling by independently acting on effectors, but the mechanisms by which response fidelity is ensured by coordinating G and G{beta}{gamma} responses remain unknown. Here, we reveal a paradigm of G-protein regulation whereby the neuronal protein GINIP biases inhibitory GPCR responses to favor G{beta}{gamma} over G signaling. Tight binding of GINIP to Gi-GTP precludes its association with effectors (adenylyl cyclase) and, simultaneously, with Regulator-of-G-protein-Signaling (RGS) proteins that accelerate deactivation. As a consequence, Gi-GTP signaling is dampened whereas G{beta}{gamma} signaling is enhanced. We show that this mechanism is essential to prevent imbalances of neurotransmission that underlie increased seizure susceptibility in vivo. Our findings reveal an additional layer of regulation within a quintessential mechanism of signal transduction that sets the tone of neurotransmission.

biochemistry↗

bioRxiv2020

Retinal circuits driving a non-image forming visual behavior

Outer retinal circuits that drive non-image forming vision in mammals are unknown. Rods and cones signal light increments and decrements to the brain through the ON and OFF pathways, respectively. Although their contribution to image-forming vision is known, the contributions of the ON and OFF pathway to the pupillary light response (PLR), a non-image forming behavior, are unexplored. Here we use genetically modified mouse lines, to comprehensively define the outer retinal circuits driving the PLR. The OFF pathway, which mirrors the ON pathway in image-forming vision, plays no role in the PLR. We found that rods use the primary rod pathway to drive the PLR at scotopic light levels. At photopic light levels, the primary and secondary rod pathways drive normal PLR. Importantly, we find that cones are unable to compensate for rods. Thus, retinal circuit dynamics allow rods to drive the PLR across a wide range of light intensities.

neuroscience↗