Biology subjects

Goldman, Y.

Publications and source records attributed to Goldman, Y..

3 recordsLinked to original sources

bioRxiv2025

Suppression of nonsense mutations by small, cyclic peptides

Premature termination codons in mRNAs result from nonsense mutations and hinder the translation of full-length, functional proteins. Nonsense mutations cause numerous serious genetic diseases, including cystic fibrosis and Duchenne muscular dystrophy. Several small-molecule drugs have been reported that could potentially ameliorate these diseases by promoting translational readthrough at the premature termination codon. However, utilization of many of these molecules faces problems such as limited efficacy or high cellular toxicity. Using a selection strategy in Saccharomyces cerevisiae coupling suppression of endogenous nonsense mutations to cell survival, we identified ten readthrough-promoting cyclic peptides from a DNA-encoded library. The selected cyclic peptides suppress nonsense mutations in various reporter genes, and the candidates inducing the highest readthrough levels display no observable cytotoxicity in yeast. Mutational analysis of the most promising cyclic peptide demonstrate that most amino acid side chains contribute to the readthrough-stimulating activity. Importantly, this cyclic peptide appears to bind directly to the eukaryotic core translation machinery and promotes readthrough in vitro by interfering with ribosomal decoding. Our results suggest that small, cyclic peptides selected in vivo could represent a novel drug type to treat the many incurable human genetic diseases that are caused by nonsense mutations.

molecular biology↗

bioRxiv2019

Processivity and Velocity for Motors Stepping on Periodic Tracks

Processive molecular motors enable cargo transportation by assembling into dimers capable of taking several consecutive steps along a cytoskeletal filament. In the well-accepted hand-over-hand stepping mechanism the trailing motor detaches from the track and binds the filament again in leading position. This requires fuel consumption in the form of ATP hydrolysis, and coordination of the catalytic cycles between the leading and the trailing heads. However, alternative stepping mechanisms exist, including inchworm-like movements, backward steps, and foot stomps. Whether all of these pathways are coupled to ATP hydrolysis remains to be determined. Here, in order to establish the principles governing the dynamics of processive movement, we present a theoretical framework which includes all of the alternative stepping mechanisms. Our theory bridges the gap between the elemental rates describing the biochemical and structural transitions in each head, and the experimentally measurable quantities, such as velocity, processivity, and probability of backward stepping. Our results, obtained under the assumption that the track is periodic and infinite, provide expressions which hold regardless of the topology of the network connecting the intermediate states, and are therefore capable of describing the function of any molecular motor. We apply the theory to myosin VI, a motor that takes frequent backward steps, and moves forward with a combination of hand-over-hand and inchworm-like steps. Our model reproduces quantitatively various observables of myosin VI motility measured experimentally from two groups. The theory is used to predict the gating mechanism, the pathway for backward stepping, and the energy consumption as a function of ATP concentration.\n\nSignificance StatementMolecular motors harness the energy released by ATP hydrolysis to transport cargo along cytoskeletal filaments. The two identical heads in the motor step alternatively on the polar track by communicating with each other. Our goal is to elucidate how the coordination between the two heads emerges from the catalytic cycles. To do so, we created a theoretical framework that allows us to relate the measurable features of motility, such as motor velocity, with the biochemical rates in the leading and trailing heads, thereby connecting biochemical activity and motility. We illustrate the efficacy of the theory by analyzing experimental data for myosin VI, which takes frequent backward steps, and moves forward by a hand-over-hand and inchworm-like steps.

biophysics↗

bioRxiv2018

A new in vitro assay measuring direct interaction of nonsense suppressors with the eukaryotic protein synthesis machinery

Nonsense suppressors (NonSups) induce \"readthrough\", i.e., the selection of near cognate tRNAs at premature termination codons and insertion of the corresponding amino acid into nascent polypeptide. Prior readthrough measurements utilized contexts in which NonSups can promote readthrough directly, by binding to one or more of the components of the protein synthesis machinery, or indirectly, by several other mechanisms. Here we utilize a new, highly-purified in vitro assay to measure exclusively direct nonsense suppressor-induced readthrough. Of 16 NonSups tested, 12 display direct readthrough, with results suggesting that such NonSups act by at least two different mechanisms. In preliminary work we demonstrate the potential of single molecule fluorescence energy transfer measurements to elucidate mechanisms of NonSup-induced direct readthrough, which will aid efforts to identify NonSups having improved clinical efficacy.\n\nTable of Contents artwork\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC=\"FIGDIR/small/330506_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@a548dborg.highwire.dtl.DTLVardef@15237bcorg.highwire.dtl.DTLVardef@c93d3forg.highwire.dtl.DTLVardef@1d40e2c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗