Biology subjects

Goldman, Y. E.

Publications and source records attributed to Goldman, Y. E..

13 recordsLinked to original sources

bioRxiv2026

Biased stochastic motor dynamics drive bidirectional, processive translocation by the AAA+ disaggregase Hsp104.

Protein aggregation disrupts proteostasis and drives neurodegeneration. Hsp104 is a hexameric, ring-shaped AAA+ ATPase that dissolves protein aggregates, yet how hexamers translocate and extract polypeptides trapped in mechanically resistant aggregates remains unclear. Using substrates that recapitulate the physical constraints of aggregates, we establish that Hsp104 is a processive, bidirectional translocase that can dynamically switch direction while threading a single polypeptide. On mechanically restrained substrates and prions, Hsp104 hexamers execute biased stochastic transitions among three conformational states at individual interprotomer interfaces: closed, extended, and a previously unobserved hyperextended form. These transitions follow kinetically favored paths rather than a rigid rotary sequence. The resulting biased stochastic stepping, enabled by the conformational plasticity of Hsp104 hexamers, underpins operational adaptability and redefines the functional logic of AAA+ motors.

biochemistry↗

bioRxiv2026

Nanometer-scale RNA protein clusters (RPCs) Foster Helicase Activity of DEAD-box eIF4A

DEAD-box RNA helicases are central regulators of RNA metabolism, employing ATP-dependent mechanisms to remodel RNA structure and RNA-protein interactions, yet how helicase catalysis is coordinated with multi-subunit interactions between RNA and protein remains unresolved. Translation initiation helicase, eukaryotic initiation factor 4A (eIF4A), which acts as an intrinsically non-processive enzyme, is essential for unwinding structured mRNAs, relies on cofactors to achieve physiological activity. Here we uncover an unexpected RNA-helicase state of eIF4A, demonstrating that eIF4A forms nanometer-scale RNA-protein clusters (RPCs) of [~]2-5 MDa in presence of its physiological cofactors eIF4B and eIF4G, RNA and ATP under near-physiological concentrations. Using a single molecule approach, we directly resolve the formation of discrete clusters that recruit multiple copies of proteins with RNA upon ATP addition and show that RPC formation correlates with helicase activity in vitro. Further, we find eIF4B as a key determinant of this multi-subunit assembly. Its intrinsically disordered regions (IDRs) together with structured RNA-recognition motifs (RRMs) drive multivalent RNA-dependent clustering, critical for efficient helicase activity. Disrupting eIF4B-RNA interactions through a targeted point mutation (F139A) in the RRM reduces both the cluster size and the helicase activity, further establishing a functional link between cluster formation and catalytic activity. Consistent with these findings, in-cell diffusion measurements reveal markedly slower diffusion of wild-type eIF4B compared with the RNA-binding-deficient mutant, indicative of RPC formation within the cellular environment. Together, our results reveal regulated helicase clustering as a previously unrecognized characteristic of the translation initiation machinery, linking ATP-dependent DEAD-box helicase activity to nanometer-scale RNA-protein clusters and translation initiation regulation.

biophysics↗

bioRxiv2025

A myosin hypertrophic cardiomyopathy mutation disrupts the super-relaxed state and boosts contractility by enhanced actin attachment

Hypertrophic cardiomyopathy (HCM) is a leading cause of cardiac failure among individuals under 35. Many genetic mutations that cause HCM enhance ventricular systolic function, suggesting that these HCM mutations are hypercontractile. Among the most common causes of HCM are mutations in the gene MYH7, which encodes for {beta}-cardiac myosin, the principal human ventricular myosin. Previous work has demonstrated that, for purified myosins, some MYH7 mutations are gain-of-function while others cause reduced function, so how they lead to enhanced contractility is not clear. Here, we have characterized the mechanics and kinetics of the severe HCM-causing mutation M493I. Motility assays demonstrate a 70% reduction of actin filament gliding velocities on M493I-coated surfaces relative to WT. This mutation slows ADP release from actomyosin{middle dot}ADP 5-fold without affecting phosphate release or ATP binding. Yet it enhances steady-state ATPase Vmax 2-fold. Through single-molecule mechanical studies, we find that M493I myosin has a normal working stroke of 5 nm but a significantly prolonged actin attachment duration. Under isometric feedback, M493I myosins produce high, sustained force, with an actin detachment rate that is less sensitive to force than that of WT myosin. We also report direct measurement of the equilibrium state of the super-relaxed to disordered relaxed (SRX-DRX) regulatory transition and show its disruption in M493I, with a concomitant enhancement to actin attachment kinetics. Together, these data demonstrate that enhanced myosin binding from inhibition of myosins off state, combined with slow ADP release and enhanced force production, underlie the enhanced function and etiology of this HCM mutation. Significance StatementHypertrophic cardiomyopathy (HCM) is a leading genetic cause of sudden cardiac death in young individuals. Although often described as a hypercontractile disease, the molecular basis for this remains unclear, especially for mutations with inhibitory effects in various in vitro assays. We show that the severe HCM mutation M493I in {beta}-cardiac myosin slows ADP release yet enhances force output and actin attachment through multiple mechanisms, including disrupted autoinhibition via the super-relaxed state. Our findings unify seemingly contradictory biophysical changes into a coherent mechanistic model and support the hypothesis that increased myosin head availability, rather than enhanced individual kinetics alone, underlies HCM hypercontractility.

biophysics↗

bioRxiv2025

S2Tag, a novel affinity tag for the capture and immobilization of coiled-coil proteins: application to the study of human β-cardiac myosin

Single molecule and ensemble motility assays are powerful tools for investigating myosin activity. A key requirement for the quality and reproducibility of the data obtained with these methods is the mode of attachment of myosin to assay surfaces. We previously characterized the ability of a monoclonal antibody (10F12.3) to tether skeletal muscle myosin to nitrocellulose coated glass. Here, we identify the 11 amino-acid epitope (S2Tag) recognized by 10F12.3 in the coiled-coil S2 domain of myosin. To test the transferability of S2Tag, we inserted it into a wild-type {beta}-cardiac myosin construct (WT-{beta}CM) and evaluated its mechanochemistry. WT-{beta}CM immobilized via S2Tag robustly propelled actin filaments in gliding assays and showed single-molecule actin displacements and attachment kinetics by optical trapping. Thus, the antibody attachment is effective for ensemble and single molecule assays. We inserted the S2Tag into a {beta}CM construct containing a penetrant mutation (S532P-{beta}CM) that causes dilated cardiomyopathy. Inclusion of S2Tag enabled quantitative mixed-motor gliding filament assays with WT-{beta}CM. The analysis shows the S532P mutation results in a 60% decrease in gliding speed, yet the motor seems to produce the same force as WT-{beta}CM. Importantly, S2Tag is a useful new tool for affinity capture of alpha-helical coiled coil proteins.

biophysics↗

bioRxiv2024

Dynamics of β-cardiac myosin between the super-relaxed and disordered-relaxed states

The super-relaxed (SRX) state of myosin ATPase activity is critical for striated muscle function, and its dysregulation is linked to cardiomyopathies. It is unclear whether the SRX state exchanges readily with the disordered-relaxed (DRX) state, and whether the SRX state directly corresponds to the folded back interacting-head motif (IHM). Using recombinant {beta}-cardiac heavy meromyosin (HMM) and subfragment 1 (S1), which cannot form the IHM, we show that the SRX and DRX populations are in rapid equilibrium, dependent on myosin head-tail interactions. Some mutations which cause hypertrophic (HCM) or dilated (DCM) cardiomyopathies alter the SRX-DRX equilibrium, but not all mutations. The cardiac myosin inhibitor mavacamten slows nucleotide release by an equal factor for both HMM and S1, thus only indirectly influencing the occupancy time of the SRX state. These findings suggest that purified myosins undergo rapid switching between SRX and DRX states, refining our understanding of cardiomyopathy mechanisms.

biochemistry↗

bioRxiv2024

Mechanism-based approach in designing patient-specific combination therapies for nonsense mutation diseases

Premature termination codon (PTC) diseases, arising as a consequence of nonsense mutations in a patients DNA, account for approximately 12% of all human disease mutations. Currently there are no FDA approved treatments for increasing PTC readthrough in nonsense mutation diseases, although one translational readthrough inducing drug, ataluren, has had conditional approval for treatment of Duchenne muscular dystrophy in Europe and elsewhere for 10 years. Ataluren displays consistent low toxicity in clinical trials for treatment of several different PTC diseases, but its therapeutic effects on such diseases are inconsistent. The identity of the stop codon and its sequence context are major determinants of PTC readthrough efficiency in both the absence and presence of nonsense suppressors. Previously we have shown that ataluren stimulates readthrough exclusively by competitively inhibiting release factor complex (RFC, eRF1.eRF3.GTP)-dependent catalysis of translation termination. Here, using an in vitro reconstituted system (PURE-LITE) and both ensemble and single molecule assays, we demonstrate that PTC identity and the immediately adjacent mRNA sequence contexts modulate the catalytic activity of RFC in terminating peptide elongation. Such modulation largely determines the effectiveness of ataluren in stimulating readthrough, whether added alone or in combination with either the aminoglycoside G418 or an anticodon edited aa-tRNA, each of which stimulate readthrough by mechanisms orthogonal to that of ataluren. Our results provide an attractive rationale for the variability of ataluren effectiveness in stimulating readthrough in clinical trials. Patients harboring a PTC mutation with a sequence context promoting strong interaction with RFC are predicted to be resistant to ataluren, whereas ataluren treatment should be more effective for patient sequences conferring weaker interaction with RFC.

biochemistry↗

bioRxiv2024

Single-Molecule Studies of Cognate and Near-Cognate Elongation in an in vitro Eukaryotic Translation System

The ribosome plays a central role in translation of the genetic code into amino acid sequences during synthesis of polypeptides. During each cycle of peptide elongation, the ribosome must discriminate between correct and incorrect aminoacyl-tRNAs according to the codon present in its A-site. Ribosomes rely on a complex sequence of proofreading mechanisms to minimize erroneous selection of incorrect aminoacyl-tRNAs that would lead to mistakes in translation. These mechanisms have been studied extensively in prokaryotic organisms, but eukaryotic elongation is less well understood. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) with an in vitro eukaryotic translation system to investigate tRNA selection and subsequent steps during peptide elongation. We compared accommodation of a tryptophan-aminoacyl-tRNA into the ribosomal A-site containing either a cognate or near-cognate codon and unexpectedly found that, following an initial slow sampling event, subsequent near-cognate sampling events proceeded more rapidly than the initial event. Further, we found a strong negative correlation between the concentration of near-cognate aminoacyl-tRNA and the efficiency of tRNA accommodation. These novel characteristics of near-cognate interaction with the eukaryotic ribosome suggest that rejection of a near-cognate tRNAs leads to formation of an altered ribosomal conformation that assists in rejecting subsequent incorrect tRNA interactions.

biophysics↗

bioRxiv2023

DDX3X and DDX3Y constitutively form nano-sized RNA-protein clusters that foster enzymatic activity

DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous RNA helicases, DDX3X and DDX3Y, form nano-sized RNA-protein clusters (RPCs) that foster their catalytic activities in vitro and in cells. The IDRs are critical for the formation of these RPCs. A thorough analysis of the catalytic cycle of DDX3X and DDX3Y by ensemble biochemistry and single molecule photon bursts in the confocal microscope showed that RNA release is a major step that differentiates the unwinding activities of DDX3X and DDX3Y. Our findings provide new insights that the nano-sized helicase RPCs may be the normal state of these helicases under non-stressed conditions that promote their RNA unwinding and act as nucleation points for liquid-liquid phase separation under stress. This mechanism may apply broadly among other members of the DEAD-box helicase family.

biophysics↗

bioRxiv2020

Human hypertrophic cardiomyopathy mutation R712L suppresses the working stroke of cardiac myosin and can be rescued by omecamtiv mecarbil

Hypertrophic cardiomyopathies (HCMs) are the leading cause of acute cardiac failure in young individuals. Over 300 mutations throughout {beta}-cardiac myosin, including in the motor domain, are associated with HCM. A {beta}-cardiac myosin motor mutation (R712L) leads to a severe form of HCM. Actin-gliding motility of R712L-myosin is inhibited, despite near normal ATPase kinetics. By optical trapping, the working stroke of R712L-myosin was decreased 4-fold, but actin-attachment durations were normal. A prevalent hypothesis that HCM mutants are hypercontractile is thus not universal. R712 is adjacent to the binding site of the heart failure drug omecamtiv mecarbil (OM). OM suppresses the working stroke of normal {beta}-cardiac myosin, but remarkably, OM rescues the R712L-myosin working stroke. Using a flow chamber to interrogate a single molecule during buffer exchange, we found OM rescue to be reversible. Thus, the R712L mutation uncouples lever arm rotation from ATPase activity and this inhibition is rescued by OM.

biophysics↗

bioRxiv2019

Strain-Dependent Kinetic Properties of KIF3A and KIF3C Tune the Mechanochemistry of the KIF3AC Heterodimer

KIF3AC is a mammalian neuron-specific kinesin-2 implicated in intracellular cargo transport. It is a heterodimer of KIF3A and KIF3C motor polypeptides which have distinct biochemical and motile properties as engineered homodimers. Single-molecule motility assays show that KIF3AC moves processively along microtubules at a rate faster than expected given the motility rates of the KIF3AA and much slower KIF3CC homodimers. To resolve the stepping kinetics of KIF3A and KIF3C motors in homo-and heterodimeric constructs, and to determine their transport potential under mechanical load, we assayed motor activity using interferometric scattering (iSCAT) microscopy and optical trapping. The distribution of stepping durations of KIF3AC molecules is described by a rate (k1 = 11 s-1) without apparent kinetic asymmetry in stepping. Asymmetry was also not apparent under hindering or assisting mechanical loads of 1 pN in the optical trap. KIF3AC shows increased force sensitivity relative to KIF3AA, yet is more capable of stepping against mechanical load than KIF3CC. Microtubule gliding assays containing 1:1 mixtures of KIF3AA and KIF3CC result in speeds similar to KIF3AC, indicating the homodimers mechanically impact each others motility to reproduce the behavior of the heterodimer. We conclude that the stepping of KIF3C can be activated by KIF3A in a strain-dependent manner which is similar to application of an assisting load, and the behavior of KIF3C mirrors prior studies of kinesins with increased interhead compliance. These results suggest that KIF3AC-based cargo transport likely requires multiple motors, and its mechanochemical properties arise due to the strain-dependences of KIF3A and KIF3C.\n\nSignificance StatementKinesins are important long-range intracellular transporters in neurons required by the extended length of the axon and dendrites and selective cargo transport to each. The mammalian kinesin-2, KIF3AC, is a neuronal heterodimer of fast and slow motor polypeptides. Our results show that KIF3AC has a single observed stepping rate in the presence and absence of load and detaches from the microtubule rapidly under load. Interestingly, both KIF3A and assisting loads accelerate the kinetics of KIF3C. These results suggest that KIF3AC is an unconventional cargo transporter and its motile properties do not represent a combination of alternating fast and slow step kinetics. We demonstrate that the motile properties of KIF3AC represent a mechanochemistry that is specific to KIF3AC and may provide functional advantages in neurons.

biophysics↗

bioRxiv2019

Single molecule mechanics resolves the earliest events in force generation by cardiac myosin

Key steps of cardiac mechanochemistry, including the force-generating working stroke and the release of phosphate (Pi), occur rapidly after myosin-actin attachment. An ultra-high-speed optical trap enabled direct observation of the timing and amplitude of the working stroke, which can occur within <200 s of actin binding by {beta}-cardiac myosin. The initial actomyosin state can sustain loads of at least 4.5 pN and proceeds directly to the stroke or detaches before releasing ATP hydrolysis products. The rates of these processes depend on the force. The time between binding and stroke is unaffected by 10 mM Pi which, along with other findings, indicates the stroke precedes phosphate release. After Pi release, Pi can rebind enabling reversal of the working stroke. Detecting these rapid events under physiological loads provides definitive indication of the dynamics by which actomyosin converts biochemical energy into mechanical work.

biochemistry↗

bioRxiv2019

Nanoaperture fabrication via colloidal lithography for single molecule fluorescence imaging

In single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling fabrication of thousands of ZMWs in parallel without sophisticated equipment. Polystyrene 1 m dia. microbeads self-assemble on a glass slide into a hexagonal array, forming a mask for the deposition of metallic posts in the inter-bead interstices. The width of those interstices (and subsequent posts) is adjusted within 100-300 nm by partially fusing the beads at the polystyrene glass transition temperature. The beads are dissolved in toluene, aluminum or gold cladding is deposited around the posts, and those are dissolved, leaving behind an array ZMWs. Parameter optimization and the performance of the ZMWs are presented. By using colloidal self-assembly, typical laboratories can make use of sub-wavelength ZMW technology avoiding the availability and expense of sophisticated clean-room environments and equipment.

biophysics↗

bioRxiv2018

Positive Cardiac Inotrope, Omecamtiv Mecarbil, Activates Muscle Despite Suppressing the Myosin Working Stroke

Omecamtiv mecarbil (OM) is a positive cardiac inotrope in phase-3 clinical trials for treatment of heart failure. Although initially described as a direct myosin activator, subsequent studies are at odds with this description and do not explain OM-mediated increases in cardiac output. Single-molecule, biophysical experiments on cardiac myosin show that OM suppresses myosins working stroke and prolongs actomyosin attachment 5-fold, which explain inhibitory actions of the drug observed in vitro. Surprisingly, the increased myocardial force output in the presence of OM can be explained by cooperative thin filament activation by OM-inhibited myosin molecules. Selective suppression of myosin is an unanticipated route to muscle activation that may guide future development of therapeutic drugs.

biophysics↗