Mechanism of Cardiac Tropomyosin Transitions on Filamentous Actin As Revealed by All-Atom Steered Molecular Dynamics Simulations

Williams, Michael R.; Tardiff, Jil C.; Schwartz, Steven D.

doi:10.1021/acs.jpclett.8b00958

Cited by 12 publications

(13 citation statements)

References 25 publications

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“…MD simulation has become a method of choice to construct models for the purpose of studying the flexural and torsional flexibility of coiledcoil tropomyosin (11,20,23,27,(30)(31)(32). MD provides a dynamic threedimensional structural readout of the coiled coils not easily obtained experimentally.…”

Section: Tropomyosin Modelsmentioning

confidence: 99%

Precise Binding of Tropomyosin on Actin Involves Sequence-Dependent Variance in Coiled-Coil Twisting

Lehman

Kiani

et al. 2018

Biophysical Journal

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Often considered an archetypal dimeric coiled coil, tropomyosin nonetheless exhibits distinctive "noncanonical" core residues located at the hydrophobic interface between its component α-helices. Notably, a charged aspartate, D137, takes the place of nonpolar residues otherwise present. Much speculation has been offered to rationalize potential local coiled-coil instability stemming from D137 and its effect on regulatory transitions of tropomyosin over actin filaments. Although experimental approaches such as electron cryomicroscopy reconstruction are optimal for defining average tropomyosin positions on actin filaments, to date, these methods have not captured the dynamics of tropomyosin residues clustered around position 137 or elsewhere. In contrast, computational biochemistry, involving molecular dynamics simulation, is a compelling choice to extend the understanding of local and global tropomyosin behavior on actin filaments at high resolution. Here, we report on molecular dynamics simulation of actin-free and actin-associated tropomyosin, showing noncanonical residue D137 as a locus for tropomyosin twist variation, with marked effects on actin-tropomyosin interactions. We conclude that D137-sponsored coiled-coil twisting is likely to optimize electrostatic side-chain contacts between tropomyosin and actin on the assembled thin filament, while offsetting disparities between tropomyosin pseudorepeat and actin subunit periodicities. We find that D137 has only minor local effects on tropomyosin coiled-coil flexibility, (i.e., on its flexural mobility). Indeed, D137-associated overtwisting may actually augment tropomyosin stiffness on actin filaments. Accordingly, such twisting-induced stiffness of tropomyosin is expected to enhance cooperative regulatory translocation of the tropomyosin cable over actin.

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Section: Tropomyosin Modelsmentioning

confidence: 99%

Precise Binding of Tropomyosin on Actin Involves Sequence-Dependent Variance in Coiled-Coil Twisting

Lehman

Kiani

et al. 2018

Biophysical Journal

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“…In principle, computationally directed steered docking of tropomyosin onto the F-actin surface can offer clues into the actin-tropomyosin assembly process (26). However, the number of choices involved in steering conformationally variable tropomyosin onto an actin model, to say nothing of scoring respective pathways, seemingly is limitless.…”

Section: Introductionmentioning

confidence: 99%

The Effect of Tropomyosin Mutations on Actin-Tropomyosin Binding: In Search of Lost Time

Lehman

Moore

Campbell

et al. 2019

Biophysical Journal

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The initial binding of tropomyosin onto actin filaments and then its polymerization into continuous cables on the filament surface must be precisely tuned to overall thin-filament structure, function, and performance. Low-affinity interaction of tropomyosin with actin has to be sufficiently strong to localize the tropomyosin on actin, yet not so tight that regulatory movement on filaments is curtailed. Likewise, head-to-tail association of tropomyosin molecules must be favorable enough to promote tropomyosin cable formation but not so tenacious that polymerization precedes filament binding. Arguably, little molecular detail on early tropomyosin binding steps has been revealed since Wegner's seminal studies on filament assembly almost 40 years ago. Thus, interpretation of mutation-based actin-tropomyosin binding anomalies leading to cardiomyopathies cannot be described fully. In vitro, tropomyosin binding is masked by explosive tropomyosin polymerization once cable formation is initiated on actin filaments. In contrast, in silico analysis, characterizing molecular dynamics simulations of single wild-type and mutant tropomyosin molecules on F-actin, is not complicated by tropomyosin polymerization at all. In fact, molecular dynamics performed here demonstrates that a midpiece tropomyosin domain is essential for normal actin-tropomyosin interaction and that this interaction is strictly conserved in a number of tropomyosin mutant species. Elsewhere along these mutant molecules, twisting and bending corrupts the tropomyosin superhelices as they ''lose their grip'' on F-actin. We propose that residual interactions displayed by these mutant tropomyosin structures with actin mimic ones that occur in early stages of thin-filament generation, as if the mutants are recapitulating the assembly process but in reverse. We conclude therefore that an initial binding step in tropomyosin assembly onto actin involves interaction of the essential centrally located domain.

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“…This method is highly focused on the local structural environment and therefore is more accurate than the PolyPhen-2 algorithm. However, it cannot determine alterations to structure or function long distances from the mutational site, which have been shown to be significant (9,21,22). Homology modeling of pre-and post-powerstroke states of myosin was utilized in an attempt to find regions of disease-causing variants (44).This highly static approach was able to identify regions of variant clusters, however it is left unexplained how these variants will affect the protein function or other conformations of myosin.…”

Section: Discussionmentioning

confidence: 99%

“…We note that the function of the three-state model requires complex allosteric interactions between the multiple components that make up the thick and thin filaments, with the effect propagating over long distances (e.g., Ca 2+ binding; refs. 9 , 21 , 22 ). While each method has advantages, they all focus purely on local effects and are inherently static, neglecting fundamental protein dynamics and the importance of allostery.…”

Section: Discussionmentioning

confidence: 99%

“…The full atomistic model has previously been used as a mechanistic probe to simulate structural and dynamic changes induced by mutations that are not addressable by experiment. These studies have revealed that point mutations in the CTF can result in structural and dynamic changes propagated over hundreds of angstroms (4,9,(21)(22)(23). While elucidating the primary mechanisms underlying pathogenic remodeling is crucial , from the clinical standpoint, rigorous assignment of pathogenic potential to de novo variants or those where existing information is conflicting has emerged as a central challenge to the use of genetic information in the care of families with HCM (7).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Computational and biophysical determination of pathogenicity of variants of unknown significance in cardiac thin filament

Mason¹,

Lynn²,

Baldo³

et al. 2021

JCI Insight

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Point mutations within sarcomeric proteins have been associated with altered function and cardiomyopathy development. Difficulties remain, however, in establishing the pathogenic potential of individual mutations, often limiting the use of genotype in management of affected families. To directly address this challenge, we utilized our all-atom computational model of the human full cardiac thin filament (CTF) to predict how sequence substitutions in CTF proteins might affect structure and dynamics on an atomistic level.Utilizing molecular dynamics (MD) calculations, we simulated 21 well-defined genetic pathogenic cardiac troponin T and tropomyosin variants to establish a baseline of pathogenic changes induced in computational observables. Computational results were verified via differential scanning calorimetry on a subset of variants to develop an experimental correlation.Calculations were performed on 9 independent variants of unknown significance (VUS) and results were compared to pathogenic variants to identify high resolution pathogenic signatures.Results for VUS were compared to the baseline set to determine induced structural and dynamic changes and potential variant reclassifications were proposed. This unbiased, highresolution computational methodology can provide unique structural and dynamic information that can be incorporated into existing analyses to facilitate classification both for de novo variants and those where established approaches have provided conflicting information.

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Mechanism of Cardiac Tropomyosin Transitions on Filamentous Actin As Revealed by All-Atom Steered Molecular Dynamics Simulations

Cited by 12 publications

References 25 publications

Precise Binding of Tropomyosin on Actin Involves Sequence-Dependent Variance in Coiled-Coil Twisting

Precise Binding of Tropomyosin on Actin Involves Sequence-Dependent Variance in Coiled-Coil Twisting

The Effect of Tropomyosin Mutations on Actin-Tropomyosin Binding: In Search of Lost Time

Computational and biophysical determination of pathogenicity of variants of unknown significance in cardiac thin filament

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