Transport properties of rigid bent-rod macromolecules and of semiflexible broken rods in the rigid-body treatment. Analysis of the flexibility of myosin rod

Iniesta, A.; Díaz, Francisco Antonio González; Torre, José Garcı́a de la

doi:10.1016/s0006-3495(88)82956-4

Cited by 32 publications

(26 citation statements)

References 38 publications

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“…On the other hand, it is well known that this property is least sensitive to modeling and theoretical refinements. While the problem of the proper reference point was unclear, it was speculated that the rigid body treatment (Harvey et al 1983;Iniesta et al 1988) could be a good approximation. When Wegener (1985) finally solved rigorously that problem it turned out that the rigid-body results were indeed excellent.…”

Section: Translational Diffusionmentioning

confidence: 99%

“…Indeed, much experimental and theoretical effort has been devoted to detect the possible flexibility at the joint between the heads ($1 subfragments) and the rod, and, more importantly, at the region connecting the two subfragments ($2 and LMM) that make the myosin rod. While some works suggest that there may be a fairly large flexibility within the rod (Highsmith et al 1982;Cardinaud and Bernengo 1985;Iniesta et al 1988), others indicate that the rod is nearly rigid (Hvidt et al 1982(Hvidt et al , 1984Curry and Krause 1991). Even if the rod is somewhat flexible, it is not clear whether flexibility is localized at a hinge or distributed along the rod contour, as in a wormlike rod.…”

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

“…The differences arise from sample preparation and handling as well as from fitting of the observed decays (Cardinaud and Bernengo 1985;Hvidt et al 1984;Curry and Krause 1991). c) Two different theoretical treatment have been applied: the rigid-body procedure (Garcia de la Torte and Bloomfield 1980; Iniesta et al 1988), and the Harvey-Wegener formalism (Wegener 1982 b). As is emphasized in the present review, the different relaxation times resulting from the two approaches have different physical meanings and are valid in different situations.…”

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

“…In Table 3 we collect experimental values of these properties and the longest relaxation time, [t/]. Data are taken from previous compilations (Garcia de la Torre and Bloomfield 1981; Iniesta et al 1988), with the addition of some newer values (Hvidt et al 1984;Curry and Krause 1991). These values are compared with those calculated for assuming a rigid, straight rod, with various choices for the length.…”

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

“…Commonly accepted experimental values for the longest z 1 had been 26 gs for the myosin rod and 38 gs for whole myosin (see Iniesta et al 1988). These values are more or less (depending on length choices) smaller than the theoretical predictions for a straight, rigid rod, which had been interpreted in terms of some flexibility within the rod.…”

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

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Hydrodynamics of segmentally flexible macromolecules

1994

Eur Biophys J

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Segmentally flexible macromolecules are composed of a few rigid subunits linked by joints which are more or less flexible. The dynamics in solution of this type of macromolecule present special aspects that are reviewed here. Three alternative approaches are described. One is the rigid-body treatment, which is shown to be valid for overall dynamic properties such as translational diffusion and intrinsic viscosity. Another approach is the Harvey-Wegener treatment, which is particularly suited for rotational diffusion. The simplest version of this treatment, which ignores hydrodynamic interaction (HI) effects, is found to be quite accurate when compared to a more rigorous version including HI. A third approach is the Brownian dynamics simulation that, albeit at some computational cost, might describe rigorously cases of arbitrary complexity. This technique has been used to test the approximations in the rigid-body and Harvey-Wegener treatments, thus allowing a better understanding of their validity. Brownian trajectories of simplified models such as the trumbbell and the broken rod have been simulated. The comparison of the decay rates of some correlation functions with the predictions of the two treatments leads to a general conclusion: the Harvey-Wegener treatment determines the initial rate, while the long-time behavior is dominated by the rigid-body relaxation time. As an example of application to a specific biological macromolecule, we present a simulation of an immunoglobulin molecule, showing how Brownian Dynamics can be used to predict rotational and internal dynamics. Another typical example is myosin. Literature data of hydrodynamic properties of whole myosin and the myosin rod are compared with predictions from the Harvey-Wegener and rigid-body treatments. The present situation of the problem on myosin flexibility is analyzed, and some indications are given for future experimental and simulation work.

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Section: Translational Diffusionmentioning

confidence: 99%

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

Section: Myosin and Its Fragmentsmentioning

confidence: 99%

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Hydrodynamics of segmentally flexible macromolecules

1994

Eur Biophys J

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Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits

Torre

Carrasco

2002

Biopolymers

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Diffusion coefficients of segmentally flexible macromolecules with two subunits: A study of broken rods

et al. 1988

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SynopsisA general treatment for the solution dynamics of segmentally flexible macromolecules having two subunits is presented. Bead modeling allows for a complete inclusion of hydrodynamic interactions in this treatment. "he finite size of the beads is also considered, so that it is therefore possible to account properly for torsional motions of the subunits. Expressions for the components of the resistance matrix are derived. From them, the translational and rotational diffusion coefEcients can be calculated. Distinction is made between hinged macromolecules, whose only internal motion is bending, and swivel-jointed macromolecules, for which torsions of the subunits are also allowed. Numerical results are presented for broken rods with the two types of flexibility.The effects of hydrodynamic interaction between arms of broken rods are about 25% for translation and under 10% for rotation. These findings give support to the treatments of Harvey, Wegener, and co-workers in which interactions were neglected. The rotational dynamics of hinged and swivel-jointed rods are compared. Although there are differences in the short-time behavior, the longest relaxation time is the same for the two cases. Finally, the validity of Wegener's rotational diffusion constants is discussed.

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Transport properties of rigid bent-rod macromolecules and of semiflexible broken rods in the rigid-body treatment. Analysis of the flexibility of myosin rod

Cited by 32 publications

References 38 publications

Hydrodynamics of segmentally flexible macromolecules

Hydrodynamics of segmentally flexible macromolecules

Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits

Diffusion coefficients of segmentally flexible macromolecules with two subunits: A study of broken rods

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