A swivel‐jointed formalism for segmentally flexible macromolecules and its application to the rotational behavior of myosin

Wegener, William A.

doi:10.1002/bip.360210605

Cited by 39 publications

(18 citation statements)

References 37 publications

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“…At 20"C, calculation shows that the relaxation time would be approximately 25% of the rigid rod value for a molecule the length of tropomyosin with a completely flexible hinge at the center. 29 The observed relaxation times for nonpolymerizable skeletal and smooth muscle tropomyosins are respectively, 97 and 85% of the rigid rod value, which suggests that the solution structures of these tropomyosins do not contain a flexible hinge in the center. The next least stable block of the tropomyosins is at the C-terminal end of the coiled coil.…”

Section: Discussionmentioning

confidence: 95%

Flexibility of smooth and skletal tropomyosins

Swenson

Stellwagen

1989

Biopolymers

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The rotational relaxation times of nonpolymerizable skeletal and smooth muscle tropomyosin were measured by analysis of the decay of the zero-field birefringence at different temperatures and salt concentrations. Skeletal tropomyosin in solution is equally well modeled as a rigid rod or as a semiflexible rod with a persistence length of 150 nm. Smooth muscle tropomyosin does not fit the rigid rod model but is well approximated by a semiflexible rod model with a persistence length of 55 nm. The results indicate that smooth muscle tropomyosin is either a more flexible molecule than skeletal muscle tropomyosin or is a curved structure with an end-to-end length shorter than the coiled-coil contour length. Smooth muscle tropomyosin controls the actomyosin ATPase differently from skeletal muscle tropomyosin and it had been suggested that the reason is because it is more rigid; clearly, another explanation must be sought.

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Section: Discussionmentioning

confidence: 95%

Flexibility of smooth and skletal tropomyosins

Swenson

Stellwagen

1989

Biopolymers

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“…Also, the analyses of our simple 2D system indicates that the methods of the solution of the DEM can quite straightforwardly be generalized to real, 3D, nonrigid macromolecules. Work is currently in progress to extend the results of the present article to the consideration of inertial effects for more general macromolecular chains, consisting of an arbitrary number of rigid bodies 7,22,80) .…”

Section: Resultsmentioning

confidence: 94%

“…Indeed, Here it is enough to evaluate Z À1 q in the zero order, i. e. by putting k = 0. Summarizing, the FPE (A17), as compared with its counterpart (22,23), possesses a new nondissipative solvent-induced term (see also ref. 19) for the special case of butane).…”

Section: A9mentioning

confidence: 99%

“…In order to compare such a FPE with that derived in section 3 (Eqs. (22) and (23)), we restrict ourselves to the consideration of a dilute solution of macromolecules in the bath of an atomic solvent under (global) equilibrium conditions.…”

Section: Appendixmentioning

confidence: 99%

“…To derive a closed form equation for the reduced probability density function q (q, t) from the FPE (22), it is enough to realize that the problem possesses a large parameter, viz., friction, which is proportional to the solvent viscosity g. Further, it is convenient to invoke the projection operator technique and introduce the operators R q eq p v Àv dp I 1 À R By assuming that the initial condition for Eq. (22) is written as q (q, p, 0) = q eq (p) U (q), one arrives at the following exact equation for the probability density R q (q, p, t) 3 q eq (q) q (q, t):…”

Section: Diffusion Limitmentioning

confidence: 99%

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Inertial effects in the Brownian dynamics with rigid constraints

Gelin¹

1999

Macromol. Theory Simul.

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SUMMARY: To investigate the influence of inertial effects on the dynamics of an assembly of beads subjected to rigid constraints and placed in a buffer medium, a convenient method to introduce suitable generalized coordinates is presented. Without any restriction on the nature of the soft forces involved (both stochastic and deterministic), pertinent Langevin equations are derived. Provided that the Brownian forces are Gaussian and Markovian, the corresponding Fokker-Planck equation (FPE) is obtained in the complete phase space of generalized coordinates and momenta. The correct short time behavior for correlation functions (CFs) of generalized coordinates is established, and the diffusion equation with memory (DEM) is deduced from the FPE in the high friction limit. The DEM is invoked to perform illustrative calculations in two dimensions of the orientational CFs for once broken nonrigid rods immobilized on a surface. These calculations reveal that the CFs under certain conditions exhibit an oscillatory behavior, which is irreproducible within the standard diffusion equation. Several methods are considered for the approximate solution of the DEM, and their application to three dimensional DEMs is discussed.

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Transport properties of rigid and flexible macromolecules by brownian dynamics simulation

Allison

McCammon

1984

Biopolymers

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SynopsisThe Phys. 69,1352-13601 is used to simulate the Brownian dynamics of a system of identical, interacting beads. In the present study, we use the method to obtain transport coefficients for a variety of rigid and flexible structures modeled as arrays of spherical subunits. Constraints are enforced using the SHAKE algorithm or a modification, SHAKE-HI, that is described for the first time. In SHAKE-HI, hydrodynamic interactions between subunits are taken into account when the constraints are enforced. Use of SHAKE-HI yields transport coefficients that are in perfect agreement with those obtained by other methods. The primary advantage of the present method is its generality. We also propose that multistep Brownian dynamics may be important in simulating actual experiments (such as fluorescence depolarization) on well-defined model systems that possess an arbitrary degree of internal flexibility.

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A swivel‐jointed formalism for segmentally flexible macromolecules and its application to the rotational behavior of myosin

Cited by 39 publications

References 37 publications

Flexibility of smooth and skletal tropomyosins

Flexibility of smooth and skletal tropomyosins

Inertial effects in the Brownian dynamics with rigid constraints

Transport properties of rigid and flexible macromolecules by brownian dynamics simulation

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