Radius of gyration of multisubunit macromolecules: application to myosin heads, myosin rod and whole myosin

Solvez, Juan A.; Iniesta, A.; Torre, Jose Garciáde la

doi:10.1016/0141-8130(88)90065-7

Cited by 16 publications

(11 citation statements)

References 15 publications

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“…As the time required for evaluating one conformation is so short in present computers, one could think of an alternative procedure in which a sample containing a moderate number (a few hundred) conformations is generated by simple Monte Carlo procedures, and the average is carried our over the sample. This idea has been applied in the calculation of the radius of gyration (Solvez et al 1988 …”

Section: Rotational Diffusionmentioning

confidence: 99%

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: Rotational Diffusionmentioning

confidence: 99%

Hydrodynamics of segmentally flexible macromolecules

1994

Eur Biophys J

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“…The relative orientation of the monomers, which determines the final structure, influences the d i parameter. As a matter of fact, as underlined in Solvez et al (1988), Eq. (3) tells us that R g depends on the dimension of the monomers and the position of their centers, but, if the latter are fixed, R g does not depend on the monomers orientation.…”

Section: The Fractal Mass Dimensionmentioning

confidence: 99%

“…When dealing with ellipsoidal monomers, we can use an average value for R g,i , following the method used in macromolecular physics by Solvez et al (1988), Kerfelec et al (1988), and Garcia de la Torre & Carrasco (2002). The relative orientation of the monomers, which determines the final structure, influences the d i parameter.…”

Section: The Fractal Mass Dimensionmentioning

confidence: 99%

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The influence of the monomer shape in the first stage of dust growth in the protoplanetary disk

Bertini

Gutiérrez

Sabolo

2009

A&A

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Context. Laboratory experiments have shown that the initial stage of the dust growth in the protoplanetary disk starts with low-velocity hit-and-stick collisions between sub-micron grains, before the relative impact energy becomes large enough to cause the morphological restructuring of the forming aggregates. The results of these collisions are loose aggregates characterized by fractal dimensions ≤2. Numerical studies generally model this early stage with colliding clusters made of monodisperse spherical monomers. Aims. In this paper we aimed to investigate how a more complex representation of the monodisperse monomers structure influences the morphology of the final aggregate particles in terms of fractal dimension, porosity, cross-section, and friction time. This study had also the purpose of testing the validity of the current fractal models in representing irregular particles. Methods. We used three kinds of hit-and-stick aggregation methods: two particle-cluster aggregations producing compact and extremely loose aggregates, respectively, and simplified cluster-cluster aggregation as intermediate class in terms of fluffyness and porosity. In our measures, we used two kinds of monomer shapes: spheres and elongated prolate ellipsoids with axis ratio 3:1 resembling the ones used to model interstellar dust grains. Results. We found that the monomer shape has little influence ( 2%) on the fractal dimension of the final aggregate, once large particles are taken into account, independently on the morphological class. Elongated monomers produce structures with larger fractal dimension in the limit of small particles. For loose objects the influence on the porosity is even smaller, whereas elongated monomers give particles with ∼5% higher porosity in the case of large compact fractals. Regardless the ellipsoidal monomer used has, by construction, a cross-section ∼26% larger than the one of the volume-equivalent sphere, the difference in cross-section per unit mass is decreasing when aggregates are considered. Clusters made by elliptical monomers result much coupled to the surrounding gas than objects made by spherical monomers belonging to the same morphological class. Differences in the friction time are estimated to be below 15%. We conclude that the monomer shape influence on the morphology of the final particles during the hit-and-stick aggregation step is much lower than the differences due to considering different morphological classes in modeling and the uncertainties produced in a realistic accretion scenario, where a wide distribution of morphologies is expected. Present models of irregular particles as fractals made by spherical monomers can therefore also represent well more complex shapes, before the restructuring phase is taken into account.

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“…The peptides are expected to be very flexible due to the lack of a rigid secondary structure, making their geometrical size difficult to determine. Thus, the radius of gyration is used as a statistical measure for the size of the peptides, a method that is used to represent the size of macromolecules [27]. Using Molecular Dynamics (MD), see Computational methods section, the radius of gyration is calculated based on the most often occurring conformations.…”

Section: Methodsmentioning

confidence: 99%

Separation of Peptides with Forward Osmosis Biomimetic Membranes

et al. 2016

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Forward osmosis (FO) membranes have gained interest in several disciplines for the rejection and concentration of various molecules. One application area for FO membranes that is becoming increasingly popular is the use of the membranes to concentrate or dilute high value compound solutions such as pharmaceuticals. It is crucial in such settings to control the transport over the membrane to avoid losses of valuable compounds, but little is known about the rejection and transport mechanisms of larger biomolecules with often flexible conformations. In this study, transport of two chemically similar peptides with molecular weight (Mw) of 375 and 692 Da across a thin film composite Aquaporin Inside™ Membrane (AIM) FO membrane was investigated. Despite the relative large size, both peptides were able to permeate the dense active layer of the AIM membrane and the transport mechanism was determined to be diffusion-based. Interestingly, the membrane permeability increased 3.65 times for the 692 Da peptide (1.39 × 10−12 m2·s−1) compared to the 375 Da peptide (0.38 × 10−12 m2·s−1). This increase thus occurs for an 85% increase in Mw but only for a 34% increase in peptide radius of gyration (Rg) as determined from molecular dynamics (MD) simulations. This suggests that Rg is a strong influencing factor for membrane permeability. Thus, an increased Rg reflects the larger peptide chains ability to sample a larger conformational space when interacting with the nanostructured active layer increasing the likelihood for permeation.

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Radius of gyration of multisubunit macromolecules: application to myosin heads, myosin rod and whole myosin

Cited by 16 publications

References 15 publications

Hydrodynamics of segmentally flexible macromolecules

Hydrodynamics of segmentally flexible macromolecules

The influence of the monomer shape in the first stage of dust growth in the protoplanetary disk

Separation of Peptides with Forward Osmosis Biomimetic Membranes

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