Universal features of polymer shapes

Aronovitz, Joseph A.; Nelson, David R.

doi:10.1051/jphys:019860047090144500

Cited by 235 publications

(225 citation statements)

References 10 publications

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“…To determine the shape of a given conformation we use two rotationally invariant quantities S and ∆ that are determined using the inertia tensor [10,11,12,13],…”

Section: Shape Parametersmentioning

confidence: 99%

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Asymmetry in the Shapes of Folded and Denatured States of Proteins

2004

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The asymmetry in the shapes of folded and unfolded states are probed using two parameters, ∆ (a measure of the sphericity) and S that describes the shape (S > 0 corresponds to prolate and S < 0 represents oblate). For the folded states, whose interiors are densely packed, the radii of gyration (R g ), ∆, and S are calculated using the coordinates of the experimentally determined structures. Although R g scales as N 1/3 , as expected for maximally compact structures, the distributions of ∆ and S show that there is considerable asymmetry in the shapes of folded structures. The degree of asymmetry is greater for proteins that form oligomers. Analysis of the two-and three-body contacts in the native structures shows that the presence of near equal number of contacts between backbone and side-chains and between side-chains gives rise to dense packing. We suggest that proteins with relatively large values of ∆ and S can tolerate volume mutations without greatly affecting the network of contacts or their stability. Mutagenesis data on T4 lysozyme and λ-repressor support this conclusion. To probe shape characteristics of denatured states we have developed a C α − C β model of a WW-like domain.The shape parameters, which are calculated using Langevin simulations, change dramatically in the course of coil to globule transition. Comparison of the values of ∆ and S between the globular state and the folded state of WW domain shows that both energetic (especially dispersion in the hydrophobic interactions) and steric effects are important in determining packing in proteins.

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“…To determine the shape of a given conformation we use two rotationally invariant quantities S and ∆ that are determined using the inertia tensor [10,11,12,13],…”

Section: Shape Parametersmentioning

confidence: 99%

“…The purpose of this paper is two fold: (a) We use ideas familiar in polymer physics [9,10,11] to describe shape parameters of proteins using only the coordinates of the native structure. Examination of the asymmetry in the overall shapes gives insights into the extent to which a protein can tolerate volume mutations.…”

Section: Introductionmentioning

confidence: 99%

Asymmetry in the Shapes of Folded and Denatured States of Proteins

2004

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“…which is bounded to the interval [-0.25, 2] with negative values referring to predominantly oblate shapes and positive values representing prolate molecules [13,14].…”

Section: Resultsmentioning

confidence: 99%

Molecular dynamics simulation of configurational properties of complexes between β-cyclodextrin and 2,6-diaziadamantane in water

Zifferer

Kornherr²,

Brinker

2008

Molecular Simulation

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“…Nevertheless, it is difficult to treat analytically. A more tractable approach has been suggested by Aronovitz et al [23] and Rudnick et al [24] based on the definition of the asphericity ∆ D as…”

Section: Introductionmentioning

confidence: 99%

The shape of invasion percolation clusters in random and correlated media

Ebrahimi

2008

J. Stat. Mech.

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The shape of two-dimensional invasion percolation clusters are studied numerically for both nontrapping (NTIP) and trapping (TIP) invasion percolation processes. Two different anisotropy quantifiers, the anisotropy parameter and the asphericity are used for probing the degree of anisotropy of clusters. We observe that in spite of the difference in scaling properties of NTIP and TIP, there is no difference in the values of anisotropy quantifiers of these processes. Furthermore, we find that in completely random media, the invasion percolation clusters are on average slightly less isotropic than standard percolation clusters. Introducing isotropic long-range correlations into the media reduces the isotropy of the invasion percolation clusters. The effect is more pronounced for the case of persisting long-range correlations. The implication of boundary conditions on the shape of clusters is another subject of interest. Compared to the case of free boundary conditions, IP clusters of conventional rectangular geometry turn out to be more isotropic. Moreover, we see that in conventional rectangular geometry the NTIP clusters are more isotropic than the TIP clusters.

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Universal features of polymer shapes

Cited by 235 publications

References 10 publications

Asymmetry in the Shapes of Folded and Denatured States of Proteins

Asymmetry in the Shapes of Folded and Denatured States of Proteins

Molecular dynamics simulation of configurational properties of complexes between β-cyclodextrin and 2,6-diaziadamantane in water

The shape of invasion percolation clusters in random and correlated media

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