Asymmetry in the shapes of folded and denatured states of proteins

By Ruxandra I. Dima, D. Thirumalai. 2003

166 citations recorded by the source corpus.

The asymmetry in the shapes of folded and unfolded states are probed using two parameters, Δ (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 (Rg), Δ, and S are calculated using the coordinates of the experimentally determined structures. Although Rg scales as N1/3, as expected for maximally compact structures, the distributions of Δ 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 Δ and S can tolerate volume mutations without greatly affecting the network of contacts or their stability. ...

Subfields: Biotechnology, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0ab5f67c8b3c7df20bab820da8c5be1c425c5780

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In Materials Chemistry

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  2. Rohit V. Pappu

In Molecular Biology

  1. Rahul K. Das
  2. Rohit V. Pappu
  3. Vladimir N Uversky

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