![]() ![]() A fully extended chain has C=0 (right-hand edge of surface), and a maximally compact 3 × 3 × 3 cube has C=28 (left-hand edge of surface). The contours are spaced 0.5 units apart, so that each level is a factor of e 0.5=1.6 times more probable than the previous (lower) one.įigure 2 Free-energy (F) surface of a 27-mer as a function of the number of native contacts (Q 0) and the total number of (native and non-native) contacts (C) obtained by sampling the accessible configuration space with Monte Carlo simulations (see Ref. The diagram was obtained by taking the natural logarithm of the observed frequency of each pair of main-chain dihedral angles (φ,ψ) in a set of 1000 representative protein structures (A. The surface features result primarily from steric repulsions between the various atoms and lead to a distribution of conformations in the coil state that corresponds locally to an average over the low-energy regions of the conformational space for each amino acid. (b) Chemical structure of an alanine residue and the Ramachandran diagram representing its free-energy surface in a protein environment. The different species within each ensemble interconvert rapidly. ![]() Figure 1 (a) Schematic representation of the global distribution of conformations of a polypeptide chain in a random-coil state, a partially collapsed denatured state and a compact non-native state. ![]()
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