Conformational entropy

Conformational entropy

Conformational entropy is the entropy associated with the physical arrangement of a polymer chain that assumes a compact or globular state in solution. The concept is most commonly applied to biological macromolecules such as proteins and RNA, but can also be used for polysaccharides and other polymeric organic compounds. To calculate the conformational entropy, the possible conformations assumed by the polymer may first be discretized into a finite number of states, usually characterized by unique combinations of certain structural parameters, each of which has been assigned an energy level. In proteins, backbone dihedral angles and side chain rotamers are commonly used as descriptors, and in RNA the base pairing pattern is used. These characteristics are used to define the degrees of freedom (in the statistical mechanics sense of a possible "microstate"). The conformational entropy associated with a particular conformation is then dependent on the probability associated with the occupancy of that state, as determined by the sum of the energies associated with the value of each parameter assumed in the state.

The entropy of heterogeneous random coil or denatured proteins is significantly higher than that of the folded native state tertiary structure. In particular, the conformational entropy of the amino acid side chains in a protein is thought to be a major contributor to the energetic stabilization of the denatured state and thus a barrier to protein folding.[1] However, a recent study has shown that side-chain conformational entropy can stabilize native structures among alternative compact structures.[2] The conformational entropy of RNA and proteins can be estimated; for example, empirical methods to estimate the loss of conformational entropy in a particular side chain on incorporation into a folded protein can roughly predict the effects of particular point mutations in a protein. Side-chain conformational entropies can be defined as Boltzmann sampling over all possible rotameric states:[3]

S = − RΣipiln(pi)

where R is the gas constant and pi is the probability of a residue being in rotamer i.[3]

The limited conformational range of proline residues lowers the conformational entropy of the denatured state and thus increases the energy difference between the denatured and native states. A correlation has been observed between the thermostability of a protein and its proline residue content.[4]


  1. ^ Doig AJ, Sternberg MJE. (1995). Side-chain conformational entropy in protein folding. Protein Science 4:2247-51.
  2. ^ Zhang J, Liu JS (2006) On Side-Chain Conformational Entropy of Proteins. PLoS Comput Biol 2(12): e168. doi:10.1371/journal.pcbi.0020168
  3. ^ a b Pickett SD, Sternberg MJ. (1993). Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 231(3):825-39.
  4. ^ Watanabe K., Masuda T., Ohashi H., Mihara H. & Suzuki Y. Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. Eur J Biochem 226,277-83 (1994).

See also

Wikimedia Foundation. 2010.

Игры ⚽ Нужно решить контрольную?

Look at other dictionaries:

  • conformational entropy — noun entropy calculated from the probability that a state could be reached by chance alone • Hypernyms: ↑randomness, ↑entropy, ↑S …   Useful english dictionary

  • Entropy — This article is about entropy in thermodynamics. For entropy in information theory, see Entropy (information theory). For a comparison of entropy in information theory with entropy in thermodynamics, see Entropy in thermodynamics and information… …   Wikipedia

  • Configuration entropy — In statistical mechanics, configuration entropy is the portion of a system s entropy that is related to the position of its constituent particles rather than to their velocity or momentum. It is physically related to the number of ways of… …   Wikipedia

  • Proline — For other uses, see Proline (disambiguation). Proline …   Wikipedia

  • Molecular dynamics — (MD) is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms. In the most common version, the trajectories of molecules… …   Wikipedia

  • Protein folding — Protein thermodynamics redirects here. For the thermodynamics of reactions catalyzed by proteins, see Enzyme. Protein before and after folding. Protein folding is the process by which a protein structure assumes its functional shape or… …   Wikipedia

  • Force field (chemistry) — In the context of molecular mechanics, a force field (also called a forcefield) refers to the functional form and parameter sets used to describe the potential energy of a system of particles (typically but not necessarily atoms). Force field… …   Wikipedia

  • Self-consistent mean field (biology) — The self consistent mean field (SCMF) method is an adaptation of mean field theory used in protein structure prediction to determine the optimal amino acid side chain packing given a fixed protein backboneref|Koehl. It is faster but less accurate …   Wikipedia

  • randomness — noun 1. (thermodynamics) a thermodynamic quantity representing the amount of energy in a system that is no longer available for doing mechanical work entropy increases as matter and energy in the universe degrade to an ultimate state of inert… …   Useful english dictionary

  • Folding funnel — The folding funnel hypothesis is a specific version of the energy landscape theory of protein folding, which assumes that a protein s native state corresponds to its free energy minimum under the solution conditions usually encountered in cells.… …   Wikipedia

Share the article and excerpts

Direct link
Do a right-click on the link above
and select “Copy Link”