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Statistical mechanics of noncovalent bonds in polyamino acids. VIII. Covalent loops in proteins
Author(s) -
Poland Douglas C.,
Scheraga Harold A.
Publication year - 1965
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1965.360030404
Subject(s) - covalent bond , chemistry , random coil , ribonuclease , entropy (arrow of time) , conformational entropy , side chain , residue (chemistry) , statistical mechanics , configuration entropy , crystallography , thermodynamics , rna , molecule , polymer , physics , circular dichroism , organic chemistry , biochemistry , gene
The effect of covalently crosslinked loops on the entropy of polypeptide chains is discussed. Since the available theory applies to single, independent loops, this theory has been extended to cases where the chains are multiply crosslinked and, therefore, dependent. Multiply crosslinked loops are present in many proteins, e.g., ribonuclease. It is shown that, whereas in general there is a significant difference between the entropy computed with the present treatment of dependent chains and that incorrectly computed by applying the theory of independent chains to multiply crosslinked loops, the difference in the two procedures is not very great for ribonuclease (and well within the uncertainty of our knowledge of the residue conformational entropy) because the chains of ribonuclease are only slightly dependent even though they are multiply crosslinked. Specifically, estimates of the entropy losses per residue are: −0.45 e.u. for chains in a single, independent loop, −0.58 to −0.66 e.u. for dependent chains in multiply crosslinked loops, and −0.51 e.u. for a simplified model of ribonuclease. With this information, a treatment is given of a helix–coil transition in two chains, assumed to be polyglycine, connected at each end by disulfide bonds. The results of a previous theory for short chains are combined here with the results for the entropy loss on loop formation. It is seen that the presence of the loop stabilizes the helical forms (because of the lowering of the entropy of the random state) and broadens the transition (because of the increased importance of intermediate states).