- Zimm-Bragg model
statistical mechanics, the Zimm-Bragg model is a helix-coil transition modelthat describes helix-coil transitions of macromolecules, usually polymerchains. Most models provide a reasonable approximation of the fractional helicity of a given polypeptide; the Zimm-Bragg model differs by incorporating the ease of propagationwith respect to nucleation.
Helix-coil transition models
Helix-coil transition models assume that
polypeptidesare linear chains composed of interconnected segments. Further, models group these sections into two broad categories: "coils", random conglomerations of disparate unbound pieces, are represented by the letter 'C', and "helices", ordered states where the chain has assumed a structure stabilized by hydrogen bonding, are represented by the letter 'H'.cite journal|author=Samuel Kutter|coauthors=Eugene M. Terentjev|journal=The European Physical Journal E - Soft Matter|date=16 October 2002|title=Networks of helix-forming polymers|volume=8|issue=5|pages=539–47|pmid=15015126|publisher=EDP Sciences|doi=10.1140/epje/i2002-10044-x]
Thus, it is possible to loosely represent a macromolecule as a string such as CCCCHCCHCHHHHHCHCCC and so forth. The number of coils and helices factors into the calculation of fractional helicity, , defined as :where: is the average helicity and: is the number of helix or coil units.
The Zimm-Bragg model takes the cooperativity of each segment into consideration when calculating fractional helicity. The probability of any given
monomerbeing a helix or coil is affected by which the previous monomer is; that is, whether the new site is a nucleation or propagation.
By convention, a coil unit ('C') is always of statistical weight 1. Addition of a helix state ('H') to a previously coiled state (nucleation) is assigned a statistical weight , where is the nucleation parameter and:.Adding a helix state to a site that is already a helix (propagation) has a statistical weight of . For most
proteins,:which makes the propagation of a helix more favorable than nucleation of a helix from coil state.cite book|author=Ken A. Dill|coauthors=Sarina Bromberg|title=Molecular Driving Forces - Statistical Thermodynamics in Chemistry and Biology|pages=505|publisher=Garland Publishing, Inc.|date=2002]
From these parameters, it is possible to compute the fractional helicity . The average helicity is given by:where is the statistical weight and is the partition function given by the sum of the probabilities of each site on the polypeptide. The fractional helicity is thus given by the equation:.
The Zimm-Bragg model is equivalent to a one-dimensional
Ising modeland has no long-range interactions, i.e., interactions between residues well separated along the backbone; therefore, by the famous argument of Rudolf Peierls, it cannot undergo a phase transition.
The statistical mechanics of the Zimm-Bragg model [cite journal | last = Zimm | first = BH | author link = Bruno Zimm | coauthors = Bragg JK | year = 1959 | title = Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains | journal = Journal of Chemical Physics | volume = 31 | pages = 526–531 | doi = 10.1063/1.1730390] may be solved exactly using the transfer-matrix method. The two parameters of the Zimm-Bragg model are σ, the
statistical weightfor nucleating a helix and "s", the statistical weight for propagating a helix. These parameters may depend on the residue "j"; for example, a prolineresidue may easily nucleate a helix but not propagate one; a leucineresidue may nucleate and propagate a helix easily; whereas glycine may disfavor both the nucleation and propagation of a helix. Since only nearest-neighbour interactions are considered in the Zimm-Bragg model, the full partition functionfor a chain of "N" residues can be written as follows
where the 2x2 transfer matrix W"j" of the "j"th residue equals the matrix of statistical weights for the state transitions
The "row-column" entry in the transfer matrix equals the statistical weight for making a transition from state "row" in residue "j-1" to state "column" in residue "j". The two states here are "helix" (the first) and "coil" (the second). Thus, the upper left entry "s" is the statistical weight for transitioning from helix to helix, whereas the lower left entry "σs" is that for transitioning from coil to helix.
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