Helix-coil transition model
Encyclopedia
Helix–coil transition models are formalized techniques in statistical mechanics
developed to describe conformations of linear polymer
s in solution. The models are usually but not exclusively applied to polypeptides as a measure of the relative fraction of the molecule in an alpha helix
conformation versus turn
or random coil
. The main attraction in investigating alpha helix
formation is that one encounters many of the features of protein folding
but in their simplest version. Most of the helix–coil models contain parameters for the likelihood of helix nucleation
from a coil region, and helix propagation along the sequence once nucleated; because polypeptides are directional and have distinct N-terminal and C-terminal ends, propagation parameters may differ in each direction.
The two states are
Common transition models include the Zimm-Bragg model
and the Lifson-Roig model
, and their extensions and variations.
Energy of host poly-alanine helix in aqueous solution:
where m is number of residues in the helix.
Statistical mechanics
Statistical mechanics or statistical thermodynamicsThe terms statistical mechanics and statistical thermodynamics are used interchangeably...
developed to describe conformations of linear polymer
Polymer
A polymer is a large molecule composed of repeating structural units. These subunits are typically connected by covalent chemical bonds...
s in solution. The models are usually but not exclusively applied to polypeptides as a measure of the relative fraction of the molecule in an alpha helix
Alpha helix
A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...
conformation versus turn
Turn (biochemistry)
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.- Definition :According to the most common definition, a turn is a structural motif where the Cα atoms of two residues separated by few peptide bonds are in close approach A turn is...
or random coil
Random coil
A random coil is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules...
. The main attraction in investigating alpha helix
Alpha helix
A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...
formation is that one encounters many of the features of protein folding
Protein folding
Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
but in their simplest version. Most of the helix–coil models contain parameters for the likelihood of helix nucleation
Nucleation
Nucleation is the extremely localized budding of a distinct thermodynamic phase. Some examples of phases that may form by way of nucleation in liquids are gaseous bubbles, crystals or glassy regions. Creation of liquid droplets in saturated vapor is also characterized by nucleation...
from a coil region, and helix propagation along the sequence once nucleated; because polypeptides are directional and have distinct N-terminal and C-terminal ends, propagation parameters may differ in each direction.
The two states are
- helix state: characterized by a common rotating pattern kept together by hydrogen bondHydrogen bondA hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
s, (see alpha-helix). - coil state: conglomerate of randomly ordered sequence of atoms (see random coilRandom coilA random coil is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules...
).
Common transition models include the Zimm-Bragg model
Zimm-Bragg model
In statistical mechanics, the Zimm–Bragg model is a helix-coil transition model that describes helix-coil transitions of macromolecules, usually polymer chains...
and the Lifson-Roig model
Lifson-Roig model
In polymer science, the Lifson-Roig model is a helix-coil transition model applied to the alpha helix-random coil transition of polypeptides; it is a refinement of the Zimm-Bragg model that recognizes that a polypeptide alpha helix is only stabilized by a hydrogen bond only once three consecutive...
, and their extensions and variations.
Energy of host poly-alanine helix in aqueous solution:
where m is number of residues in the helix.