How general is the nucleation-condensation mechanism?

Combined with previous studies on six proteins, the analysis suggests that at least 10 of the 15 small globular proteins fold via a nucleation-condensation mechanism with a concurrent build-up of secondary and tertiary structure contacts, but a structural consolidation that is clearly nonuniformly distributed over the …

What is the framework model of protein folding?

a) Framework model. Protein folding is thought to start with the formation of elements of secondary structure independently of tertiary structure, or at least before tertiary structure is locked in place.

What is hydrophobic collapse in protein folding?

Hydrophobic collapse is a proposed process for the production of the 3-D conformation adopted by polypeptides and other molecules in polar solvents. Incidentally, polar residues interact favourably with water, thus the solvent-facing surface of the peptide is usually composed of predominantly hydrophilic regions.

What is the diffusion collision model?

The diffusion-collision model proposes that the folding process for a four-helix bundle protein be divided into a sequence of random helix-helix collisions, some of which result in coalescence of the helices.

What is the meaning of nucleation?

Nucleation, the initial process that occurs in the formation of a crystal from a solution, a liquid, or a vapour, in which a small number of ions, atoms, or molecules become arranged in a pattern characteristic of a crystalline solid, forming a site upon which additional particles are deposited as the crystal grows.

What is nucleation condensation model of protein folding?

The nucleation-condensation model postulates the existence of a folding nucleus whose formation stabilizes the transition state. As the propensity for forming secondary structure increases, the mechanism slides from nucleation-condensation to the diffusion-collision/framework model (Fig. 6).

What is nucleation in protein folding?

A nucleation-like pathway of protein folding involves the formation of a cluster containing native residues that grows by including residues from the unfolded part of the protein. The resulting average dihedral potential depends on the distance between the selected residue and the cluster center.

What is meant by hydrophobic collapse?

The medicinal chemical use of the term hydrophobic collapse is defined here to mean a significant conformational change in a molecule produced by dissolving the molecule in water, relative to the conformation observed for this same molecule in organic solution or in vacuo.

What is an example of nucleation?

Nucleation is the process where droplets of liquid can condense from a vapor, or bubbles of gas can form in a boiling liquid. For example, sugar crystals growing on a string is an example of heterogeneous nucleation. Another example is the crystallization of a snowflake around a dust particle.

What happens during nucleation?

Nucleation occurs when a small nucleus begins to form in the liquid, the nuclei then grows as atoms from the liquid are attached to it. The crucial point is to understand it as a balance between the free energy available from the driving force, and the energy consumed in forming new interface.

What is the nucleation model?

Classical nucleation theory (CNT) is the most common theoretical model used to quantitatively study the kinetics of nucleation. Nucleation is the first step in the spontaneous formation of a new thermodynamic phase or a new structure, starting from a state of metastability.