Protein folding
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Protein folding is the process by which a protein assumes its characteristic functional shape or tertiary structure, also known as the native state. All protein molecules are linear heteropolymers composed of amino acids; this sequence is known as the primary structure. Most proteins can carry out their biological functions only when folding has been completed, because three-dimensional shape of the proteins in the native state is critical to their function. For example, many enzymes have deep clefts or pockets on their surfaces that act as binding sites for substrates, and membrane proteins often have central channels through which they allow certain organic compounds or ions to pass. Most folded proteins have a hydrophobic core in which side chain packing stabilizes the folded state, and charged or polar side chains on the solvent-exposed surface where they interact with surrounding water molecules.
The process of folding in vivo often begins co-translationally, so that the N-terminus of the protein begins to fold while the C-terminal portion of the protein is still being synthesized by the ribosome. Cells express specialized proteins called chaperones whose function is to aid in the folding of other proteins. A major example is the bacterial GroEL system, which assists in the folding of globular proteins.
The "reverse" of the folding process is called protein denaturation, whereby the native structure of a protein is disrupted and a random coil ensemble of unfolded structures is formed instead. Denaturation can be carried out chemically by the addition of denaturants or thermally by heating (and sometimes cooling). Many denatured proteins precipitate into insoluble amorphous aggregates. Some proteins denatured under some conditions can reversibly refold; however, in many cases denaturation is irreversible.
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[edit] Known facts about the process
[edit] The relationship between folding and amino acid sequence
The particular amino-acid sequence (or "primary structure") of a protein predisposes it to fold into its native conformation or conformations. Proteins do so spontaneously during or after their synthesis inside cells. While these macromolecules may be seen as "folding themselves," their folding depends on the characteristics of their surrounding solution, including the identity of the primary solvent (either water or lipid inside cells), the concentration of salts, the temperature, and molecular chaperones.
For the most part, scientists have been able to study many identical molecules folding together en masse. It appears that in transitioning to the native state, a given amino acid sequence always takes roughly the same route and proceeds through roughly the same intermediates and transition states. At the coarsest level, folding involves first the establishment of regular secondary and supersecondary structures, particularly alpha helices and beta sheets, and only afterwards tertiary structure. Formation of quaternary structure usually involves the "assembly" or "coassembly" of subunits that have already folded. The regular alpha helix and beta sheet structures fold first because they are stabilized by intramolecular hydrogen bonds, as was first realized by Linus Pauling. Protein folding may involve covalent bonding in the form of disulfide bridges formed between two cysteine residues or formation of metal clusters. Shortly before settling into their more stable native conformation, molecules may pass through an intermediate "molten globule" state.
The essential fact of folding, however, remains that the amino acid sequence of each protein contains the information that specifies both the native structure and the pathway to attain that state: Folding is a spontaneous process. The passage of the folded state is mainly guided by the hydrophobic interactions, formation of intramolecular hydrogen bonds, and van der Waals forces, and it is opposed by conformational entropy of the polypeptide chain.
[edit] Preconditions for correct folding
In certain solutions and under some conditions proteins will not fold at all. Temperatures above or below the range that cells tend to live in will cause proteins to unfold or "denature" (this is why boiling makes the white of an egg opaque). High concentrations of solutes and extremes of pH can do the same. A fully denatured protein lacks both tertiary and secondary structure, and exists as a so-called random coil. Cells sometimes protect their proteins against the denaturing influence of heat with enzymes known as chaperones or heat shock proteins, which assist other proteins both in folding and in remaining folded. Some proteins never fold in cells at all except with the assistance of chaperone molecules, that either isolate individual proteins so that their folding is not interrupted by interactions with other proteins or help to unfold misfolded proteins, giving them a second chance to refold properly.
[edit] Incorrect protein folding and neurodegenerative disease
Incorrectly folded proteins are responsible for prion related illness such as Creutzfeldt-Jakob disease and Bovine spongiform encephalopathy (mad cow disease), and amyloid related illnesses such as Alzheimer's Disease. These diseases are associated with the aggregation of misfolded proteins into insoluble plaques; it is not known whether the plaques are the cause or merely a symptom of illness.
[edit] Time scales of protein folding and the Levinthal paradox
The entire duration of the folding process varies dramatically depending on the protein of interest. The slowest folding proteins require many minutes or hours to fold, primarily due to steric hindrances. However, small proteins, with lengths of a hundred or so amino acids, typically fold on time scales of milliseconds. The very fastest known protein folding reactions are complete within a few microseconds. The Levinthal paradox, proposed by Cyrus Levinthal in 1969, states that, if a protein were to fold by sequentially sampling all possible conformations, it would take an astronomical amount of time to do so, even if the conformations were sampled at a rapid rate (on the nanosecond or picosecond scale). Based upon the observation that proteins fold much faster than this, Levinthal then proposed that a random conformational search does not occur in folding, and the protein must, therefore, fold by a directed process.
Folding and unfolding rates also depend on environment conditions like temperature, solvent viscosity, pH and more. The folding process can also be slowed down (and the unfolding sped up) by applying mechanical forces, as revealed by single-molecule experiments.
[edit] Techniques for studying protein folding
[edit] Modern studies of folding with high time resolution
The study of protein folding has been greatly advanced in recent years by the development of fast, time-resolved techniques. These are experimental methods for rapidly triggering the folding of a sample of unfolded protein, and then observing the resulting dynamics. Fast techniques in widespread use include ultrafast mixing of solutions, photochemical methods, and laser temperature jump spectroscopy. Among the many scientists who have contributed to the development of these techniques are Heinrich Roder, Harry Gray, Martin Gruebele, Brian Dyer, William Eaton, Sir Alan R. Fersht and Bengt Nölting. [please note, that is becoming a dead end path for understand protein folding. The reason is that protein do not always fold in the same manner, resulting in a different transition state being observed.]
[edit] Energy landscape theory of protein folding
The protein folding phenomenon was largely an experimental endeavor until the formulation of energy landscape theory by Joseph Bryngelson and Peter Wolynes in the late 1980's and early 1990's. This approach introduced the principle of minimal frustration, which asserts that evolutionary selection has designed the amino acid sequences of natural proteins so that interactions between side chains largely favor the molecule's acquisition of the folded state. Interactions that do not favor folding are selected against, although some residual frustration is expected to exist. A consequence of these evolutionarily designed sequences is that proteins are generally thought to have globally "funneled energy landscapes" (coined by José Onuchic) that are largely directed towards the native state. This "folding funnel" landscape allows the protein to fold to the native state through any of a large number of pathways and intermediates, rather than being restricted to a single mechanism. The theory is supported by computational simulations of model proteins and has been used to improve methods for protein structure prediction and design.
[edit] Computational prediction of protein tertiary structure
De novo or ab initio techniques for computational protein structure prediction employ simulations of protein folding to determine the protein's final folded shape.
[edit] Techniques for determination of protein structure
The determination of the folded structure of a protein is a lengthy and complicated process, involving methods like X-ray crystallography and NMR. In bioinformatics, one of the major areas of interest is the prediction of native structure from amino-acid sequences alone.
[edit] See also
- Anfinsen's dogma
- Denatured protein
- Protein design
- Chevron plot
- Denaturation midpoint
- Equilibrium unfolding
[edit] External links
- Folding @ Home Help decode the riddles of protein folding.
- Rosetta @ Home Help predict protein structures and complexes.
| Protein tertiary structure | ||
|---|---|---|
| General: | Structural domain | Protein folding | |
| All-α folds: | Helix bundle | Globin fold | Homeodomain fold | Alpha solenoid | |
| All-β folds: | Immunoglobulin fold | Beta barrel | Beta-propeller domain | |
| α/β folds: | TIM barrel | Leucine-rich repeat | Flavodoxin fold | Thioredoxin fold | Trefoil knot fold | |
| α+β folds: | Ferredoxin fold | Ribonuclease A | SH2-like fold | |
| Irregular folds: | Conotoxin | |
| ←Secondary structure | Structure determination methods | Quaternary structure→ |
