Protein folding

foldfoldingfoldedmisfoldingmisfoldedmisfolded proteinsprotein foldfoldsprotein stabilityprotein misfolding
Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner.wikipedia
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Protein

proteinsproteinaceousstructural proteins
Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner. Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids.
Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity.

Amyloid

amyloid plaquesamyloid plaqueamyloids
Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Aggregated proteins are associated with prion-related illnesses such as Creutzfeldt–Jakob disease, bovine spongiform encephalopathy (mad cow disease), amyloid-related illnesses such as Alzheimer's disease and familial amyloid cardiomyopathy or polyneuropathy, as well as intracellular aggregation diseases such as Huntington's and Parkinson's disease.
Amyloids are aggregates of proteins that become folded into a shape that allows many copies of that protein to stick together, forming fibrils.

Ribosome

ribosomesribosomal70S
As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure.
Once the protein is produced, it can then fold to produce a specific functional three-dimensional structure although during synthesis some proteins start folding into their correct form.

Neurodegeneration

neurodegenerativeneurodegenerative diseaseneurodegenerative diseases
Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins.
Alzheimer's disease has been hypothesized to be a protein misfolding disease (proteopathy), caused by accumulation of abnormally folded A-beta and tau proteins in the brain.

Protein domain

domainsdomainstructural domain
On the other hand, very small single-domain proteins with lengths of up to a hundred amino acids typically fold in a single step.
Each domain forms a compact three-dimensional structure and often can be independently stable and folded.

Denaturation (biochemistry)

denaturationdenatureddenature
Denaturation of proteins is a process of transition from the folded to the unfolded state.
Protein folding is key to whether a globular or membrane protein can do its job correctly; it must be folded into the right shape to function.

Protein secondary structure

secondary structuresecondarystructure
Formation of a secondary structure is the first step in the folding process that a protein takes to assume its native structure.
Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure.

Protein quaternary structure

quaternary structuremultiprotein complexesmonomer
Tertiary structure may give way to the formation of quaternary structure in some proteins, which usually involves the "assembly" or "coassembly" of subunits that have already folded; in other words, multiple polypeptide chains could interact to form a fully functional quaternary protein.
Protein quaternary structure is the number and arrangement of multiple folded protein subunits in a multi-subunit complex.

Native state

nativenative conformationfinal structure
Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner.
However, "native state" is used almost exclusively in the singular, typically to distinguish properly folded proteins from denatured or unfolded ones.

Random coil

randomly coiledcoilcoils
Denaturation of proteins is a process of transition from the folded to the unfolded state. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from a random coil.
The conformational entropy associated with the random-coil state significantly contributes to its energetic stabilization and accounts for much of the energy barrier to protein folding.

Anfinsen's dogma

thermodynamic hypothesispostulateproteins fold spontaneously
The resulting three-dimensional structure is determined by the amino acid sequence or primary structure (Anfinsen's dogma).
How the protein reaches this structure is the subject of the field of protein folding, which has a related concept called Levinthal's paradox.

Translation (biology)

translationtranslatedprotein translation
Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids.
The polypeptide later folds into an active protein and performs its functions in the cell. The ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons.

Chaperone (protein)

chaperonechaperone proteinchaperones
While these macromolecules may be regarded as "folding themselves", the process also depends on the solvent (water or lipid bilayer), the concentration of salts, the pH, the temperature, the possible presence of cofactors and of molecular chaperones.
The chaperones are concerned primarily with protein folding.

Hydrophobic effect

hydrophobichydrophobic interactionshydrophobic core
The hydrophobic effect exists as a driving force in thermodynamics only if there is the presence of an aqueous medium with an amphiphilic molecule containing a large hydrophobic region.
It is also responsible for effects related to biology, including: cell membrane and vesicle formation, protein folding, insertion of membrane proteins into the nonpolar lipid environment and protein-small molecule associations.

Prion

prionsprion diseasePrion diseases
Aggregated proteins are associated with prion-related illnesses such as Creutzfeldt–Jakob disease, bovine spongiform encephalopathy (mad cow disease), amyloid-related illnesses such as Alzheimer's disease and familial amyloid cardiomyopathy or polyneuropathy, as well as intracellular aggregation diseases such as Huntington's and Parkinson's disease.
Prions are misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein.

Water

H 2 OHOliquid water
While these macromolecules may be regarded as "folding themselves", the process also depends on the solvent (water or lipid bilayer), the concentration of salts, the pH, the temperature, the possible presence of cofactors and of molecular chaperones.
The interactions between water and the subunits of these biomacromolecules shape protein folding, DNA base pairing, and other phenomena crucial to life (hydrophobic effect).

Creutzfeldt–Jakob disease

Creutzfeldt-Jakob diseaseCJDcreutzfeldt-jakob syndrome
Aggregated proteins are associated with prion-related illnesses such as Creutzfeldt–Jakob disease, bovine spongiform encephalopathy (mad cow disease), amyloid-related illnesses such as Alzheimer's disease and familial amyloid cardiomyopathy or polyneuropathy, as well as intracellular aggregation diseases such as Huntington's and Parkinson's disease.
Infectious prions are misfolded proteins that can cause normally folded proteins to become misfolded.

Hydrophobic collapse

The water molecules are fixed in these water cages which drives the hydrophobic collapse, or the inward folding of the hydrophobic groups.
Partial hydrophobic collapse is an experimentally accepted model for the folding kinetics of many globular proteins, such as myoglobin, alpha-lactalbumin, barstar, and staphylococcal nuclease.

Thermostability

thermostableheat stabilitythermally unstable
Temperatures above or below the range that cells tend to live in will cause thermally unstable proteins to unfold or denature (this is why boiling makes an egg white turn opaque).
Above the native temperature of the organism, thermal energy may cause the unfolding and denaturation, as the heat can disrupt the intramolecular bonds in the tertiary and quaternary structure.

Hydrogen bond

hydrogen bondinghydrogen bondshydrogen-bonding
Characteristic of secondary structure are the structures known as alpha helices and beta sheets that fold rapidly because they are stabilized by intramolecular hydrogen bonds, as was first characterized by Linus Pauling.
(See also protein folding).

Proline

ProL-proline L -proline
When studied outside the cell, the slowest folding proteins require many minutes or hours to fold primarily due to proline isomerization, and must pass through a number of intermediate states, like checkpoints, before the process is complete.
From a kinetic standpoint, cis-trans proline isomerization is a very slow process that can impede the progress of protein folding by trapping one or more proline residues crucial for folding in the non-native isomer, especially when the native protein requires the cis isomer.

Equilibrium unfolding

gradual unfolding
While inferences about protein folding can be made through mutation studies, typically, experimental techniques for studying protein folding rely on the gradual unfolding or folding of proteins and observing conformational changes using standard non-crystallographic techniques.
In biochemistry, equilibrium unfolding is the process of unfolding a protein or RNA molecule by gradually changing its environment, such as by changing the temperature or pressure, adding chemical denaturants, or applying force as with an atomic force microscope tip.

Phi value analysis

mutation studiesphi valuestransition state
While inferences about protein folding can be made through mutation studies, typically, experimental techniques for studying protein folding rely on the gradual unfolding or folding of proteins and observing conformational changes using standard non-crystallographic techniques. Fluorescence spectroscopy can be combined with fast-mixing devices such as stopped flow, to measure protein folding kinetics, generate a chevron plot and derive a Phi value analysis.
Phi value analysis, \phi analysis, or \phi-value analysis is an experimental protein engineering technique for studying the structure of the folding transition state of small protein domains that fold in a two-state manner.

Chevron plot

Fluorescence spectroscopy can be combined with fast-mixing devices such as stopped flow, to measure protein folding kinetics, generate a chevron plot and derive a Phi value analysis.
A chevron plot is a way of representing protein folding kinetic data in the presence of varying concentrations of denaturant that disrupts the protein's native tertiary structure.

Proteopathy

protein misfoldingproteinopathiesproteotoxicity
It happens in cooking, in burns, in proteinopathies, and in other contexts.
It is hypothesized that chaperones and co-chaperones (proteins that assist protein folding) may antagonize proteotoxicity during aging and in protein misfolding-diseases to maintain proteostasis.