Protein before and after folding.

Protein folding is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure. Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino Proteins are an important class of biological Macromolecules present in all biological organisms made up of such elements as Carbon, Hydrogen ^[1]

Each protein begins as a polypeptide, translated from a sequence of mRNA as a linear chain of amino acids. Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this This polypeptide lacks any developed three-dimensional structure (the left hand side of the neighboring figure). However each amino acid in the chain can be thought of having certain 'gross' chemical features. These may be hydrophobic, hydrophilic, or electrically charged, for example. In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of Hydrophile, from the Greek (hydros "water" and φιλια (philia "friendship" refers to a physical property of a Molecule These interact with each other and their surroundings in the cell to produce a well-defined, three dimensional shape, the folded protein (the right hand side of the figure), known as the native state. In Biochemistry, the native state of a Protein is its operative or functional form The resulting three-dimensional structure is determined by the sequence of the amino acids. ^[2] The mechanism of protein folding is not completely understood.

Experimentally determining the three dimensional structure of a protein is often very difficult and expensive. However the sequence of that protein is often known. Therefore scientists have tried to use different biophysical techniques to manually fold a protein, that is, to predict the structure of the complete protein from the sequence of the protein. Biophysics (also biological physics) is an Interdisciplinary Science that employs and develops theories and methods of the Physical sciences for

For many proteins the correct three dimensional structure is essential to function. ^[3] Failure to fold into the intended shape usually produces inactive proteins with different properties (details found under prion). A prion (ˈpriːɒn is thought to be an infectious agent that according to current scientific consensus is comprised entirely of a propagated, mis-folded Several neurodegenerative and other diseases are believed to result from the accumulation of misfolded (incorrectly folded) proteins. Neurodegenerative Disease ( Greek νέυρο- néuro-, "nerval" and Latin dēgenerāre, "to decline" or "to A disease is an abnormal condition of an organism that impairs bodily functions and can be deadly ^[4]

Known facts about the process

The relationship between folding and amino acid sequence

Illustration of the main driving force behind protein structure formation. In the compact fold (to the right), the hydrophobic amino acids (shown as black spheres) are in general shielded from the solvent.

The amino-acid sequence (or primary structure) of a protein predisposes it towards its native conformation or conformations. In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including It will fold spontaneously during or after synthesis. Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) While these macromolecules may be regarded as "folding themselves", the mechanism depends equally on the characteristics of the cytosol, including the nature of the primary solvent (water or lipid), the concentration of salts, the temperature, and molecular chaperones. The term macromolecule by definition implies "large Molecule " The cytosol or intracellular fluid (or cytoplasmic matrix) is the liquid found inside cells. A solvent is a liquid or gas that dissolves a solid liquid or gaseous Solute, resulting in a Solution. Water is a common Chemical substance that is essential for the survival of all known forms of Life. Lipids are broadly defined as any fat- Soluble ( lipophilic) naturally-occurring Molecule, such as fats oils waxes cholesterol sterols fat-soluble Salt is a Dietary mineral composed primarily of Sodium chloride that is essential for Animal life but toxic to most land plants Temperature is a physical property of a system that underlies the common notions of hot and cold something that is hotter generally has the greater temperature This article is about the protein For other uses see Chaperone, a disambiguation page

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 hydrophobic effect is the property that non-polar molecules tend to form intermolecular aggregates in an aqueous medium and analogous intramolecular interactions "Polar molecule" and "Non-polar" redirect here It is generally accepted that minimizing the number of hydrophobic side-chains exposed to water is the principal driving force behind the folding process,^[5] although a recent theory has been proposed which reassesses the contributions made by hydrogen bonding. ^[6]The strengths of hydrogen bonds in a protein vary, i. e. they are dependent on their microenvironment, thus H-bonds enveloped in a hydrophobic core contribute more than H-bonds exposed to the aqueous environment to the stability of the native state. ^[7]

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. In vivo ( Latin: within the living means that which takes place inside an organism. Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal end, or Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that Specialized proteins called chaperones assist in the folding of other proteins. This article is about the protein For other uses see Chaperone, a disambiguation page ^[8] A well studied example is the bacterial GroEL system, which assists in the folding of globular proteins. The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have GroEL belongs to the Chaperonin family of Molecular chaperones, and is found in a large number of bacteria Globular proteins, or spheroproteins are one of the two main Protein classes comprising "globe" -like proteins that are more or less soluble in In eukaryotic organisms chaperones are known as heat shock proteins. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex Heat shock proteins ( HSP) are a group of Proteins whose expression is increased when the cells are exposed to elevated temperatures or other stress Although most globular proteins are able to assume their native state unassisted, chaperone-assisted folding is often necessary in the crowded intracellular environment to prevent aggregation; chaperones are also used to prevent misfolding and aggregation which may occur as a consequence of exposure to heat or other changes in the cellular environment.

For the most part, scientists have been able to study many identical molecules folding together en masse. At the coarsest level, it appears that in transitioning to the native state, a given amino acid sequence takes on roughly the same route and proceeds through roughly the same intermediates and transition states. Often folding involves first the establishment of regular secondary and supersecondary structures, particularly alpha helices and beta sheets, and afterwards tertiary structure. A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which The β sheet (also β-pleated sheet) is the second form of regular Secondary structure in Proteins consisting of beta strands connected laterally In Biochemistry and Chemistry, the tertiary structure of a Protein or any other Macromolecule is its three-dimensional structure as defined Formation of quaternary structure usually involves the "assembly" or "coassembly" of subunits that have already folded. In Biochemistry, quaternary structure is the arrangement of multiple folded Protein molecules in a multi-subunit complex The regular alpha helix and beta sheet structures fold rapidly because they are stabilized by intramolecular hydrogen bonds, as was first characterized by Linus Pauling. A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which The β sheet (also β-pleated sheet) is the second form of regular Secondary structure in Proteins consisting of beta strands connected laterally A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen Linus Carl Pauling (February 28 1901 – August 19 1994 was an American Scientist, Peace activist, Author and educator. Protein folding may involve covalent bonding in the form of disulfide bridges formed between two cysteine residues or the formation of metal clusters. In Chemistry, a disulfide bond is a single Covalent bond derived from the coupling of Thiol groups Not to be confused with Cystine, its oxidized dimer Cysteine (abbreviated as Cys or C) is an α- Amino acid with Shortly before settling into their more energetically favourable native conformation, molecules may pass through an intermediate "molten globule" state. In Thermodynamics, the Gibbs free energy ( IUPAC recommended name Gibbs energy or Gibbs function) is a Thermodynamic potential which A molten globule ( MG) is a stable partially folded Protein state found in mildly denaturing conditions such as low PH (generally pH = 2 mild

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. This is not to say that identical amino acid sequences always fold similarly. ^[9] Conformations differ based on environmental factors as well; similar proteins fold differently based on where they are found. Folding is a spontaneous process independent of energy inputs from nucleoside triphosphates. A spontaneous process is the time-evolution of a system in which it releases free energy (most often as heat and moves to a lower more thermodynamically stable energy state Nucleoside triphosphate (NTP is a Nucleoside with three Phosphates Natural nucleoside triphosphates include Adenosine triphosphate (ATP Guanosine The passage of the folded state is mainly guided by hydrophobic interactions, formation of intramolecular hydrogen bonds, and van der Waals forces, and it is opposed by conformational entropy. A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen The Van der Waals equation is an Equation of state that can be derived from a special form of the potential between a pair of molecules (hard-sphere repulsion Conformational entropy is the Entropy associated with the physical arrangement of a Polymer chain that assumes a compact or globular state in solution

Disruption of the native state

In certain solutions and under some conditions proteins will not fold into their biochemically functional forms. Temperatures above (and sometimes those 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). Thermostability is the quality of a substance to resist irreversible change in its chemical or physical structure at a high relative temperature Denaturation is a process in which Proteins or Nucleic acids lose their structure (tertiary structure by application of some external stress or compound for Albumen redirects here For other uses see Albumen (disambiguation. High concentrations of solutes, extremes of pH, mechanical forces, and the presence of chemical denaturants can do the same. In Chemistry, a solution is a Homogeneous Mixture composed of two or more substances pH is the measure of the acidity or alkalinity of a Solution. A fully denatured protein lacks both tertiary and secondary structure, and exists as a so-called random coil. A random coil is a Polymer Conformation where the Monomer subunits are oriented randomly while still being bonded to adjacent Under certain conditions some proteins can refold; however, in many cases denaturation is irreversible. ^[10] 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. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins This article is about the protein For other uses see Chaperone, a disambiguation page Heat shock proteins ( HSP) are a group of Proteins whose expression is increased when the cells are exposed to elevated temperatures or other stress Some proteins never fold in cells at all except with the assistance of chaperone molecules, which 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. This function is crucial to prevent the risk of precipitation into insoluble amorphous aggregates. Precipitation is the formation of a Solid in a Solution during a Chemical reaction. Solubility is the characteristic Physical property referring to the ability of a given substance the Solute, to dissolve in a Solvent.

Incorrect protein folding and neurodegenerative disease

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 intracytoplasmic aggregation diseases such as Huntington's and Parkinson's disease. A prion (ˈpriːɒn is thought to be an infectious agent that according to current scientific consensus is comprised entirely of a propagated, mis-folded Creutzfeldt-Jakob disease ( CJD) is a very rare and incurable degenerative neurological disorder ( Brain Disease) that is ultimately Bovine Spongiform Encephalopathy ( BSE) commonly known as Mad-Cow Disease ( MCD) is a fatal Neurodegenerative disease in Cattle Amyloids are insoluble fibrous Protein aggregates sharing specific structural traits Alzheimer's disease ( AD) also called Alzheimer disease or simply Alzheimer's, is the most common form of Dementia. These age onset degenerative diseases are associated with the multimerization of misfolded proteins into insoluble, extracellular aggregates and/or intracellular inclusions including cross-beta sheet amyloid fibrils; it is not clear whether the aggregates are the cause or merely a reflection of the loss of proteostasis, the balance between synthesis, folding, aggregation and protein turnover. Amyloids are insoluble fibrous Protein aggregates sharing specific structural traits Misfolding and excessive degradation in lieu of folding and function leads to a number of proteopathy diseases such as antitrypsin-associated Emphysema, cystic fibrosis and the lysosomal storage diseases, where loss of function is the origin of the disorder. Proteopathy (Proteo- protein -pathy disease proteopathies pl. Emphysema is a chronic obstructive Pulmonary disease ( COPD) formerly termed a chronic obstructive Lung disease (COLD Cystic fibrosis (also known as CF, mucoviscoidosis, or mucoviscidosis) is a hereditary disease affecting the exocrine (mucus glands of the lungs The lysosomal storage diseases are a group of over forty human Genetic disorders that result from defects in lysosomal function While protein replacement therapy has historically been used to correct the latter disorders, an emerging approach is to use proteostasis regulators to fold mutated proteins to render them functional. Christopher M. Dobson, Jeffery W. Kelly, Dennis Selkoe, Stanley Pruisner, Peter T. Jeffery W Kelly (born August 23, 1960 in Medina New York) is the Dean of Graduate Studies and the Lita Annenberg Professor of Chemistry within the Lansbury, William E. Balch, Richard I. Morimoto, Susan L. Lindquist and Byron C. Caughey have all contributed to this emerging understanding of diseases that are some of the most menacing of our era.

Kinetics 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 proline isomerizations or wrong disulfide bond formations, and must pass through a number of intermediate states, like checkpoints, before the process is complete. ^[11] On the other hand, very small single-domain proteins with lengths of up to a hundred amino acids typically fold in a single step. A protein domain is a part of protein sequence and structure that can evolve, function and exist independently of the rest of the protein chain ^[12] Time scales of milliseconds are the norm and the very fastest known protein folding reactions are complete within a few microseconds. ^[13]

The Levinthal paradox^[14] observes 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). The Levinthal paradox is a Thought experiment in the theory of Protein folding dynamics A nanosecond ( ns) is one billionth of a second See also times of other orders of magnitude. To help compare Orders of magnitude of different Times this page lists times between 10&minus12 seconds and 10&minus11 seconds (1 Pico 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.

Techniques for studying protein folding

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, Sheena Radford, Chris Dobson, Sir Alan R. Fersht and Bengt Nölting. Harry Barkus Gray (b 14 November 1935 in Woodburn, Kentucky, U Sir Alan Roy Fersht FIC FRS (born April 21, 1943) is a British chemist distinguished for his pioneering work on protein folding Bengt Nölting (born May 1 1962) is a German physicist and biophysicist who pioneered various methods in Biophysics and engineering

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 1980s and early 1990s. In Physics, an energy landscape is a pair ( X, f) consisting of a Topological space X representing the physical states or parameters This approach introduced the principle of minimal frustration, which asserts that evolution has selected 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 selected 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 folding funnel hypothesis is a specific version of the Energy landscape theory of Protein folding, which assumes that a Protein 's Native state The theory is supported by both computational simulations of model proteins and numerous experimental studies, and it has been used to improve methods for protein structure prediction and design. Lattice proteins are highly simplified computer models of Proteins which are used to investigate Protein folding. Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. Protein design is the design of new Protein molecules from scratch or the deliberate design of a new molecule by making calculated variations on a known structure

Computational prediction of protein tertiary structure

De novo or ab initio techniques for computational protein structure prediction is related to, but strictly distinct from, studies involving protein folding. Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. Molecular Dynamics (MD) is an important tool for studying protein folding and dynamics in silico. Molecular dynamics ( MD) is a form of Computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of In Silico is the second full-length studio album by Australian Drum and bass band Pendulum, released in Australia and Because of computational cost, ab initio MD folding simulations with explicit water are limited to peptides and very small proteins. MD simulations of larger proteins remain restricted to dynamics of the experimental structure or its high-temperature unfolding. In order to simulate long time folding processes (beyond about 1 microsecond), like folding of small-size proteins (about 50 residues) or larger, some approximations or simplifications in protein models need to be introduced. An approach using reduced protein representation (pseudo-atoms representing groups of atoms are defined) and statistical potential is not only useful in protein structure prediction, but is also capable of reproducing the folding pathways. In Protein structure prediction, a statistical potential (also knowledge-based potential, empirical potential, or residue contact potential) Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. ^[15]

Because of the many possible ways of folding, there can be many possible structures. A peptide consisting of just five amino acids can fold into over 100 billion possible structures. ^[16]

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. X-ray crystallography is a method of determining the arrangement of Atoms within a Crystal, in which a beam of X-rays strikes a crystal and scatters Protein nuclear magnetic resonance spectroscopy (usually abbreviated protein NMR) is a field of Structural biology in which NMR spectroscopy is used One of the major areas of interest is the prediction of native structure from amino-acid sequences alone using bioinformatics and computational simulation methods. Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. Bioinformatics is the application of information technology to the field of molecular biology

There are distributed computing projects which use idle CPU time of personal computers to solve problems such as protein folding or prediction of protein structure. A Computer processor is described as idle when it is not being used by any program. People can run these programs on their computer or PlayStation 3 to support them. See links below (for example Folding@Home) to get information about how to participate in these projects. Folding@home (sometimes abbreviated as FAH or F@h) is a Distributed computing (DC project designed to perform computationally intensive simulations

See also

• Protein structure prediction
• Folding (chemistry)
• Anfinsen's dogma
• Levinthal paradox
• Denaturation (biochemistry)
• Protein design
• Molecular modelling
• Chevron plot
• Denaturation midpoint
• Equilibrium unfolding
• Folding@Home
• Downhill folding
• Foldit computer game

References

External links

• FoldIt - Folding Protein Game
• Folding@Home
• Rosetta@Home