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Protein

2007 Schools Wikipedia Selection. Related subjects: General Biology

   A representation of the 3D structure of myoglobin, showing coloured
   alpha helices. This protein was the first to have its structure solved
   by X-ray crystallography.
   Enlarge
   A representation of the 3D structure of myoglobin, showing coloured
   alpha helices. This protein was the first to have its structure solved
   by X-ray crystallography.

   Proteins are large organic compounds made of amino acids arranged in a
   linear chain and joined together between the carboxyl atom of one amino
   acid and the amine nitrogen of another. This bond is called a peptide
   bond. The sequence of amino acids in a protein is defined by a gene and
   encoded in the genetic code. Although this genetic code specifies 20
   "standard" amino acids, the residues in a protein are often chemically
   altered in post-translational modification: either before the protein
   can function in the cell, or as part of control mechanisms. Proteins
   can also work together to achieve a particular function, and they often
   associate to form stable complexes.

   Like other biological macromolecules such as polysaccharides and
   nucleic acids, proteins are essential parts of all living organisms and
   participate in every process within cells. Many proteins are enzymes
   that catalyze biochemical reactions, and are vital to metabolism. Other
   proteins have structural or mechanical functions, such as the proteins
   in the cytoskeleton, which forms a system of scaffolding that maintains
   cell shape. Proteins are also important in cell signaling, immune
   responses, cell adhesion, and the cell cycle. Protein is also a
   necessary component in our diet, since animals cannot synthesise all
   the amino acids and must obtain essential amino acids from food.
   Through the process of digestion, animals break down ingested protein
   into free amino acids that can be used for protein synthesis.

   The name protein comes from the Greek πρώτα ("prota"), meaning "of
   primary importance" and were first described and named by Jöns Jakob
   Berzelius in 1838. However, their central role in living organisms was
   not fully appreciated until 1926, when James B. Sumner showed that the
   enzyme urease was a protein. The first protein structures to be solved
   included insulin and myoglobin; the first was by Sir Frederick Sanger
   who won a 1958 Nobel Prize for it, and the second by Max Perutz and Sir
   John Cowdery Kendrew in 1958. Both proteins' three-dimensional
   structures were amongst the first determined by x-ray diffraction
   analysis; the myoglobin structure won the Nobel Prize in Chemistry for
   its discoverers.

Biochemistry

   Resonance structures of the peptide bond that links individual amino
   acids to form a protein polymer.
   Enlarge
   Resonance structures of the peptide bond that links individual amino
   acids to form a protein polymer.
   Section of a protein structure showing serine and alanine residues
   linked together by peptide bonds. Carbons are shown in white and
   hydrogens are omitted for clarity.
   Enlarge
   Section of a protein structure showing serine and alanine residues
   linked together by peptide bonds. Carbons are shown in white and
   hydrogens are omitted for clarity.

   Proteins are linear polymers built from 20 different L-alpha- amino
   acids. All amino acids share common structural features including an
   alpha carbon to which an amino group, a carboxyl group, and a variable
   side chain are bonded. Only proline shows little difference in a
   fashion by containing an unusual ring to the N-end amine group, which
   forces the CO-NH amide sequence into a fixed conformation. The side
   chains of the standard amino acids, detailed in the list of standard
   amino acids, have varying chemical properties that produce proteins'
   three-dimensional structure and are therefore critical to protein
   function. The amino acids in a polypeptide chain are linked by peptide
   bonds formed in a dehydration reaction. Once linked in the protein
   chain, an individual amino acid is called a residue and the linked
   series of carbon, nitrogen, and oxygen atoms are known as the main
   chain or protein backbone. The peptide bond has two resonance forms
   that contribute some double bond character and inhibit rotation around
   its axis, so that the alpha carbons are roughly coplanar. The other two
   dihedral angles in the peptide bond determine the local shape assumed
   by the protein backbone.

   Due to the chemical structure of the individual amino acids, the
   protein chain has directionality. The end of the protein with a free
   carboxyl group is known as the C-terminus or carboxy terminus, while
   the end with a free amino group is known as the N-terminus or amino
   terminus.

   There is some ambiguity between the usage of the words protein,
   polypeptide, and peptide. Protein is generally used to refer to the
   complete biological molecule in a stable conformation, while peptide is
   generally reserved for a short amino acid oligomers often lacking a
   stable 3-dimensional structure. However, the boundary between the two
   is ill-defined and usually lies near 20-30 residues. Polypeptide can
   refer to any single linear chain of amino acids, usually regardless of
   length, but often implies an absence of a single defined conformation.

Synthesis

   Proteins are assembled from amino acids using information encoded in
   genes. Each protein has its own unique amino acid sequence that is
   specified by the nucleotide sequence of the gene encoding this protein.
   The genetic code is a set of three-nucleotide sets called codons and
   each three-nucleotide combination stands for an amino acid, for example
   ATG stands for methionine. Because DNA contains four nucleotides, the
   total number of possible codons is 64; hence, there is some redundancy
   in the genetic code and some amino acids are specified by more than one
   codon. Genes encoded in DNA are first transcribed into pre- messenger
   RNA (mRNA) by proteins such as RNA polymerase. Most organisms then
   process the pre-mRNA (also known as a primary transcript) using various
   forms of post-transcriptional modification to form the mature mRNA,
   which is then used as a template for protein synthesis by the ribosome.
   In prokaryotes the mRNA may either be used as soon as it is produced,
   or be bound by a ribosome after having moved away from the nucleoid. In
   contrast, eukaryotes make mRNA in the cell nucleus and then translocate
   it across the nuclear membrane into the cytoplasm, where protein
   synthesis then takes place. The rate of protein synthesis is higher in
   prokaryotes than eukaryotes and can reach up to 20 amino acids per
   second.

   The process of synthesizing a protein from an mRNA template is known as
   translation. The mRNA is loaded onto the ribosome and is read three
   nucleotides at a time by matching each codon to its base pairing
   anticodon located on a transfer RNA molecule, which carries the amino
   acid corresponding to the codon it recognizes. The enzyme aminoacyl
   tRNA synthetase "charges" the tRNA molecules with the correct amino
   acids. The growing polypeptide is often termed the nascent chain.
   Proteins are always biosynthesized from N-terminus to C-terminus.

   The size of a synthesized protein can be measured by the number of
   amino acids it contains and by its total molecular mass, which is
   normally reported in units of daltons (synonymous with atomic mass
   units), or the derivative unit kilodalton (kDa). Yeast proteins are on
   average 466 amino acids long and 53 kDa in mass. The largest known
   proteins are the titins, a component of the muscle sarcomere, with a
   molecular mass of almost 3,000 kDa and a total length of almost 27,000
   amino acids.

Chemical synthesis

   Short proteins can also be synthesized chemically in the laboratory by
   a family of methods known as peptide synthesis, which rely on organic
   synthesis techniques such as chemical ligation to produce peptides in
   high yield. Chemical synthesis allows for the introduction of
   non-natural amino acids into polypeptide chains, such as attachment of
   fluorescent probes to amino acid side chains. These methods are useful
   in laboratory biochemistry and cell biology, though generally not for
   commercial applications. Chemical synthesis is inefficient for
   polypeptides longer than about 300 amino acids, and the synthesized
   proteins may not readily assume their native tertiary structure. Most
   chemical synthesis methods proceed from C-terminus to N-terminus,
   opposite the biological reaction.

Structure of proteins

   Three possible representations of the three-dimensional structure of
   the protein triose phosphate isomerase. Left: all-atom representation
   colored by atom type. Middle: "cartoon" representation illustrating the
   backbone conformation, colored by secondary structure. Right:
   Solvent-accessible surface representation colored by residue type
   (acidic residues red, basic residues blue, polar residues green,
   nonpolar residues white).
   Enlarge
   Three possible representations of the three-dimensional structure of
   the protein triose phosphate isomerase. Left: all-atom representation
   colored by atom type. Middle: "cartoon" representation illustrating the
   backbone conformation, colored by secondary structure. Right:
   Solvent-accessible surface representation colored by residue type
   (acidic residues red, basic residues blue, polar residues green,
   nonpolar residues white).

   Most proteins fold into unique 3-dimensional structures. The shape into
   which a protein naturally folds is known as its native state. Although
   many proteins can fold unassisted simply through the structural
   propensities of their component amino acids, others require the aid of
   molecular chaperones to efficiently fold to their native states.
   Biochemists often refer to four distinct aspects of a protein's
   structure:
     * Primary structure: the amino acid sequence
     * Secondary structure: regularly repeating local structures
       stabilized by hydrogen bonds. The most common examples are the
       alpha helix and beta sheet. Because secondary structures are local,
       many regions of different secondary structure can be present in the
       same protein molecule.
     * Tertiary structure: the overall shape of a single protein molecule;
       the spatial relationship of the secondary structures to one
       another. Tertiary structure is generally stabilized by nonlocal
       interactions, most commonly the formation of a hydrophobic core,
       but also through salt bridges, hydrogen bonds, disulfide bonds, and
       even post-translational modifications. The term "tertiary
       structure" is often used as synonymous with the term fold.
     * Quaternary structure: the shape or structure that results from the
       interaction of more than one protein molecule, usually called
       protein subunits in this context, which function as part of the
       larger assembly or protein complex.

   In addition to these levels of structure, proteins may shift between
   several related structures in performing their biological function. In
   the context of these functional rearrangements, these tertiary or
   quaternary structures are usually referred to as " conformations," and
   transitions between them are called conformational changes. Such
   changes are often induced by the binding of a substrate molecule to an
   enzyme's active site, or the physical region of the protein that
   participates in chemical catalysis.
   Molecular surface of several proteins showing their comparative sizes.
   From left to right are: Antibody (IgG), Hemoglobin, Insulin (a
   hormone), Adenylate kinase (an enzyme), and Glutamine synthetase (an
   enzyme).
   Enlarge
   Molecular surface of several proteins showing their comparative sizes.
   From left to right are: Antibody (IgG), Hemoglobin, Insulin (a
   hormone), Adenylate kinase (an enzyme), and Glutamine synthetase (an
   enzyme).

   Proteins can be informally divided into three main classes, which
   correlate with typical tertiary structures: globular proteins, fibrous
   proteins, and membrane proteins. Almost all globular proteins are
   soluble and many are enzymes. Fibrous proteins are often structural;
   membrane proteins often serve as receptors or provide channels for
   polar or charged molecules to pass through the cell membrane.

   A special case of intramolecular hydrogen bonds within proteins, poorly
   shielded from water attack and hence promoting their own dehydration,
   are called dehydrons.

Structure determination

   Discovering the tertiary structure of a protein, or the quaternary
   structure of its complexes, can provide important clues about how the
   protein performs its function. Common experimental methods of structure
   determination include X-ray crystallography and NMR spectroscopy, both
   of which can produce information at atomic resolution. Cryoelectron
   microscopy is used to produce lower-resolution structural information
   about very large protein complexes, including assembled viruses; a
   variant known as electron crystallography can also produce
   high-resolution information in some cases, especially for
   two-dimensional crystals of membrane proteins. Solved structures are
   usually deposited in the Protein Data Bank (PDB), a freely available
   resource from which structural data about thousands of proteins can be
   obtained in the form of Cartesian coordinates for each atom in the
   protein.

   There are many more known gene sequences than there are solved protein
   structures. Further, the set of solved structures is biased toward
   those proteins that can be easily subjected to the experimental
   conditions required by one of the major structure determination
   methods. In particular, globular proteins are comparatively easy to
   crystallize in preparation for X-ray crystallography, which remains the
   oldest and most common structure determination technique. Membrane
   proteins, by contrast, are difficult to crystallize and are
   underrepresented in the PDB. Structural genomics initiatives have
   attempted to remedy these deficiencies by systematically solving
   representative structures of major fold classes. Protein structure
   prediction methods attempt to provide a means of generating a plausible
   structure for a proteins whose structures have not been experimentally
   determined.

Cellular functions

   Proteins are the chief actors within the cell, said to be carrying out
   the duties specified by the information encoded in genes. With the
   exception of certain types of RNA, most other biological molecules are
   relatively inert elements upon which proteins act. Proteins make up
   half the dry weight of an E. coli cell, while other macromolecules such
   as DNA and RNA make up only 3% and 20% respectively. The total
   complement of proteins expressed in a particular cell or cell type is
   known as its proteome.
   The enzyme hexokinase is shown as a simple ball-and-stick molecular
   model. To scale in the top right-hand corner are its two substrates,
   ATP and glucose.
   Enlarge
   The enzyme hexokinase is shown as a simple ball-and-stick molecular
   model. To scale in the top right-hand corner are its two substrates,
   ATP and glucose.

   The chief characteristic of proteins that enables them to carry out
   their diverse cellular functions is their ability to bind other
   molecules specifically and tightly. The region of the protein
   responsible for binding another molecule is known as the binding site
   and is often a depression or "pocket" on the molecular surface. This
   binding ability is mediated by the tertiary structure of the protein,
   which defines the binding site pocket, and by the chemical properties
   of the surrounding amino acids' side chains. Protein binding can be
   extraordinarily tight and specific; for example, the ribonuclease
   inhibitor protein binds to human angiogenin with a sub-femtomolar
   dissociation constant (<10^-15 M) but does not bind at all to its
   amphibian homolog onconase (>1 M). Extremely minor chemical changes
   such as the addition of a single methyl group to a binding partner can
   sometimes suffice to nearly eliminate binding; for example, the
   aminoacyl tRNA synthetase specific to the amino acid valine
   discriminates against the very similar side chain of the amino acid
   isoleucine.

   Proteins can bind to other proteins as well as to small-molecule
   substrates. When proteins bind specifically to other copies of the same
   molecule, they can oligomerize to form fibrils; this process occurs
   often in structural proteins that consist of globular monomers that
   self-associate to form rigid fibers. Protein-protein interactions also
   regulate enzymatic activity, control progression through the cell
   cycle, and allow the assembly of large protein complexes that carry out
   many closely related reactions with a common biological function.
   Proteins can also bind to, or even be integrated into, cell membranes.
   The ability of binding partners to induce conformational changes in
   proteins allows the construction of enormously complex signaling
   networks.

Enzymes

   The best-known role of proteins in the cell is their duty as enzymes,
   which catalyze chemical reactions. Enzymes are usually highly specific
   catalysts that accelerate only one or a few chemical reactions. Enzymes
   effect most of the reactions involved in metabolism and catabolism as
   well as DNA replication, DNA repair, and RNA synthesis. Some enzymes
   act on other proteins to add or remove chemical groups in a process
   known as post-translational modification. About 4,000 reactions are
   known to be catalyzed by enzymes. The rate acceleration conferred by
   enzymatic catalysis is often enormous - as much as 10^17-fold increase
   in rate over the uncatalyzed reaction in the case of orotate
   decarboxylase.

   The molecules bound and acted upon by enzymes are known as substrates.
   Although enzymes can consist of hundreds of amino acids, it is usually
   only a small fraction of the residues that come in contact with the
   substrate. and an even smaller fraction - 3-4 residues on average -
   that are directly involved in catalysis. The region of the enzyme that
   binds the substrate and contains the catalytic residues is known as the
   active site.

Cell signalling and ligand transport

   A mouse antibody against cholera that binds a carbohydrate antigen.
   Enlarge
   A mouse antibody against cholera that binds a carbohydrate antigen.

   Many proteins are involved in the process of cell signaling and signal
   transduction. Some proteins, such as insulin, are extracellular
   proteins that transmit a signal from the cell in which they were
   synthesized to other cells in distant tissues. Others are membrane
   proteins that act as receptors whose main function is to bind a
   signaling molecule and induce a biochemical response in the cell. Many
   receptors are membrane proteins that have a binding site exposed on the
   cell surface and an effector domain within the cell, which may have
   enzymatic activity or may undergo a conformational change detected by
   other proteins within the cell.

   Antibodies are protein components of adaptive immune system whose main
   function is to bind antigens, or foreign substances in the body, and
   target them for destruction. Antibodies can be secreted into the
   extracellular environment or anchored in the membranes of specialized B
   cells known as plasma cells. While enzymes are limited in their binding
   affinity for their substrates by the necessity of conducting their
   reaction, antibodies have no such constraints. An antibody's binding
   affinity to its target is extraordinarily high.

   Many ligand transport proteins bind particular small biomolecules and
   transport them to other locations in the body of a multicellular
   organism. These proteins must have a high binding affinity when their
   ligand is present in high concentrations but must also release the
   ligand when it is present at low concentrations in the target tissues.
   The canonical example of a ligand-binding protein is haemoglobin, which
   transports oxygen from the lungs to other organs and tissues in all
   vertebrates and has close homologs in every biological kingdom.

   Transmembrane proteins can also serve as ligand transport proteins that
   alter the permeability of the cell's membrane to small molecules and
   ions. The membrane alone has a hydrophobic core through which polar or
   charged molecules cannot diffuse. Membrane proteins contain internal
   channels that allow such molecules to enter and exit the cell. Many ion
   channel proteins are specialized to select for only a particular ion;
   for example, potassium and sodium channels often discriminate for only
   one of the two ions.

Structural proteins

   Structural proteins confer stiffness and rigidity to otherwise fluid
   biological components. Most structural proteins are fibrous proteins;
   for example, actin and tubulin are globular and soluble as monomers but
   polymerize to form long, stiff fibers that comprise the cytoskeleton,
   which allows the cell to maintain its shape and size. Collagen and
   elastin are critical components of connective tissue such as cartilage,
   and keratin is found in hard or filamentous structures such as hair,
   nails, feathers, hooves, and some animal shells.

   Other proteins that serve structural functions are motor proteins such
   as myosin, kinesin, and dynein, which are capable of generating
   mechanical forces. These proteins are crucial for cellular motility of
   single-celled organisms and the sperm of many sexually reproducing
   multicellular organisms. They also generate the forces exerted by
   contracting muscles.

Methods of study

   As some of the most commonly studied biological molecules, the
   activities and structures of proteins are examined both in vitro and in
   vivo. In vitro studies of purified proteins in controlled environments
   are useful for learning how a protein carries out its function: for
   example, enzyme kinetics studies explore the chemical mechanism of an
   enzyme's catalytic activity and its relative affinity for various
   possible substrate molecules. By contrast, in vivo experiments on
   proteins' activities within cells or even within whole organisms can
   provide complementary information about where a protein functions and
   how it is regulated.

Protein purification

   In order to perform in vitro analyses, a protein must be purified away
   from other cellular components. This process usually begins with cell
   lysis, in which a cell's membrane is disrupted and its internal
   contents released into a solution known as a crude lysate. The
   resulting mixture can be purified using ultracentrifugation, which
   fractionates the various cellular components into fractions containing
   soluble proteins; membrane lipids and proteins; cellular organelles,
   and nucleic acids. Precipitation by a method known as salting out can
   concentrate the proteins from this lysate. Various types of
   chromatography are then used to isolate the protein or proteins of
   interest based on properties such as molecular weight, net charge and
   binding affinity. The level of purification can be monitored using gel
   electrophoresis if the desired protein's molecular weight is known, by
   spectroscopy if the protein has distinguishable spectroscopic features,
   or by enzyme assays if the protein has enzymatic activity.

   For natural proteins, a series of purification steps may be necessary
   to obtain protein sufficiently pure for laboratory applications. To
   simplify this process, genetic engineering is often used to add
   chemical features to proteins that make them easier to purify without
   affecting their structure or activity. Here, a "tag" consisting of a
   specific amino acid sequence, often a series of histidine residues (a "
   His-tag"), is attached to one terminus of the protein. As a result,
   when the lysate is passed over a chromatography column containing
   nickel, the histidine residues ligate the nickel and attach to the
   column while the untagged components of the lysate pass unimpeded.

Cellular localization

   Proteins in different cellular compartments and structures tagged with
   green fluorescent protein.
   Enlarge
   Proteins in different cellular compartments and structures tagged with
   green fluorescent protein.

   The study of proteins in vivo is often concerned with the synthesis and
   localization of the protein within the cell. Although many
   intracellular proteins are synthesized in the cytoplasm and
   membrane-bound or secreted proteins in the endoplasmic reticulum, the
   specifics of how proteins are targeted to specific organelles or
   cellular structures is often unclear. A useful technique for assessing
   cellular localization uses genetic engineering to express in a cell a
   fusion protein or chimera consisting of the natural protein of interest
   linked to a " reporter" such as green fluorescent protein (GFP). The
   fused protein's position within the cell can be cleanly and efficiently
   visualized using microscopy, as shown in the figure opposite.

   Through another genetic engineering application known as site-directed
   mutagenesis, researchers can alter the protein sequence and hence its
   structure, cellular localization, and susceptibility to regulation,
   which can be followed in vivo by GFP tagging or in vitro by enzyme
   kinetics and binding studies.

Proteomics and bioinformatics

   The total complement of proteins present in a cell or cell type is
   known as its proteome, and the study of such large-scale data sets
   defines the field of proteomics, named by analogy to the related field
   of genomics. Key experimental techniques in proteomics include protein
   microarrays, which allow the detection of the relative levels of a
   large number of proteins present in a cell, and two-hybrid screening,
   which allows the systematic exploration of protein-protein
   interactions. The total complement of biologically possible such
   interactions is known as the interactome. A systematic attempt to
   determine the structures of proteins representing every possible fold
   is known as structural genomics.

   The large amount of genomic and proteomic data available for a variety
   of organisms, including the human genome, allows researchers to
   efficiently identify homologous proteins in distantly related organisms
   by sequence alignment. Sequence profiling tools can perform more
   specific sequence manipulations such as restriction enzyme maps, open
   reading frame analyses for nucleotide sequences, and secondary
   structure prediction. From this data phylogenetic trees can be
   constructed and evolutionary hypotheses developed using special
   software like ClustalW regarding the ancestry of modern organisms and
   the genes they express. The field of bioinformatics seeks to assemble,
   annotate, and analyze genomic and proteomic data, applying
   computational techniques to biological problems such as gene finding
   and cladistics.

Structure prediction and simulation

   Complementary to the field of structural genomics, protein structure
   prediction seeks to develop efficient ways to provide plausible models
   for proteins whose structures have not yet been determined
   experimentally. The most successful type of structure prediction, known
   as homology modeling, relies on the existence of a "template" structure
   with sequence similarity to the protein being modeled; structural
   genomics' goal is to provide sufficient representation in solved
   structures to model most of those that remain. Although producing
   accurate models remains a challenge when only distantly related
   template structures are available, it has been suggested that sequence
   alignment is the bottleneck in this process, as quite accurate models
   can be produced if a "perfect" sequence alignment is known. Many
   structure prediction methods have served to inform the emerging field
   of protein engineering, in which novel protein folds have already been
   designed. A more complex computational problem is the prediction of
   intermolecular interactions, such as in molecular docking and
   protein-protein interaction prediction.

   The processes of protein folding and binding can be simulated using
   techniques derived from molecular dynamics, which increasingly take
   advantage of distributed computing as in the Folding@Home project. The
   folding of small alpha-helical protein domains such as the villin
   headpiece and the HIV accessory protein have been successfully
   simulated in silico, and hybrid methods that combine standard molecular
   dynamics with quantum mechanics calculations have allowed exploration
   of the electronic states of rhodopsins.

Nutrition

   Most microorganisms and plants can biosynthesize all 20 standard amino
   acids, while animals must obtain some of the amino acids from the diet.
   Key enzymes in the biosynthetic pathways that synthesize certain amino
   acids - such as aspartokinase, which catalyzes the first step in the
   synthesis of lysine, methionine, and threonine from aspartate - are not
   present in animals. The amino acids that an organism cannot synthesize
   on its own are referred to as essential amino acids. (This designation
   is often used to specifically identify those essential to humans.) If
   amino acids are present in the environment, most microorganisms can
   conserve energy by taking up the amino acids from the environment and
   downregulating their own biosynthetic pathways. Bacteria are often
   engineered in the laboratory to lack the genes necessary for
   synthesizing a particular amino acid, providing a selectable marker for
   the success of transfection, or the introduction of foreign DNA.

   In animals, amino acids are obtained through the consumption of foods
   containing protein. Ingested proteins are broken down through
   digestion, which typically involves denaturation of the protein through
   exposure to acid and degradation by the action of enzymes called
   proteases. Ingestion of essential amino acids is critical to the health
   of the organism, since the biosynthesis of proteins that include these
   amino acids is inhibited by their low concentration. Amino acids are
   also an important dietary source of nitrogen. Some ingested amino
   acids, especially those that are not essential, are not used directly
   for protein biosynthesis. Instead, they are converted to carbohydrates
   through gluconeogenesis, which is also used under starvation conditions
   to generate glucose from the body's own proteins, particularly those
   found in muscle.

History

   Proteins were recognized as a distinct class of biological molecules in
   the eighteenth century by Antoine Fourcroy and others. Members of this
   class (called the "albuminoids", Eiweisskörper, or matières
   albuminoides) were recognized by their ability to coagulate or
   flocculate under various treatments such as heat or acid; well-known
   examples at the start of the nineteenth century included albumen from
   egg whites, blood serum albumin, fibrin, and wheat gluten. The
   similarity between the cooking of egg whites and the curdling of milk
   was recognized even in ancient times; for example, the name albumen for
   the egg-white protein was coined by Pliny the Elder from the Latin
   albus ovi (egg white).

   With the advice of Jöns Jakob Berzelius, the Dutch chemist Gerhardus
   Johannes Mulder carried out elemental analyses of common animal and
   plant proteins. To everyone's surprise, all proteins had nearly the
   same empirical formula, roughly C[400]H[620]N[100]O[120] with
   individual sulfur and phosphorus atoms. Mulder published his findings
   in two papers (1837,1838) and hypothesized that there was one basic
   substance (Grundstoff) of proteins, and that it was synthesized by
   plants and absorbed from them by animals in digestion. Berzelius was an
   early proponent of this theory and proposed the name "protein" for this
   substance in a letter dated 10 July 1838

     The name protein that I propose for the organic oxide of fibrin and
     albumin, I wanted to derive from [the Greek word] πρωτειος, because
     it appears to be the primitive or principal substance of animal
     nutrition.

   Mulder went on to identify the products of protein degradation such as
   the amino acid, leucine, for which he found a (nearly correct)
   molecular weight of 131 Da.

   The minimum molecular weight suggested by Mulder's analyses was roughly
   9 kDa, hundreds of times larger than other molecules being studied.
   Hence, the chemical structure of proteins (their primary structure) was
   an active area of research until 1949, when Fred Sanger sequenced
   insulin. The (correct) theory that proteins were linear polymers of
   amino acids linked by peptide bonds was proposed independently and
   simultaneously by Franz Hofmeister and Emil Fischer at the same
   conference in 1902. However, some scientists were sceptical that such
   long macromolecules could be stable in solution. Consequently, numerous
   alternative theories of the protein primary structure were proposed,
   e.g., the colloidal hypothesis that proteins were assemblies of small
   molecules, the cyclol hypothesis of Dorothy Wrinch, the
   diketopiperazine hypothesis of Emil Abderhalden and the
   pyrrol/piperidine hypothesis of Troensgard (1942). Most of these
   theories had difficulties in accounting for the fact that the digestion
   of proteins yielded peptides and amino acids. Proteins were finally
   shown to be macromolecules of well-defined composition (and not
   colloidal mixtures) by Theodor Svedberg using analytical
   ultracentrifugation. The possibility that some proteins are
   non-covalent associations of such macromolecules was shown by Gilbert
   Smithson Adair (by measuring the osmotic pressure of hemoglobin) and,
   later, by Frederic M. Richards in his studies of ribonuclease S. The
   mass spectrometry of proteins has long been a useful technique for
   identifying posttranslational modifications and, more recently, for
   probing protein structure.

   Most proteins are difficult to purify in more than milligram
   quantities, even using the most modern methods. Hence, early studies
   focused on proteins that could be purified in large quantities, e.g.,
   those of blood, egg white, various toxins, and digestive/metabolic
   enzymes obtained from slaughterhouses. Many techniques of protein
   purification were developed during World War II in a project led by
   Edwin Joseph Cohn to purify blood proteins to help keep soldiers alive.
   In the late 1950's, the Armour Hot Dog Co. purified 1 kg (= one million
   milligrams) of pure bovine pancreatic ribonuclease A and made it freely
   available to scientists around the world. This generous act made RNase
   A the main protein for basic research for the next few decades,
   resulting in several Nobel Prizes.

   The study of protein folding began in 1910 with a famous paper by
   Henrietta Chick and C. J. Martin, in which they showed that the
   flocculation of a protein was composed of two distinct processes: the
   precipitation of a protein from solution was preceded by another
   process called denaturation, in which the protein became much less
   soluble, lost its enzymatic activity and became more chemically
   reactive. In the mid-1920's, Tim Anson and Alfred Mirsky proposed that
   denaturation was a reversible process, a correct hypothesis that was
   initially lampooned by some scientists as "unboiling the egg". Anson
   also suggested that denaturation was a two-state ("all-or-none")
   process, in which one fundamental molecular transition resulted in the
   drastic changes in solubility, enzymatic activity and chemical
   reactivity; he further noted that the free energy changes upon
   denaturation were much smaller than those typically involved in
   chemical reactions. In 1929, Hsien Wu hypothesized that denaturation
   was protein folding, a purely conformational change that resulted in
   the exposure of amino acid side chains to the solvent. According to
   this (correct) hypothesis, exposure of aliphatic and reactive side
   chains to solvent rendered the protein less soluble and more reactive,
   whereas the loss of a specific conformation caused the loss of
   enzymatic activity. Although considered plausible, Wu's hypothesis was
   not immediately accepted, since so little was known of protein
   structure and enzymology and other factors could account for the
   changes in solubility, enzymatic activity and chemical reactivity. In
   the early 1960's, Chris Anfinsen showed that the folding of
   ribonuclease A was fully reversible with no external cofactors needed,
   verifying the "thermodynamic hypothesis" of protein folding that the
   folded state represents the global minimum of free energy for the
   protein.

   The hypothesis of protein folding was followed by research into the
   physical interactions that stabilize folded protein structures. The
   crucial role of hydrophobic interactions was hypothesized by Dorothy
   Wrinch and Irving Langmuir, as a mechanism that might stabilize her
   cyclol structures. Although supported by J. D. Bernal and others, this
   (correct) hypothesis was rejected along with the cyclol hypothesis,
   which was disproven in the 1930's by Linus Pauling (among others).
   Instead, Pauling championed the idea that protein structure was
   stabilized mainly by hydrogen bonds, an idea advanced initially by
   William Astbury (1933). Remarkably, Pauling's incorrect theory about
   H-bonds resulted in his correct models for the secondary structure
   elements of proteins, the alpha helix and the beta sheet. The
   hydrophobic interaction was restored to its correct prominence by a
   famous article in 1959 by Walter Kauzman on denaturation, based partly
   on work by Kaj Linderstrom-Lang. The ionic nature of proteins was
   demonstrated by Bjerrum, Weber and Arne Tiselius, but Linderstrom-Lang
   showed that the charges were generally accessible to solvent and not
   bound to each other (1949).

   The secondary and low-resolution tertiary structure of globular
   proteins was investigated initially by hydrodynamic methods, such as
   analytical ultracentrifugation and flow birefringence. Spectroscopic
   methods to probe protein structure (such as circular dichroism,
   fluorescence, near-ultraviolet and infrared absorbance) were developed
   in the 1950's. The first atomic-resolution structures of proteins were
   solved by X-ray crystallography in the 1960's and by NMR in the 1980's.
   As of 2006, the Protein Data Bank has nearly 40,000 atomic-resolution
   structures of proteins. In more recent times, cryo-electron microscopy
   of large macromolecular assemblies and computational protein structure
   prediction of small protein domains are two methods approaching atomic
   resolution.

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