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Classification
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Biochemistry

Synthesis

Structure

Cellular functions

Methods of study

Digestion

Mechanical properties

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From Wikipedia, the free encyclopedia

This article is about a class of molecules. For protein as a nutrient, see Protein (nutrient). For
other uses, see Protein (disambiguation).
 A representation of the 3D structure of the protein
myoglobin showing turquoise α-helices. This protein was the first to have its structure solved
by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called
a heme group (shown in gray) with a bound oxygen molecule (red).

Proteins are large biomolecules and macromolecules that comprise one or more long chains
of amino acid residues. Proteins perform a vast array of functions within organisms,
including catalysing metabolic reactions, DNA replication, responding to stimuli, providing
structure to cells and organisms, and transporting molecules from one location to another.
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 3D structure that determines its activity.

A linear chain of amino acid residues is called a polypeptide. A protein contains at least one
long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely
considered to be proteins and are commonly called peptides. The individual amino acid
residues are bonded together by peptide bonds and adjacent amino acid residues. The
sequence of amino acid residues in a protein is defined by the sequence of a gene, which is
encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids;
but in certain organisms the genetic code can include selenocysteine and—in certain archaea
—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often
chemically modified by post-translational modification, which alters the physical and
chemical properties, folding, stability, activity, and ultimately, the function of the proteins.
Some proteins have non-peptide groups attached, which can be called prosthetic groups or
cofactors. Proteins can work together to achieve a particular function, and they often
associate to form stable protein complexes.

Once formed, proteins only exist for a certain period and are then degraded and recycled by
the cell's machinery through the process of protein turnover. A protein's lifespan is measured
in terms of its half-life and covers a wide range. They can exist for minutes or years with an
average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are
degraded more rapidly either due to being targeted for destruction or due to being unstable.

Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are
essential parts of organisms and participate in virtually every process within cells. Many
proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Some
proteins have structural or mechanical functions, such as actin and myosin in muscle, and the
cytoskeleton's scaffolding proteins that maintain cell shape. Other proteins are important in
cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are
needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion
breaks the proteins down for metabolic use.

History and etymology

Further information: History of molecular biology

Discovery and early studies

Proteins have been studied and recognized since the 1700s by Antoine Fourcroy and others,[1]
[2]
who often collectively called them "albumins", or "albuminous materials" (Eiweisskörper,
in German).[2] Gluten, for example, was first separated from wheat in published research
around 1747, and later determined to exist in many plants.[1] In 1789, Antoine Fourcroy
recognized three distinct varieties of animal proteins: albumin, fibrin, and gelatin.[3]
Vegetable (plant) proteins studied in the late 1700s and early 1800s included gluten, plant
albumin, gliadin, and legumin.[1]

Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by
the Swedish chemist Jöns Jacob Berzelius in 1838.[4][5] Mulder carried out elemental analysis
of common proteins and found that nearly all proteins had the same empirical formula,
C400H620N100O120P1S1.[6] He came to the erroneous conclusion that they might be composed of a
single type of (very large) molecule. The term "protein" to describe these molecules was
proposed by Mulder's associate Berzelius; protein is derived from the Greek word πρώτειος
(proteios), meaning "primary",[7] "in the lead", or "standing in front",[2] + -in. 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.[6]

Early nutritional scientists such as the German Carl von Voit believed that protein was the
most important nutrient for maintaining the structure of the body, because it was generally
believed that "flesh makes flesh".[8] Around 1862, Karl Heinrich Ritthausen isolated the
amino acid glutamic acid.[9] Thomas Burr Osborne compiled a detailed review of the
vegetable proteins at the Connecticut Agricultural Experiment Station. Osborne, alongside
Lafayette Mendel, established several nutritionally essential amino acids in feeding
experiments with laboratory rats.[10] Diets lacking an essential amino acid stunts the rats'
growth, consistent with Liebig's law of the minimum.[11] The final essential amino acid to be
discovered, threonine, was identified by William Cumming Rose.[12]

The difficulty in purifying proteins impeded work by early protein biochemists. Proteins
could be obtained in large quantities from blood, egg whites, and keratin, but individual
proteins were unavailable. In the 1950s, the Armour Hot Dog Company purified 1 kg of
bovine pancreatic ribonuclease A and made it freely available to scientists. This gesture
helped ribonuclease A become a major target for biochemical study for the following
decades.[6]

Polypeptides
 polypeptide

The understanding of proteins as polypeptides, or chains of amino acids, came through the
work of Franz Hofmeister and Hermann Emil Fischer in 1902.[13][14] The central role of
proteins as enzymes in living organisms that catalyzed reactions was not fully appreciated
until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein.[15]

Linus Pauling is credited with the successful prediction of regular protein secondary
structures based on hydrogen bonding, an idea first put forth by William Astbury in 1933.[16]
Later work by Walter Kauzmann on denaturation,[17][18] based partly on previous studies by
Kaj Linderstrøm-Lang,[19] contributed an understanding of protein folding and structure
mediated by hydrophobic interactions.[20]

The first protein to have its amino acid chain sequenced was insulin, by Frederick Sanger, in
1949. Sanger correctly determined the amino acid sequence of insulin, thus conclusively
demonstrating that proteins consisted of linear polymers of amino acids rather than branched
chains, colloids, or cyclols.[21] He won the Nobel Prize for this achievement in 1958.[22]
Christian Anfinsen's studies of the oxidative folding process of ribonuclease A, for which he
won the nobel prize in 1972, solidified the thermodynamic hypothesis of protein folding,
according to which the folded form of a protein represents its free energy minimum.[23][24]

Structure

John Kendrew with model of myoglobin in

progress

With the development of X-ray crystallography, it became possible to determine protein

structures as well as their sequences.[25] The first protein structures to be solved were
hemoglobin by Max Perutz and myoglobin by John Kendrew, in 1958.[26][27] The use of
computers and increasing computing power has supported the sequencing of complex
proteins. In 1999, Roger Kornberg sequenced the highly complex structure of RNA
polymerase using high intensity X-rays from synchrotrons.[25]

Since then, cryo-electron microscopy (cryo-EM) of large macromolecular assemblies[28] has

been developed. Cryo-EM uses protein samples that are frozen rather than crystals, and
beams of electrons rather than X-rays. It causes less damage to the sample, allowing scientists
to obtain more information and analyze larger structures.[25] Computational protein structure
prediction of small protein structural domains[29] has helped researchers to approach atomic-
level resolution of protein structures. As of April 2024, the Protein Data Bank contains
181,018 X-ray, 19,809 EM and 12,697 NMR protein structures.[30]

Classification
Main articles: Protein family, Gene Ontology, and Enzyme Commission number

Proteins are primarily classified by sequence and structure, although other classifications are
commonly used. Especially for enzymes the EC number system provides a functional
classification scheme.[31] Similarly, gene ontology classifies both genes and proteins by their
biological and biochemical function, and by their intracellular location.[32]

Sequence similarity is used to classify proteins both in terms of evolutionary and functional
similarity. This may use either whole proteins or protein domains, especially in multi-domain
proteins. Protein domains allow protein classification by a combination of sequence, structure
and function, and they can be combined in many ways. In an early study of 170,000 proteins,
about two-thirds were assigned at least one domain, with larger proteins containing more
domains (e.g. proteins larger than 600 amino acids having an average of more than 5
domains).[33]

Biochemistry

Chemical structure of the peptide bond

(bottom) and the three-dimensional structure of a peptide bond between an alanine and an
adjacent amino acid (top/inset). The bond itself is made of the CHON elements.
 Resonance structures of the peptide
bond that links individual amino acids to form a protein polymer
Main articles: Biochemistry, Amino acid, and Peptide bond

Most proteins consist of linear polymers built from series of up to 20 L-α-amino acids. All
proteinogenic amino acids have a common structure where an α-carbon is bonded to an
amino group, a carboxyl group, and a variable side chain. Only proline differs from this basic
structure as its side chain is cyclical, bonding to the amino group, limiting protein chain
flexibility.[34] The side chains of the standard amino acids have a variety of chemical
structures and properties, and it is the combined effect of all amino acids that determines its
three-dimensional structure and chemical reactivity.[35]

The amino acids in a polypeptide chain are linked by peptide bonds between amino and
carboxyl group. An individual amino acid in a chain is called a residue, and the linked series
of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone.[36]: 19
The peptide bond has two resonance forms that confer some double-bond character to the
backbone. The alpha carbons are roughly coplanar with the nitrogen and the carbonyl (C=O)
group. The other two dihedral angles in the peptide bond determine the local shape assumed
by the protein backbone. One consequence of the N-C(O) double bond character is that
proteins are somewhat rigid.[36]: 31 A polypeptide chain ends with a free amino group, known
as the N-terminus or amino terminus, and a free carboxyl group, known as the C-terminus or
carboxy terminus.[37] By convention, peptide sequences are written N-terminus to C-terminus,
correlating with the order in which proteins are synthesized by ribosomes.[37][38]

The words protein, polypeptide, and peptide are a little ambiguous and can overlap in
meaning. Protein is generally used to refer to the complete biological molecule in a stable
conformation, whereas peptide is generally reserved for a short amino acid oligomers often
lacking a stable 3D structure. But the boundary between the two is not well defined and
usually lies near 20–30 residues.[39]

Proteins can interact with many types of molecules and ions, including with other proteins,
with lipids, with carbohydrates, and with DNA.[40][41][42]

Abundance in cells

A typical bacterial cell, e.g. E. coli and Staphylococcus aureus, is estimated to contain about
2 million proteins. Smaller bacteria, such as Mycoplasma or spirochetes contain fewer
molecules, on the order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and
thus contain much more protein. For instance, yeast cells have been estimated to contain
about 50 million proteins and human cells on the order of 1 to 3 billion.[43] The concentration
of individual protein copies ranges from a few molecules per cell up to 20 million.[44] Not all
genes coding proteins are expressed in most cells and their number depends on, for example,
cell type and external stimuli. For instance, of the 20,000 or so proteins encoded by the
human genome, only 6,000 are detected in lymphoblastoid cells.[45] The most abundant
protein in nature is thought to be RuBisCO, an enzyme that catalyzes the incorporation of
carbon dioxide into organic matter in photosynthesis. Plants can consist of as much as 1% by
weight of this enzyme.[46]

Synthesis
Biosynthesis

A ribosome produces a protein using mRNA as

template The DNA sequence of a gene encodes the

amino acid sequence of a protein
Main article: Protein biosynthesis

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 designates an amino acid, for example AUG
(adenine–uracil–guanine) is the code for methionine. Because DNA contains four
nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the
genetic code, with some amino acids specified by more than one codon.[42]: 1002–42 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 (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.[47]

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.[42]: 1002–42
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 with the unit dalton (Da), or its
derivative unit kilodalton (kDa). The average size of a protein increases from Archaea to
Bacteria to Eukaryote (283, 311, 438 residues and 31, 34, 49 kDa respectively) due to a
bigger number of protein domains constituting proteins in higher organisms.[48] For instance,
yeast proteins are on average 466 amino acids long and 53 kDa in mass.[39] The largest known
proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost
3000 kDa and a total length of almost 27000 amino acids.[49]

Chemical synthesis

Main article: Peptide synthesis

Peptide Synthesis

Short proteins can be synthesized chemically by a family of peptide synthesis methods. These
rely on organic synthesis techniques such as chemical ligation to produce peptides in high
yield.[50] 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.[51]
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.[52]

Structure

The crystal structure of the chaperonin,

a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein

folding. Three possible representations

of the three-dimensional structure of the protein triose phosphate isomerase. Left: All-atom
representation colored by atom type. Middle: Simplified 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).
Main article: Protein structure
Further information: Protein structure prediction

Most proteins fold into unique 3D structures. The shape into which a protein naturally folds is
known as its native conformation.[36]: 36 Although many proteins can fold unassisted, simply
through the chemical properties of their amino acids, others require the aid of molecular
chaperones to fold into their native states.[36]: 37 Biochemists often refer to four distinct aspects
of a protein's structure:[36]: 30–34

 Primary structure: the amino acid sequence. A protein is a polyamide.

 Secondary structure: regularly repeating local structures stabilized by hydrogen
bonds. The most common examples are the α-helix, β-sheet and turns. Because
secondary structures are local, many regions of distinct 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. The tertiary structure is what controls the basic function of the
protein.
 Quaternary structure: the structure formed by several protein molecules (polypeptide
chains), usually called protein subunits in this context, which function as a single
protein complex.
 Quinary structure: the signatures of protein surface that organize the crowded cellular
interior. Quinary structure is dependent on transient, yet essential, macromolecular
interactions that occur inside living cells.

Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may
shift between several related structures while they perform their functions. 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. In solution,
protein structures vary because of thermal vibration and collisions with other molecules.[42]:
368–75

Molecular surface of several proteins

showing their comparative sizes. From left to right are: immunoglobulin G (IgG, an
antibody), 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,
such as collagen, the major component of connective tissue, or keratin, the protein component
of hair and nails. Membrane proteins often serve as receptors or provide channels for polar or
charged molecules to pass through the cell membrane.[42]: 165–85

A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water
attack and hence promoting their own dehydration, are called dehydrons.[53]

Protein domains

Main article: Protein domain

Many proteins are composed of several protein domains, i.e. segments of a protein that fold
into distinct structural units.[54]: 134 Domains usually have specific functions, such as enzymatic
activities (e.g. kinase) or they serve as binding modules.[54]: 155–156

Protein domains vs. motifs. Protein domains (such as the EVH1 domain) are functional
units within proteins that fold into defined 3D structures. Motifs are usually short sequences
with specific functions but without a stable 3D structure. Many motifs are binding sites for
other proteins (such as the red and green bars shown here in the context of a VASP protein).
[55]

Sequence motif

Short amino acid sequences within proteins often act as recognition sites for other proteins.[56]
For instance, SH3 domains typically bind to short PxxP motifs (i.e. 2 prolines [P], separated
by two unspecified amino acids [x], although the surrounding amino acids may determine the
exact binding specificity). Many such motifs has been collected in the Eukaryotic Linear
Motif (ELM) database.[57]

Cellular functions
Proteins are the chief actors within the cell, said to be carrying out the duties specified by the
information encoded in genes.[39] 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 Escherichia coli cell, whereas other macromolecules such as DNA
and RNA make up only 3% and 20%, respectively.[58] The set of proteins expressed in a
particular cell or cell type is known as its proteome.[54]: 120

The enzyme hexokinase is shown as a conventional

ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates,
ATP and glucose.

The chief characteristic of proteins that allows their diverse set of 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.[59]

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 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
bind to, or be integrated into, cell membranes. The ability of binding partners to induce
conformational changes in proteins allows the construction of enormously complex signaling
networks.[42]: 830–49 As interactions between proteins are reversible and depend heavily on the
availability of different groups of partner proteins to form aggregates that are capable to carry
out discrete sets of function, study of the interactions between specific proteins is a key to
understand important aspects of cellular function, and ultimately the properties that
distinguish particular cell types.[60][61]

Enzymes

Main article: Enzyme

The best-known role of proteins in the cell is as enzymes, which catalyse chemical reactions.
Enzymes are usually highly specific and accelerate only one or a few chemical reactions.
Enzymes carry out most of the reactions involved in metabolism, as well as manipulating
DNA in processes such as DNA replication, DNA repair, and transcription. Some enzymes
act on other proteins to add or remove chemical groups in a process known as
posttranslational modification. About 4,000 reactions are known to be catalysed by enzymes.
[62]
The rate acceleration conferred by enzymatic catalysis is often enormous—as much as
17
10 -fold increase in rate over the uncatalysed reaction in the case of orotate decarboxylase
(78 million years without the enzyme, 18 milliseconds with the enzyme).[63]

The molecules bound and acted upon by enzymes are called 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—three to four residues on
average—that are directly involved in catalysis.[64] The region of the enzyme that binds the
substrate and contains the catalytic residues is known as the active site.[54]: 389

Dirigent proteins are members of a class of proteins that dictate the stereochemistry of a
compound synthesized by other enzymes.[65]

Cell signaling and ligand binding

See also: Glycan-protein interactions

Ribbon diagram of 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 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.[41]: 251–81

Antibodies are protein components of an 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. Whereas 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.[42]: 275–50
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, and 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.[42]: 222–29 Lectins are sugar-
binding proteins which are highly specific for their sugar moieties. Lectins typically play a
role in biological recognition phenomena involving cells and proteins.[66] Receptors and
hormones are highly specific binding proteins.

Transmembrane proteins can serve as ligand transport proteins that alter the permeability of
the cell 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.[41]: 232–34

Structural proteins

Protein Structure

Structural proteins confer stiffness and rigidity to otherwise-fluid biological components.

Most structural proteins are fibrous proteins; for example, 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.[42]: 178–81 Some globular
proteins can play structural functions, for example, actin and tubulin are globular and soluble
as monomers, but polymerize to form long, stiff fibers that make up the cytoskeleton, which
allows the cell to maintain its shape and size.[54]: 490

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 multicellular organisms
which reproduce sexually. They generate the forces exerted by contracting muscles[42]: 258–64, 272
and play essential roles in intracellular transport.[54]: 481, 490

Methods of study
Main article: Protein methods

Methods commonly used to study protein structure and function include

immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic
resonance and mass spectrometry. The activities and structures of proteins may be examined
in vitro, in vivo, and in silico. In vitro studies of purified proteins in controlled environments
are useful for learning how a protein carries out its function:[67] for example, enzyme kinetics
studies explore the chemical mechanism of an enzyme's catalytic activity and its relative
affinity for various possible substrate molecules.[68] By contrast, in vivo experiments can
provide information about the physiological role of a protein in the context of a cell or even a
whole organism, and can often provide more information about protein behavior in different
contexts.[69] In silico studies use computational methods to study proteins.[70]

Protein purification

Main article: Protein purification

Proteins may be purified from other cellular components using a variety of techniques such as
ultracentrifugation, precipitation, electrophoresis, and chromatography;[36]: 21–24 the advent of
genetic engineering has made possible a number of methods to facilitate purification.[71]

To perform in vitro analysis, 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.[36]: 21–24 The level of purification can be monitored using various types of gel
electrophoresis if the desired protein's molecular weight and isoelectric point are known, by
spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if
the protein has enzymatic activity. Additionally, proteins can be isolated according to their
charge using electrofocusing.[72]

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. A number of tags have been developed to help
researchers purify specific proteins from complex mixtures.[71]

Cellular localization
 Proteins in various cellular
compartments and structures tagged with green fluorescent protein (here, white)

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).[73] The fused protein's position within the cell can
then be cleanly and efficiently visualized using microscopy.[74]

Other methods for elucidating the cellular location of proteins requires the use of known
compartmental markers for regions such as the ER, the Golgi, lysosomes or vacuoles,
mitochondria, chloroplasts, plasma membrane, etc. With the use of fluorescently tagged
versions of these markers or of antibodies to known markers, it becomes much simpler to
identify the localization of a protein of interest. For example, indirect immunofluorescence
will allow for fluorescence colocalization and demonstration of location. Fluorescent dyes are
used to label cellular compartments for a similar purpose.[75]

Other possibilities exist, as well. For example, immunohistochemistry usually uses an

antibody to one or more proteins of interest that are conjugated to enzymes yielding either
luminescent or chromogenic signals that can be compared between samples, allowing for
localization information.[76] Another applicable technique is cofractionation in sucrose (or
other material) gradients using isopycnic centrifugation.[77] While this technique does not
prove colocalization of a compartment of known density and the protein of interest, it
indicates an increased likelihood.[77]

Finally, the gold-standard method of cellular localization is immunoelectron microscopy.

This technique uses an antibody to the protein of interest, along with classical electron
microscopy techniques. The sample is prepared for normal electron microscopic examination,
and then treated with an antibody to the protein of interest that is conjugated to an extremely
electro-dense material, usually gold. This allows for the localization of both ultrastructural
details as well as the protein of interest.[78]

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. This technique even allows the incorporation of unnatural amino
acids into proteins, using modified tRNAs,[79] and may allow the rational design of new
proteins with novel properties.[80]

Proteomics

Main article: Proteomics

The total complement of proteins present at a time 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 2D electrophoresis,[81] which allows the separation of many proteins, mass
spectrometry,[82] which allows rapid high-throughput identification of proteins and
sequencing of peptides (most often after in-gel digestion), protein microarrays, which allow
the detection of the relative levels of the various proteins present in a cell, and two-hybrid
screening, which allows the systematic exploration of protein–protein interactions.[83] The
total complement of biologically possible such interactions is known as the interactome.[84] A
systematic attempt to determine the structures of proteins representing every possible fold is
known as structural genomics.[85]

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 and how it can be
affected, i.e. in drug design. As proteins are too small to be seen under a light microscope,
other methods have to be employed to determine their structure. Common experimental
methods include X-ray crystallography and NMR spectroscopy, both of which can produce
structural information at atomic resolution. However, NMR experiments are able to provide
information from which a subset of distances between pairs of atoms can be estimated, and
the final possible conformations for a protein are determined by solving a distance geometry
problem. Dual polarisation interferometry is a quantitative analytical method for measuring
the overall protein conformation and conformational changes due to interactions or other
stimulus. Circular dichroism is another laboratory technique for determining internal β-sheet /
α-helical composition of proteins. Cryoelectron microscopy is used to produce lower-
resolution structural information about very large protein complexes, including assembled
viruses;[41]: 340–41 a variant known as electron crystallography can produce high-resolution
information in some cases, especially for two-dimensional crystals of membrane proteins. [86]
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.[87]

Many more gene sequences are known than protein structures. Further, the set of solved
structures is biased toward proteins that can be easily subjected to the conditions required in
X-ray crystallography, one of the major structure determination methods. In particular,
globular proteins are comparatively easy to crystallize in preparation for X-ray
crystallography. Membrane proteins and large protein complexes, by contrast, are difficult to
crystallize and are underrepresented in the PDB.[88] 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 proteins whose structures have not been experimentally
determined.[89]

Structure prediction

Main articles: Protein structure prediction and List of protein structure prediction software

Constituent amino-acids can be

analyzed to predict secondary, tertiary and quaternary protein structure, in this case
hemoglobin containing heme units

Complementary to the field of structural genomics, protein structure prediction develops

efficient mathematical models of proteins to computationally predict the molecular
formations in theory, instead of detecting structures with laboratory observation.[90] 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.[91] 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.[92] Many structure prediction methods have served to
inform the emerging field of protein engineering, in which novel protein folds have already
been designed.[93] Many proteins (in eukaryotes ~33%) contain large unstructured but
biologically functional segments and can be classified as intrinsically disordered proteins.
Predicting and analysing protein disorder is an important part of protein structure
characterisation.[94]

In silico simulation of dynamical processes

A more complex computational problem is the prediction of intermolecular interactions, such

as in molecular docking,[95] protein folding, protein–protein interaction and chemical
reactivity. Mathematical models to simulate these dynamical processes involve molecular
mechanics, in particular, molecular dynamics. In this regard, in silico simulations discovered
the folding of small α-helical protein domains such as the villin headpiece,[96] the HIV
accessory protein[97] and hybrid methods combining standard molecular dynamics with
quantum mechanical mathematics have explored the electronic states of rhodopsins.[98]

Beyond classical molecular dynamics, quantum dynamics methods allow the simulation of
proteins in atomistic detail with an accurate description of quantum mechanical effects.
Examples include the multi-layer multi-configuration time-dependent Hartree method and the
hierarchical equations of motion approach, which have been applied to plant
cryptochromes[99] and bacteria light-harvesting complexes,[100] respectively. Both quantum and
classical mechanical simulations of biological-scale systems are extremely computationally
demanding, so distributed computing initiatives such as the Folding@home project facilitate
the molecular modeling by exploiting advances in GPU parallel processing and Monte Carlo
techniques.[101][102]

Chemical analysis

See also: Protein (nutrient) § Testing in foods

The total nitrogen content of organic matter is mainly formed by the amino groups in
proteins. The total Kjeldahl nitrogen (TKN) is a measure of nitrogen widely used in the
analysis of (waste) water, soil, food, feed and organic matter in general. As the name
suggests, the Kjeldahl method is applied. More sensitive methods are available.[103][104]

Digestion
Main articles: Proteolysis and Protein (nutrient)

Hydrolysis of protein. X = HCl and heat for industrial

proteolysis. X = protease for biological proteolysis

In the absence of catalysts, proteins are slow to hydrolyze.[105] The breakdown of proteins to
small peptides and amino acids (proteolysis) is a step in digestion; these breakdown products
are then absorbed in the small intestine.[106] The hydrolysis of proteins relies on enzymes
called proteases or peptidases. Proteases, which are themselves proteins, come in several
types according to the particular peptide bonds that they cleave as well as their tendency to
cleave peptide bonds at the terminus of a protein (exopeptidases) vs peptide bonds at the
interior of the protein (endopeptidases).[107] Pepsin is an endopeptidase in the stomach.
Subsequent to the stomach, the pancreas secretes other proteases to complete the hydrolysis,
these include trypsin and chymotrypsin.[108]

Protein hydrolysis is employed commercially as a means of producing amino acids from bulk
sources of protein, such as blood meal, feathers, keratin. Such materials are treated with hot
hydrochloric acid, which effects the hydrolysis of the peptide bonds.[109]

Mechanical properties
The mechanical properties of proteins are highly diverse and are often central to their
biological function, as in the case of proteins like keratin and collagen.[110] For instance, the
ability of muscle tissue to continually expand and contract is directly tied to the elastic
properties of their underlying protein makeup.[111][112] Beyond fibrous proteins, the
conformational dynamics of enzymes[113] and the structure of biological membranes, among
other biological functions, are governed by the mechanical properties of the proteins. Outside
of their biological context, the unique mechanical properties of many proteins, along with
their relative sustainability when compared to synthetic polymers, have made them desirable
targets for next-generation materials design.[114][115]

Young's modulus, E, is calculated as the axial stress σ over the resulting strain ε. It is a
measure of the relative stiffness of a material. In the context of proteins, this stiffness often
directly correlates to biological function. For example, collagen, found in connective tissue,
bones, and cartilage, and keratin, found in nails, claws, and hair, have observed stiffnesses
that are several orders of magnitude higher than that of elastin,[116] which is thought to give
elasticity to structures such as blood vessels, pulmonary tissue, and bladder tissue, among
others.[117][118] In comparison to this, globular proteins, such as Bovine Serum Albumin, which
float relatively freely in the cytosol and often function as enzymes (and thus undergoing
frequent conformational changes) have comparably much lower Young's moduli.[119][120]

The Young's modulus of a single protein can be found through molecular dynamics
simulation. Using either atomistic force-fields, such as CHARMM or GROMOS, or coarse-
grained forcefields like Martini,[121] a single protein molecule can be stretched by a uniaxial
force while the resulting extension is recorded in order to calculate the strain.[122][123]
Experimentally, methods such as atomic force microscopy can be used to obtain similar data.
[124]
The internal dynamics of proteins involve subtle elastic and plastic deformations induced
by viscoelastic forces, which can be probed by nano-rheology techniques.[125] These estimates
yield typical spring constants around k ≈ 100 pN/nm, equivalent to Young's moduli of E ≈
100 MPa, and typical friction coefficients of γ ≈ 0.1 pN·s/nm, corresponding to viscosity of η
≈ 0.01 pN·s/nm2 = 107 cP (that is, 107 times more viscous than water).

At the macroscopic level, the Young's modulus of cross-linked protein networks can be
obtained through more traditional mechanical testing. Experimentally observed values for a
few proteins can be seen below.
 Elasticity of various proteins
Protein Protein class Young's modulus
keratin (cross-linked) fibrous 1.5–10 GPa[126]
elastin (cross-linked) fibrous 1 MPa[116]
fibrin (cross-linked) fibrous 1–10 MPa[116]
collagen (cross-linked) fibrous 5–7.5 GPa[116][127]
resilin (cross-linked) fibrous 1–2 MPa[116]
bovine serum albumin (cross-linked) globular 2.5–15 kPa[119]
β-barrel outer membrane proteins membrane 20–45 GPa[128]

See also
 Deproteination – Technique in research of live materials
 DNA-binding protein – Proteins that bind with DNA
 Index of protein-related articles
 Intein
 List of proteins
 Macromolecule – Very large molecule
 Protein evolution – Study of changes in DNA and RNA over time
 Protein sequence space – Representation of possible genetic sequences
 Protein superfamily – Grouping of proteins
 Protein toxicity – Buildup of metabolic waste due to kidney dysfunction
 Proteopathy – Diseases caused by abnormal protein structure
 Proteopedia – 3D encyclopedia of proteins and other molecules

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Further reading
Textbooks

 Branden C, Tooze J (1999). Introduction to Protein Structure. New York: Garland

Pub. ISBN 978-0-8153-2305-1.
 Murray RF, Harper HW, Granner DK, Mayes PA, Rodwell VW (2006). Harper's
Illustrated Biochemistry. New York: Lange Medical Books/McGraw-Hill. ISBN 978-
0-07-146197-9.
 Van Holde KE, Mathews CK (1996). Biochemistry. Menlo Park, California:
Benjamin/Cummings Pub. Co., Inc. ISBN 978-0-8053-3931-4.

History

 Tanford C, Reynolds JA (2001). Nature's Robots: A History of Proteins. Oxford New

York: Oxford University Press, USA. ISBN 978-0-19-850466-5.

External links
Protein at Wikipedia's sister projects

 Definitions from Wiktionary

 Media from Commons

Databases and projects

 NCBI Entrez Protein database

 NCBI Protein Structure database
 Human Protein Reference Database
 Human Proteinpedia
 Folding@Home (Stanford University) Archived 2012-09-08 at the Wayback Machine
 Protein Databank in Europe (see also PDBeQuips, short articles and tutorials on
interesting PDB structures)
 Research Collaboratory for Structural Bioinformatics (see also Molecule of the Month
Archived 2020-07-24 at the Wayback Machine, presenting short accounts on selected
proteins from the PDB)
  Proteopedia – Life in 3D: rotatable, zoomable 3D model with wiki annotations for
every known protein molecular structure.
 UniProt the Universal Protein Resource

Tutorials and educational websites

 "An Introduction to Proteins" from HOPES (Huntington's Disease Outreach Project

for Education at Stanford)
 Proteins: Biogenesis to Degradation – The Virtual Library of Biochemistry and Cell
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