PROTEINS (/ˈproʊˌtiːnz/ or /ˈproʊti.ᵻnz/ ) are large
biomolecules , or macromolecules , consisting of one or more long
chains of amino acid residues . Proteins perform a vast array of
functions within organisms , including catalysing metabolic reactions
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 , or sometimes oligopeptides . 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; however, 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. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors . Proteins can also 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 of time 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 . Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton , which form a system of scaffolding that maintains 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 use in the metabolism.
Proteins may be purified from other cellular components using a
variety of techniques such as ultracentrifugation , precipitation ,
electrophoresis , and chromatography ; the advent of genetic
engineering has made possible a number of methods to facilitate
purification. Methods commonly used to study protein structure and
function include immunohistochemistry , site-directed mutagenesis ,
* 1.1 Abundance in cells
* 2 Synthesis
* 2.1 Biosynthesis * 2.2 Chemical synthesis
* 3 Structure
* 3.1 Structure determination
* 4 Cellular functions
* 4.1 Enzymes
* 5 Methods of study
* 5.4 Bioinformatics
* 5.4.1 Structure prediction and simulation
* 6 Nutrition * 7 History and etymology * 8 See also * 9 References * 10 Textbooks
* 11 External links
* 11.1 Databases and projects * 11.2 Tutorials and educational websites
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) Resonance structures of the
peptide bond that links individual amino acids to form a protein
polymer Main articles:
Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids . All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded . Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids , have a great variety of chemical structures and properties; it is the combined effect of all of the amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity. The amino acids in a polypeptide chain are linked by peptide bonds . 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. The end with a free amino group is known as the N-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus (the sequence of the protein is written from N-terminus to C-terminus, from left to right).
The words protein, polypeptide, and peptide are a little ambiguous
and can overlap in meaning.
ABUNDANCE IN CELLS
It has been estimated that average-sized bacteria contain about 2
million proteins per cell (e.g. E. coli and
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
The process of synthesizing a protein from an m
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). The average size of
protein increases from Archaea,
Short proteins can also be synthesized chemically 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.
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
Protein structure Further information:
Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native conformation . 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. Biochemists often refer to four distinct aspects of a protein's structure:
Primary structure : the amino acid sequence . A protein is a
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 different secondary structure can be present in
the same protein molecule.
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 proteins also undergo variation in structure through thermal vibration and the collision with other molecules. 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 .
A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration , are called dehydrons .
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
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
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
The chief characteristic of proteins that also 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'
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. 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.
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
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. The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site .
Dirigent proteins are members of a class of proteins that dictate the stereochemistry of a compound synthesized by other enzymes.
CELL SIGNALING AND LIGAND BINDING
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.
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 . 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. Receptors and hormones are highly specific binding proteins.
Transmembrane proteins can also 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.
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 . Some globular proteins can also 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.
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 also generate the forces exerted by contracting muscles and play essential roles in intracellular transport.
METHODS OF STUDY
Main article: Protein methods
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: 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 can provide information about the physiological role of a protein in the context of a cell or even a whole organism . IN SILICO studies use computational methods to study proteins.
Main article: Protein purification
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. 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 their charge using electrofocusing .
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 different tags have been developed to help researchers purify specific proteins from complex mixtures.
It has been suggested that this section be split out into another article titled Cellular localization . (Discuss ) (October 2016)
Proteins in different 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). The fused protein's position within the cell can be cleanly and efficiently visualized using microscopy , as shown in the figure opposite.
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.
Other possibilities exist, as well. For example, immunohistochemistry usually utilizes 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. Another applicable technique is cofractionation in sucrose (or other material) gradients using isopycnic centrifugation . While this technique does not prove colocalization of a compartment of known density and the protein of interest, it does increase the likelihood, and is more amenable to large-scale studies.
Finally, the gold-standard method of cellular localization is immunoelectron microscopy . This technique also 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.
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, and may allow the rational design of new proteins with novel properties.
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 , which allows the separation of a large number of proteins, mass spectrometry , 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 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 .
Main article: Bioinformatics
A vast array of computational methods have been developed to analyze the structure, function, and evolution of proteins.
The development of such tools has been driven by the large amount of
genomic and proteomic data available for a variety of organisms,
including the human genome . It is simply impossible to study all
proteins experimentally, hence only a few are subjected to laboratory
experiments while computational tools are used to extrapolate to
similar proteins. Such homologous proteins can be efficiently
identified in distantly related organisms by sequence alignment .
Structure Prediction And Simulation
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units Main articles: Protein structure prediction and List of protein structure prediction software
Complementary to the field of structural genomics, protein structure prediction develops efficient mathematical models of proteins to computationally predict their structures in theory, instead of detecting structures with laboratory observation. 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 .
Mathematical models to simulate dynamic processes of protein folding
and binding involve molecular mechanics , in particular, molecular
dynamics . Monte Carlo techniques facilitate the computations, which
exploit advances in parallel and distributed computing (for example,
Folding@home project which performs molecular modeling on GPUs ).
In silico simulations discovered the folding of small α-helical
protein domains such as the villin headpiece and the
Many proteins (in Eucaryota ~33%) contain large unstructured but biologically functional segments and can be classified as intrinsically disordered proteins . Predicting and analysing protein disorder is, therefore, an important part of protein structure characterisation.
Most microorganisms and plants can biosynthesize all 20 standard amino acids , while animals (including humans) must obtain some of the amino acids from the diet . The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids . Key enzymes that synthesize certain amino acids are not present in animals — such as aspartokinase , which catalyses the first step in the synthesis of lysine , methionine , and threonine from aspartate . If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways.
In animals, amino acids are obtained through the consumption of foods containing protein. Ingested proteins are then broken down into amino acids through digestion , which typically involves denaturation of the protein through exposure to acid and hydrolysis by enzymes called proteases . Some ingested amino acids are used for protein biosynthesis, while others are converted to glucose through gluconeogenesis , or fed into the citric acid cycle . This use of protein as a fuel is particularly important under starvation conditions as it allows the body's own proteins to be used to support life, particularly those found in muscle .
HISTORY AND ETYMOLOGY
Further information: History of molecular biology
Proteins were recognized as a distinct class of biological molecules in the eighteenth century by Antoine Fourcroy and others, distinguished by the molecules' ability to coagulate or flocculate under treatments with heat or acid. Noted examples at the time included albumin from egg whites , blood serum albumin , fibrin , and wheat gluten .
Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jöns Jacob Berzelius in 1838. Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula , C400H620N100O120P1S1. 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", "in the lead", or "standing in front", + -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 .
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."
Karl Heinrich Ritthausen extended known protein
forms with the identification of glutamic acid . At the Connecticut
The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study. 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 . In the 1950s, the Armour Hot Dog Co. purified 1 kg of pure 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. John Kendrew with model of myoglobin in progress
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. Later work by Walter Kauzmann on denaturation , based partly on previous studies by Kaj Linderstrøm-Lang , contributed an understanding of protein folding and structure mediated by hydrophobic interactions .
The first protein to be 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 . He won the Nobel Prize for this achievement in 1958.
The first protein structures to be solved were hemoglobin and
myoglobin , by
Max Perutz and Sir John Cowdery Kendrew , respectively,
in 1958. As of 2017 , the
Protein Data Bank
* Biology portal * Biotechnology portal * Molecular and cellular biology portal
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DATABASES AND PROJECTS