Editing Protein (section)

==Cellular functions==

Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes.<ref name=Lodish2004/> 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.<ref name="Voet">Voet D, Voet JG. (2004). ''Biochemistry'' Vol 1 3rd ed. Wiley: Hoboken, NJ.</ref> The set of proteins expressed in a particular cell or cell type is known as its [[proteome]].<ref name=Biochemistry2010/>{{rp|120}}

[[File:Hexokinase ball and stick model, with substrates to scale copy.png|thumb|right|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, [[adenosine triphosphate|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<sup>−15</sup> M) but does not bind at all to its amphibian homolog [[onconase]] (>&nbsp;1&nbsp;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]].<ref name=Sankaranarayanan2001/>

Proteins can bind to other proteins as well as to [[Small molecule|small-molecule]] substrates. When proteins bind specifically to other copies of the same molecule, they can [[oligomer]]ize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. [[Protein–protein interaction]]s regulate enzymatic activity, control progression through the [[cell cycle]], and allow the assembly of large [[protein complex]]es 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 [[cell signaling|signaling]] networks.<ref name = "Van_Holde_1996" />{{rp|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.<ref name=Copland2009/><ref name=Samarin2009/>

===Enzymes===

{{Main|Enzyme}}

The best-known role of proteins in the cell is as [[enzyme]]s, which [[catalysis|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 (genetics)|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.<ref name=EXPASY2000/> The rate acceleration conferred by enzymatic catalysis is often enormous—as much as 10<sup>17</sup>-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).<ref name=Radzicka1995/>

The molecules bound and acted upon by enzymes are called [[Substrate (biochemistry)|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.<ref name="urlEBI"/> The region of the enzyme that binds the substrate and contains the catalytic residues is known as the [[active site]].<ref name=Biochemistry2010/>{{rp|389}}

[[Dirigent protein]]s are members of a class of proteins that dictate the [[stereochemistry]] of a compound synthesized by other enzymes.<ref name="Pickel 2013"/>

===Cell signaling and ligand binding===

{{See also|Glycan-protein interactions}}

[[File:Mouse cholera antibody.png|thumb|upright|[[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 [[biological tissue|tissues]]. Others are [[membrane protein]]s that act as [[receptor (biochemistry)|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.<ref name = "Brandon_1999" />{{rp|251–81}}

[[Antibodies]] are protein components of an [[adaptive immune system]] whose main function is to bind [[antigen]]s, or foreign substances in the body, and target them for destruction. Antibodies can be [[secrete]]d into the extracellular environment or anchored in the membranes of specialized [[B cell]]s known as [[plasma cell]]s. 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.<ref name = "Van_Holde_1996" />{{rp|275–50}}

Many ligand transport proteins bind particular [[Small molecule|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 [[lung]]s to other organs and tissues in all [[vertebrate]]s and has close homologs in every biological [[kingdom (biology)|kingdom]].<ref name = "Van_Holde_1996" />{{rp|222–29}} [[Lectins]] are [[Glycan-protein interactions|sugar-binding proteins]] which are highly specific for their sugar moieties. [[Lectins]] typically play a role in biological [[Molecular recognition|recognition]] phenomena involving cells and proteins.<ref name=Rudiger2000/> [[Receptor (biochemistry)|Receptors]] and [[hormone]]s are highly specific binding proteins.

[[Transmembrane protein]]s can serve as ligand transport proteins that alter the [[Semipermeable membrane|permeability]] of the cell membrane to [[small molecule]]s and ions. The membrane alone has a [[hydrophobic]] core through which [[Chemical polarity|polar]] or charged molecules cannot [[diffusion|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.<ref name = "Brandon_1999" />{{rp|232–34}}

===Structural proteins===

[[File:CHOP protein structure.png|thumb|Protein Structure]]

Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are [[fibrous protein]]s; 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]], [[nail (anatomy)|nails]], [[feather]]s, [[hoof|hooves]], and some [[Exoskeleton|animal shell]]s.<ref name = "Van_Holde_1996" />{{rp|178–81}} Some [[globular proteins]] can play structural functions, for example, [[actin]] and [[tubulin]] are globular and soluble as monomers, but [[polymer]]ize to form long, stiff fibers that make up the [[cytoskeleton]], which allows the cell to maintain its shape and size.<ref name=Biochemistry2010/>{{rp|490}}

Other proteins that serve structural functions are [[motor protein]]s 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 [[spermatozoon|sperm]] of many multicellular organisms which reproduce [[Sexual reproduction|sexually]]. They generate the forces exerted by contracting [[muscle]]s<ref name = "Van_Holde_1996" />{{rp|258–64, 272}} and play essential roles in intracellular transport.<ref name=Biochemistry2010/>{{rp|481,490}}