Editing Protein (section)

== Structure ==

[[File:Chaperonin 1AON.png|thumb|right|upright=1.35|The crystal structure of the [[chaperonin]], a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein folding.]]
[[File:Proteinviews-1tim.png|thumb|upright=1.35|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|Protein structure prediction}}

Most proteins [[protein folding|fold]] into unique 3D structures. The shape into which a protein naturally folds is known as its [[native conformation]].<ref name = "Murray_2006" />{{rp|36}} Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular [[Chaperone (protein)|chaperones]] to fold into their native states.<ref name = "Murray_2006" />{{rp|37}} Biochemists often refer to four distinct aspects of a protein's structure:<ref name = "Murray_2006" />{{rp|30–34}}

* ''[[Primary structure]]'': the [[peptide sequence|amino acid sequence]]. A protein is a [[polyamide]].
* ''[[Secondary structure]]'': regularly repeating local structures stabilized by [[hydrogen bond]]s. The most common examples are the [[alpha helix|α-helix]], [[beta sheet|β-sheet]] and [[turn (biochemistry)|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 bridge (protein)|salt bridges]], hydrogen bonds, [[disulfide bond]]s, and even [[posttranslational modification|post-translational modification]]s. 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 subunit]]s'' in this context, which function as a single [[protein complex]].
* ''[[Protein quinary structure|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 "[[Chemical conformation|conformations]]", and transitions between them are called ''conformational changes.'' Such changes are often induced by the binding of a [[Substrate (biochemistry)|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.<ref name = "Van_Holde_1996" />{{rp|368–75}}

[[File:Protein composite.png|thumb|upright=1.35|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 protein]]s, [[fibrous protein]]s, and [[membrane protein]]s. 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 [[receptor (biochemistry)|receptors]] or provide channels for polar or charged molecules to pass through the [[cell membrane]].<ref name = "Van_Holde_1996" />{{rp|165–85}}

A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own [[dehydration]], are called [[dehydron]]s.<ref name=Fernandez2003/>

=== Protein domains ===

{{Main|Protein domain}}

Many proteins are composed of several [[protein domain]]s, i.e. segments of a protein that fold into distinct structural units.<ref name=Biochemistry2010>{{Cite book |last1=Garrett |first1=R. |title=Biochemistry |last2=Grisham |first2=Charles M. |date=2010 |publisher=Brooks/Cole, Cengage Learning |isbn=978-0-495-10935-8 |edition=4th |location=Belmont, CA}}</ref>{{rp|134}} Domains usually have specific functions, such as [[Enzyme|enzymatic]] activities (e.g. [[kinase]]) or they serve as binding modules.<ref name=Biochemistry2010 />{{rp|155–156}}

[[File:Domain organisation of EVH proteins.png|frame|'''Protein domains vs. motifs'''. Protein domains (such as the [[WH1 domain|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 [[Ena/Vasp homology proteins|VASP]] protein).<ref>{{Cite journal |last1=Drees |first1=Frauke |last2=Gertler |first2=Frank B |date=2008-02-01 |title=Ena/VASP: proteins at the tip of the nervous system |journal=Current Opinion in Neurobiology |series=Development |volume=18 |issue=1 |pages=53–59 |doi=10.1016/j.conb.2008.05.007  |pmc=2515615 |pmid=18508258}}</ref>|center]]

=== Sequence motif ===
Short amino acid sequences within proteins often act as recognition sites for other proteins.<ref>{{cite journal | vauthors = Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ | title = Attributes of short linear motifs | journal = Molecular BioSystems | volume = 8 | issue = 1 | pages = 268–281 | date = January 2012 | pmid = 21909575 | doi = 10.1039/c1mb05231d }}</ref> For instance, [[SH3 domain]]s typically bind to short PxxP motifs (i.e. 2 [[proline]]s [P], separated by two unspecified [[amino acid]]s [x], although the surrounding amino acids may determine the exact binding specificity). Many such motifs has been collected in the [[Eukaryotic Linear Motif resource|Eukaryotic Linear Motif]] (ELM) database.<ref>{{Cite journal |last1=Kumar |first1=Manjeet |last2=Gouw |first2=Marc |last3=Michael |first3=Sushama |last4=Sámano-Sánchez |first4=Hugo |last5=Pancsa |first5=Rita |last6=Glavina |first6=Juliana |last7=Diakogianni |first7=Athina |last8=Valverde |first8=Jesús Alvarado |last9=Bukirova |first9=Dayana |last10=Čalyševa |first10=Jelena |last11=Palopoli |first11=Nicolas |last12=Davey |first12=Norman E. |last13=Chemes |first13=Lucía B. |last14=Gibson |first14=Toby J. |date=2020-01-08 |title=ELM-the eukaryotic linear motif resource in 2020 |journal=Nucleic Acids Research |volume=48 |issue=D1 |pages=D296–D306 |doi=10.1093/nar/gkz1030 |pmc=7145657 |pmid=31680160}}</ref>