Editing Proteasome (section)

===Unfolding and translocation===
After a protein has been ubiquitinated, it is recognized by the 19S regulatory particle in an ATP-dependent binding step.<ref name=Liu/> The substrate protein must then enter the interior of the 20S subunit to come in contact with the proteolytic active sites. Because the 20S particle's central channel is narrow and gated by the N-terminal tails of the α ring subunits, the substrates must be at least partially unfolded before they enter the core. The passage of the unfolded substrate into the core is called ''translocation'' and necessarily occurs after deubiquitination.<ref name=Liu/> For an idealized substrate, translocation drives deubiquitination.<ref name=":7" />   However, the order in which substrates are deubiquitinated and unfolded is not yet clear.<ref name=Zhu>{{cite journal | vauthors = Zhu Q, Wani G, Wang QE, El-mahdy M, Snapka RM, Wani AA | title = Deubiquitination by proteasome is coordinated with substrate translocation for proteolysis in vivo | journal = Experimental Cell Research | volume = 307 | issue = 2 | pages = 436–51 | date = July 2005 | pmid = 15950624 | doi = 10.1016/j.yexcr.2005.03.031}}</ref> Which of these processes is the [[rate-limiting step]] in the overall proteolysis reaction depends on the specific substrate; for some proteins, the unfolding process is rate-limiting, while deubiquitination is the slowest step for other proteins.<ref name="Smith"/> The extent to which substrates must be unfolded before translocation is suggested to be around 20 amino acid residues by the atomic structure of the substrate-engaged 26S proteasome in the deubiquitylation-compatible state,<ref name=Dong /> but substantial [[tertiary structure]], and in particular nonlocal interactions such as [[disulfide bond]]s, are sufficient to inhibit degradation.<ref name=Wenzel>{{cite journal | vauthors = Wenzel T, Baumeister W | title = Conformational constraints in protein degradation by the 20S proteasome | journal = Nature Structural Biology | volume = 2 | issue = 3 | pages = 199–204 | date = March 1995 | pmid = 7773788 | doi = 10.1038/nsb0395-199 | s2cid = 41599619 }}</ref> The presence of [[Intrinsically disordered proteins|intrinsically disordered protein]] segments of sufficient size, either at the protein terminus or internally, has also been proposed to facilitate efficient initiation of degradation.<ref>{{cite journal | vauthors = Inobe T, Fishbain S, Prakash S, Matouschek A | title = Defining the geometry of the two-component proteasome degron | journal = Nature Chemical Biology | volume = 7 | issue = 3 | pages = 161–7 | date = March 2011 | pmid = 21278740 | pmc = 3129032 | doi = 10.1038/nchembio.521 }}</ref><ref>{{cite journal | vauthors = van der Lee R, Lang B, Kruse K, Gsponer J, Sánchez de Groot N, Huynen MA, Matouschek A, Fuxreiter M, Babu MM | title = Intrinsically disordered segments affect protein half-life in the cell and during evolution | journal = Cell Reports | volume = 8 | issue = 6 | pages = 1832–44 | date = September 2014 | pmid = 25220455 | pmc = 4358326 | doi = 10.1016/j.celrep.2014.07.055 }}</ref>

The gate formed by the α subunits prevents peptides longer than about four residues from entering the interior of the 20S particle. The ATP molecules bound before the initial recognition step are [[hydrolysis|hydrolyzed]] before translocation. While energy is needed for substrate unfolding, it is not required for translocation.<ref name="Smith"/><ref name="Liu"/> The assembled 26S proteasome can degrade unfolded proteins in the presence of a non-hydrolyzable [[Adenosine triphosphate#ATP analogues|ATP analog]], but cannot degrade folded proteins, indicating that energy from ATP hydrolysis is used for substrate unfolding.<ref name=Smith/> Passage of the unfolded substrate through the opened gate occurs via [[facilitated diffusion]] if the 19S cap is in the ATP-bound state.<ref name=Smith2>{{cite journal | vauthors = Smith DM, Benaroudj N, Goldberg A | title = Proteasomes and their associated ATPases: a destructive combination | journal = Journal of Structural Biology | volume = 156 | issue = 1 | pages = 72–83 | date = October 2006 | pmid = 16919475 | doi = 10.1016/j.jsb.2006.04.012 }}</ref>

The mechanism for unfolding of [[globular protein]]s is necessarily general, but somewhat dependent on the [[primary structure|amino acid sequence]]. Long sequences of alternating glycine and [[alanine]] have been shown to inhibit substrate unfolding, decreasing the efficiency of proteasomal degradation; this results in the release of partially degraded byproducts, possibly due to the decoupling of the ATP hydrolysis and unfolding steps.<ref name=Hoyt>{{cite journal | vauthors = Hoyt MA, Zich J, Takeuchi J, Zhang M, Govaerts C, Coffino P | title = Glycine-alanine repeats impair proper substrate unfolding by the proteasome | journal = The EMBO Journal | volume = 25 | issue = 8 | pages = 1720–9 | date = April 2006 | pmid = 16601692 | pmc = 1440830 | doi = 10.1038/sj.emboj.7601058 }}</ref> Such glycine-alanine repeats are also found in nature, for example in [[silk]] [[fibroin]]; in particular, certain [[Epstein–Barr virus]] gene products bearing this sequence can stall the proteasome, helping the virus propagate by preventing [[antigen presentation]] on the major histocompatibility complex.<ref name=Zhang>{{cite journal | vauthors = Zhang M, Coffino P | title = Repeat sequence of Epstein–Barr virus-encoded nuclear antigen 1 protein interrupts proteasome substrate processing | journal = The Journal of Biological Chemistry | volume = 279 | issue = 10 | pages = 8635–41 | date = March 2004 | pmid = 14688254 | doi = 10.1074/jbc.M310449200 | doi-access = free }}</ref>

[[File:Proteasome cutaway 2.png|thumb|200px|left|A cutaway view of the proteasome 20S core particle illustrating the locations of the [[active site]]s. The α subunits are represented as green spheres and the β subunits as protein backbones colored by individual [[polypeptide chain]]. The small pink spheres represent the location of the active-site [[threonine]] residue in each subunit. Light blue chemical structures are the inhibitor [[bortezomib]] bound to the active sites.]]