protease inhibitor (biology)

Protease inhibitors may be classified either by the type of protease they inhibit, or by their mechanism of action. In 2004 Rawlings and colleagues introduced a classification of protease inhibitors based on similarities detectable at the level of amino acid sequence.{{cite journal |vauthors=Rawlings ND, Tolle DP, Barrett AJ |title=Evolutionary families of peptidase inhibitors |journal=Biochem. J. |volume=378 |issue=Pt 3 |pages=705–16 |date=March 2004 |pmid=14705960 |pmc=1224039 |doi=10.1042/BJ20031825 }} This classification initially identified 48 families of inhibitors that could be grouped into 26 related superfamily (or clans) by their structure. According to the MEROPS database there are now 81 families of inhibitors. These families are named with an I followed by a number, for example, I14 contains hirudin-like inhibitors.

Classes of proteases are:

• Aspartic protease inhibitors
• Cysteine protease inhibitors
• Metalloprotease inhibitors
• Serine protease inhibitors
• Threonine protease inhibitors
• Trypsin inhibitors
• Kunitz STI protease inhibitor

Classes of inhibitor mechanisms of action are:

• Suicide inhibitor
• Transition state inhibitor
• Protein protease inhibitor (see serpins)
• Chelating agents

This is a family of protease suicide inhibitors called the serpins. It contains inhibitors of multiple cysteine and serine protease families. Their mechanism of action relies on undergoing a large conformational change which inactivates their target's catalytic triad.

{{Infobox protein family

| Symbol = Inhibitor_I9

| Name = Peptidase inhibitor I9

| image = PDB 1spb EBI.jpg

| width =

| caption = subtilisin bpn' prosegment (77 residues) complexed with a mutant subtilisin bpn' (266 residues). crystal ph 4.6. crystallization temperature 20 c diffraction temperature-160 c

| Pfam = PF05922

| Pfam_clan =

| InterPro = IPR010259

| SMART =

| PROSITE =

| MEROPS = I9

| SCOP = 1gns

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

Proteinase propeptide inhibitors (sometimes referred to as activation peptides) are responsible for the modulation of folding and activity of the peptidase pro-enzyme or zymogen. The pro-segment docks into the enzyme, shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology, despite often low sequence identities.{{cite journal |vauthors=Tangrea MA, Bryan PN, Sari N, Orban J | title = Solution structure of the pro-hormone convertase 1 pro-domain from Mus musculus | journal = J. Mol. Biol. | volume = 320 | issue = 4 | pages = 801–12 |date=July 2002 | pmid = 12095256 | doi = 10.1016/S0022-2836(02)00543-0}}{{cite journal |vauthors=Jain SC, Shinde U, Li Y, Inouye M, Berman HM | title = The crystal structure of an autoprocessed Ser221Cys-subtilisin E-propeptide complex at 2.0 A resolution | journal = J. Mol. Biol. | volume = 284 | issue = 1 | pages = 137–44 |date=November 1998 | pmid = 9811547 | doi = 10.1006/jmbi.1998.2161 }} The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology.

The peptidase inhibitor I9 family contains the propeptide domain at the N-terminus of peptidases belonging to MEROPS family S8A, subtilisins. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.

{{Infobox protein family

| Symbol = Inhibitor_I10

| Name = Serine endopeptidase inhibitors

| image = PDB 1ixu EBI.jpg

| width =

| caption = solution structure of marinostatin, a protease inhibitor, containing two ester linkages

| Pfam = PF12559

| Pfam_clan =

| InterPro = IPR022217

| SMART =

| PROSITE =

| MEROPS =

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C-terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. It is the ester linkages within the key, 12-residue region that circularise the molecule giving it its inhibitory conformation.

{{Infobox protein family

| Symbol = Inhibitor_I24

| Name = PinA peptidase inhibitor

| image =

| width =

| caption =

| Pfam = PF10465

| Pfam_clan =

| InterPro = IPR019506

| SMART =

| PROSITE =

| MEROPS = I24

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

This family includes PinA, which inhibits the endopeptidase La. It binds to the La homotetramer but does not interfere with the ATP binding site or the active site of La.

{{Infobox protein family

| Symbol = Inhibitor_I29

| Name = Cathepsin propeptide inhibitor domain (I29)

| image = PDB 1cjl EBI.jpg

| width =

| caption = crystal structure of a cysteine protease proform

| Pfam = PF08246

| Pfam_clan =

| InterPro = IPR013201

| SMART =

| PROSITE =

| MEROPS =

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

The inhibitor I29 domain, which belongs to MEROPS peptidase inhibitor family I29, is found at the N-terminus of a variety of peptidase precursors that belong to MEROPS peptidase subfamily C1A; these include cathepsin L, papain, and procaricain.{{cite journal |vauthors=Groves MR, Taylor MA, Scott M, Cummings NJ, Pickersgill RW, Jenkins JA | title = The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft | journal = Structure | volume = 4 | issue = 10 | pages = 1193–203 |date=October 1996 | pmid = 8939744 | doi = 10.1016/s0969-2126(96)00127-x| doi-access = free }} It forms an alpha-helical domain that runs through the substrate-binding site, preventing access. Removal of this region by proteolytic cleavage results in activation of the enzyme. This domain is also found, in one or more copies, in a variety of cysteine peptidase inhibitors such as salarin.{{cite journal |vauthors=Olonen A, Kalkkinen N, Paulin L | title = A new type of cysteine proteinase inhibitor--the salarin gene from Atlantic salmon (Salmo salar L.) and Arctic charr (Salvelinus alpinus) | journal = Biochimie | volume = 85 | issue = 7 | pages = 677–81 |date=July 2003 | pmid = 14505823 | doi = 10.1016/S0300-9084(03)00128-7}}

{{Infobox protein family

| Symbol = Inhibitor_I34

| Name = Saccharopepsin inhibitor I34

| image = PDB 1dp5 EBI.jpg

| width =

| caption = the structure of proteinase a complexed with an ia3 mutant inhibitor

| Pfam = PF10466

| Pfam_clan =

| InterPro = IPR019507

| SMART =

| PROSITE =

| MEROPS = I34

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

The saccharopepsin inhibitor I34 is highly specific for the aspartic peptidase saccharopepsin. In the absence of saccharopepsin it is largely unstructured,{{cite journal |vauthors=Green TB, Ganesh O, Perry K, Smith L, Phylip LH, Logan TM, Hagen SJ, Dunn BM, Edison AS | title = IA3, an aspartic proteinase inhibitor from Saccharomyces cerevisiae, is intrinsically unstructured in solution | journal = Biochemistry | volume = 43 | issue = 14 | pages = 4071–81 |date=April 2004 | pmid = 15065849 | doi = 10.1021/bi034823n }} but in its presence, the inhibitor undergoes a conformational change forming an almost perfect alpha-helix from Asn2 to Met32 in the active site cleft of the peptidase.

{{Infobox protein family

| Symbol = Inhibitor_I36

| Name = Peptidase inhibitor family I36

| image = PDB 1bhu EBI.jpg

| width =

| caption = the 3d structure of the streptomyces metalloproteinase inhibitor, smpi, isolated from streptomyces nigrescens tk-23, nmr, minimized average structure

| Pfam = PF03995

| Pfam_clan = CL0333

| InterPro = IPR007141

| SMART =

| PROSITE =

| MEROPS = I36

| SCOP = 1bhu

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

The peptidase inhibitor family I36 domain is only found in a small number of proteins restricted to Streptomyces species. All have four conserved cysteines that probably form two disulphide bonds. One of these proteins from Streptomyces nigrescens, is the well characterised metalloproteinase inhibitor SMPI.{{cite journal |vauthors=Tanaka K, Aoki H, Oda K, Murao S, Saito H, Takahashi H | title = Nucleotide sequence of the gene for a metalloproteinase inhibitor of Streptomyces nigrescens (SMPI) | journal = Nucleic Acids Res. | volume = 18 | issue = 21 | pages = 6433 |date=November 1990 | pmid = 2243793 | pmc = 332545 | doi = 10.1093/nar/18.21.6433}}{{cite journal |vauthors=Murai H, Hara S, Ikenaka T, Oda K, Murao S | title = Amino acid sequence of Streptomyces metallo-proteinase inhibitor from Streptomyces nigrescens TK-23 | journal = J. Biochem. | volume = 97 | issue = 1 | pages = 173–80 |date=January 1985 | pmid = 3888972 | doi = 10.1093/oxfordjournals.jbchem.a135041}}

The structure of SMPI has been determined. It has 102 amino acid residues with two disulphide bridges and specifically inhibits metalloproteinases such as thermolysin, which belongs to MEROPS peptidase family M4. SMPI is composed of two beta-sheets, each consisting of four antiparallel beta-strands. The structure can be considered as two Greek key motifs with 2-fold internal symmetry, a Greek key beta-barrel. One unique structural feature found in SMPI is in its extension between the first and second strands of the second Greek key motif which is known to be involved in the inhibitory activity of SMPI. In the absence of sequence similarity, the SMPI structure shows clear similarity to both domains of the eye lens crystallins, both domains of the calcium sensor protein-S, as well as the single-domain yeast killer toxin. The yeast killer toxin structure was thought to be a precursor of the two-domain beta gamma-crystallin proteins, because of its structural similarity to each domain of the beta gamma-crystallins. SMPI thus provides another example of a single-domain protein structure that corresponds to the ancestral fold from which the two-domain proteins in the beta gamma-crystallin superfamily are believed to have evolved.{{cite journal |vauthors=Ohno A, Tate S, Seeram SS, Hiraga K, Swindells MB, Oda K, Kainosho M | title = NMR structure of the Streptomyces metalloproteinase inhibitor, SMPI, isolated from Streptomyces nigrescens TK-23: another example of an ancestral beta gamma-crystallin precursor structure | journal = J. Mol. Biol. | volume = 282 | issue = 2 | pages = 421–33 |date=September 1998 | pmid = 9735297 | doi = 10.1006/jmbi.1998.2022}}

{{Infobox protein family

| Symbol = Inhibitor_I42

| Name = Chagasin family peptidase inhibitor I42

| image = PDB 2fo8 EBI.jpg

| width =

| caption = solution structure of the trypanosoma cruzi cysteine protease inhibitor chagasin

| Pfam = PF09394

| Pfam_clan =

| InterPro = IPR018990

| SMART =

| PROSITE =

| MEROPS = I42

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

Inhibitor family I42 includes chagasin, a reversible inhibitor of papain-like cysteine proteases.{{cite journal |vauthors=Monteiro AC, Abrahamson M, Lima AP, Vannier-Santos MA, Scharfstein J | title = Identification, characterization and localization of chagasin, a tight-binding cysteine protease inhibitor in Trypanosoma cruzi | journal = J. Cell Sci. | volume = 114 | issue = Pt 21 | pages = 3933–42 |date=November 2001 | doi = 10.1242/jcs.114.21.3933 | pmid = 11719560 }} Chagasin has a beta-barrel structure, which is a unique variant of the immunoglobulin fold with homology to human CD8alpha.{{cite journal |author1=Figueiredo da Silva AA |author2=de Carvalho Vieira L |author3=Krieger MA |author4=Goldenberg S |author5=Zanchin NI |author6=Guimarães BG | title = Crystal structure of chagasin, the endogenous cysteine-protease inhibitor from Trypanosoma cruzi | journal = J. Struct. Biol. | volume = 157 | issue = 2 | pages = 416–23 |date=February 2007 | pmid = 17011790 | doi = 10.1016/j.jsb.2006.07.017 }}{{cite journal |vauthors=Wang SX, Pandey KC, Scharfstein J, Whisstock J, Huang RK, Jacobelli J, Fletterick RJ, Rosenthal PJ, Abrahamson M, Brinen LS, Rossi A, Sali A, McKerrow JH | title = The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family | journal = Structure | volume = 15 | issue = 5 | pages = 535–43 |date=May 2007 | pmid = 17502099 | doi = 10.1016/j.str.2007.03.012 | doi-access = free }}

{{Infobox protein family

| Symbol = Inhibitor_I48

| Name = Peptidase inhibitor clitocypin

| image =

| width =

| caption = clitocypin, a beta-trefoil cysteine protease inhibitor

| Pfam = PF10467

| Pfam_clan =

| InterPro = IPR019508

| SMART =

| PROSITE =

| MEROPS = I48

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

Inhibitor family I48 includes clitocypin, which binds and inhibits cysteine proteinases. It has no similarity to any other known cysteine proteinase inhibitors but bears some similarity to a lectin-like family of proteins from mushrooms.{{cite journal |vauthors=Brzin J, Rogelj B, Popovic T, Strukelj B, Ritonja A | title = Clitocypin, a new type of cysteine proteinase inhibitor from fruit bodies of mushroom clitocybe nebularis | journal = J. Biol. Chem. | volume = 275 | issue = 26 | pages = 20104–9 |date=June 2000 | pmid = 10748021 | doi = 10.1074/jbc.M001392200 | doi-access = free }}

{{Infobox protein family

| Symbol = Inhibitor_I53

| Name = Thrombin inhibitor Madanin

| image =

| width =

| caption =

| Pfam = PF11714

| Pfam_clan =

| InterPro = IPR021716

| SMART =

| PROSITE =

| MEROPS = I53

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

Members of this family are the peptidase inhibitor madanin proteins. These proteins were isolated from tick saliva.{{cite journal |vauthors=Iwanaga S, Okada M, Isawa H, Morita A, Yuda M, Chinzei Y | title = Identification and characterization of novel salivary thrombin inhibitors from the ixodidae tick, Haemaphysalis longicornis | journal = Eur. J. Biochem. | volume = 270 | issue = 9 | pages = 1926–34 |date=May 2003 | pmid = 12709051 | doi = 10.1046/j.1432-1033.2003.03560.x| doi-access = free }}

{{Infobox protein family

| Symbol = Inhibitor_I67

| Name = Bromelain inhibitor VI

| image = PDB 1bi6 EBI.jpg

| width =

| caption = nmr structure of bromelain inhibitor vi from pineapple stem

| Pfam = PF11405

| Pfam_clan =

| InterPro = IPR022713

| SMART =

| PROSITE =

| MEROPS = I67

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

Bromelain inhibitor VI, in the Inhibitor I67 family, is a double-chain inhibitor consisting of an 11-residue and a 41-residue chain.

{{Infobox protein family

| Symbol = Inhibitor_I68

| Name = Carboxypeptidase inhibitor I68

| image = PDB 1zli EBI.jpg

| width =

| caption = crystal structure of the tick carboxypeptidase inhibitor in complex with human carboxypeptidase B

| Pfam = PF10468

| Pfam_clan =

| InterPro = IPR019509

| SMART =

| PROSITE =

| MEROPS = I68

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

The Carboxypeptidase inhibitor I68 family represents a family of carboxypeptidase inhibitors found in ticks.{{Cite journal |last1=Porter |first1=Lindsay M. |last2=Radulović |first2=Željko M. |last3=Mulenga |first3=Albert |date=2017 |title=A repertoire of protease inhibitor families in Amblyomma americanum and other tick species: inter-species comparative analyses |journal=Parasites & Vectors |language=en |volume=10 |issue=1 |page=152 |doi=10.1186/s13071-017-2080-1 |doi-access=free |issn=1756-3305 |pmc=5361777 |pmid=28330502}}

{{Infobox protein family

| Symbol = Inhibitor_I78

| Name = Peptidase inhibitor I78 family

| image =

| width =

| caption =

| Pfam = PF11720

| Pfam_clan = CL0367

| InterPro = IPR021719

| SMART =

| PROSITE =

| MEROPS = I78

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

The peptidase inhibitor I78 family includes Aspergillus elastase inhibitor.

• Aprotinin
• Bestatin
• Calpain inhibitor I and II
• Chymostatin
• E-64
• Leupeptin (N-acetyl-L-leucyl-L-leucyl-L-argininal)
• alpha-2-Macroglobulin
• Pefabloc SC
• Pepstatin
• PMSF (phenylmethanesulfonyl fluoride)
• TLCK
• Trypsin inhibitors

• Kunitz domain
• Pacifastin
• Proteinase inhibitors in plants

{{Reflist}}

• [http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/Enzyme_Explorer/Key_Resources/Protease_Inhibitors/Broad_Spectrum_Inhib_.html Sigma-Aldrich protease inhibitor overview]

{{Enzyme inhibition}}

{{InterPro content|IPR022217}}

{{InterPro content|IPR019506}}

{{InterPro content|IPR013201}}

{{InterPro content|IPR019507}}

{{InterPro content|IPR007141}}

{{InterPro content|IPR018990}}

{{InterPro content|IPR019508}}

{{InterPro content|IPR021716}}

{{InterPro content|IPR022713}}

{{InterPro content|IPR019509}}

{{InterPro content|IPR021719}}

{{InterPro content|IPR010259}}

{{Authority control}}

Category:Protein families