1 Introduction
Proteolytic enzymes, i.e., proteases, are among the most important enzymes active in the processes of monitoring metabolic pathways in living organisms (Drag & Salvesen, 2010; Turk, 2006). Hydrolysis of the peptide binding of the protein and peptide substrates catalyzed by them is considered the key irreversible post-translational modification. Substrate hydrolysis by proteases is strictly controlled, and any imbalance in this system leads to disorders in their functioning (Drag & Salvesen, 2010). An apt example is the process of controlled cell death, known as apoptosis. It is strictly controlled by proteases from the group of caspases (G. S. Salvesen & Dixit, 1997). Disorders of the activity of caspases may lead to two types of diseases depending on the
Proteases are classified according to their mechanism of action and the location of hydrolysis (Drag & Salvesen, 2010). In the latter classification, proteases from the group of exopeptidases hydrolyze amino acids from the N-terminus (aminopeptidases) or C-terminus (carboxypeptidases) of the substrate, while a very large group of proteases hydrolyzing substrates in the middle of the peptide chain constitute the group of endopeptidases. Recognition of substrates is based on the specific fit of the twenty amino acid residues encoded by DNA into the binding pocket of the protease. These amino acids can be bound to the C-terminus of the protein substrate, counting from the site of hydrolysis, and then depending on the pocket they are referred to as P1′, P2′ and Pn′. Amino acids that are bound to the N-terminus of the protein substrate are termed P1, P2 and Pn (Deu et al., 2012; M. Poreba & Drag, 2010).
2 From Simplicity to Complexity of Proteases and Their Binding Mechanisms
Depending on the type of protease, the mechanism of binding substrates can be relatively simple or complex. Therefore, for example, the simplest system can be distinguished in the case of the proteolytic enzymes from the group of aminopeptidases or carboxypeptidases, which hydrolyze single amino acids from the ends of the peptide chain (Drag & Salvesen, 2010). For instance, in the case of aminopeptidases, which hydrolyze amino acids from the N-terminus of the peptide, the key is to recognize first of all the amino acid binding in the S1 pocket (i.e., enzyme’s subsite/binding site), because only this one is hydrolyzed. Of course, in the aspect of the mechanism of binding of the whole substrate, a certain role may also be played by the S1′ or S2′ pocket, but it is considered that the determinant of the specificity is precisely the binding of the amino acid to the S1 pocket. This is confirmed by numerous studies on the substrate specificity of aminopeptidases applying fluorogenic substrate libraries consisting of natural as well as unnatural (not coded by DNA) amino acids and reporter groups in the form of a fluorophore (Kasperkiewicz et al., 2012). Moreover, considering the preferences of aminopeptidases, we can carry out further analysis and distinguish those proteases that are characterized by high simplicity in the aspect of substrate
The simplest proteases undoubtedly include methionine aminopeptidases. An analysis of the substrate specificity of these enzymes showed that among all natural amino acids, they practically exclusively recognize methionine, while among the unnatural ones, only a few are structural analogs of methionine (Marcin Poreba, Gajda, et al., 2012). This is not particularly surprising, as the role of methionine aminopeptidases is the hydrolysis of N-terminal methionine with freshly expressed proteins in ribosomes. A considerably more complex system can be observed in the case of such aminopeptidases as leukotriene aminopeptidase (LT4AH), aminopeptidase N (APN) or for example leucyl aminopeptidase (Byzia et al., 2014; Drag et al., 2010; Marcin Poreba, McGowan, et al., 2012; Węglarz-Tomczak et al., 2013). These enzymes demonstrate great tolerance for natural amino acids and unnatural amino acids. For example, leukotriene aminopeptidase shows several dozen times greater affinity towards selected unnatural amino acids (e.g., benzyl esters of aspartic acid and glutamic acid, homoarginine) compared to its best natural amino acid, which is arginine (Byzia et al., 2014). The increased specificity and simultaneous complexity of recognized structures result from the function of these enzymes that are not as specialized as methionine aminopeptidases. All aminopeptidases with broad substrate specificity are responsible for processing numerous types of protein substrates and peptides, necessitating their ability to recognize many types of structural amino acids.
A somewhat more complex system is observed in the case of dipeptidyl aminopeptidases, which hydrolyze the dipeptide fragment from the substrate N-terminus. A classic example is cathepsin C, a lysosomal cysteine protease belonging to the papain protease family that participates in the activation of numerous other proteases, and is also involved in the development of diseases such as Haim-Munk syndrome and Papillon-Lefèvre syndrome (Mohamed & Sloane, 2006; Yuan et al., 2006). The multitasking ability of this enzyme implicates almost automatically its broad substrate specificity, and in consequence structural complexity of recognized amino acids (Wang et al., 2011). Moreover, this enzyme is also more complex in terms of the number of amino acids that it binds to and recognizes in order to function correctly. Therefore, cathepsin C has very well-defined pockets binding S1 and S2, and also the pockets S1′ and S2′. Studies on substrate specificity using a targeted fluorogenic substrate library towards the S1 and S2 pockets applying human, bovine and malaria orthologs showed that in the S1 pocket, mammalian orthologs present a much more complex palette of recognized natural and unnatural amino acids. The most active amino acid in the case of all three enzymes was L-Nle(O-Bzl), while
Certainly, the most complex system for recognizing specific amino acids in peptide and protein substrates is that of proteolytic enzymes from the group of endopeptidases. These enzymes constitute the largest group of proteases and are involved in key processes controlling metabolic pathways. One of the more important groups within this category is caspases, which are involved in apoptosis (Pop & Salvesen, 2009).It is a very complex system of enzymes that are divided into initiator caspases (caspase 2, 8, 9 and 10) and executioner caspases (caspase 3, 6 and 7). For the apoptosis to proceed correctly, initiator caspases have to be activated by activating factors, and then active initiator caspases activate executioner procaspases into active enzymes (Riedl & Salvesen, 2007; Guy S. Salvesen & Riedl, 2008).
The whole process involves activation by hydrolysis of executioner caspases, which subsequently hydrolyze protein substrates inside the cell. A key aspect is the ability of individual caspases to recognize specific peptide sequences. Notably, all caspases have the specificity to exclusively recognize aspartic acid in position P1, while positions P2-P4 are somewhat more complex. Practically all caspases recognize the most natural amino acids in these positions. This confirms the broad range of substrates processed by them. Interestingly, many caspases have very similar profiles of substrate specificity. This was shown by the studies on the substrate specificity of all caspases using a tetrapeptide combinatorial library of fluorogenic substrates (Thornberry et al., 1997). Examples of such caspases include caspases 4 and 5, caspases 3 and 7, and caspases 6 and 8. This interesting example shows that even a complicated palette of 20 natural amino acids is not sufficient to differentiate similar enzymes in the three binding pockets (S2–S4). Interestingly, many of these sequences were used in key biological studies concerning caspases, with researchers carrying out these studies often unaware that the substrates they used were recognized by more than one enzyme. The complexity of an apoptotic system caused several caspases to be active simultaneously, and the activity registered using fluorogenic or chromogenic substrates reflects the combined activity of these caspases. A few years ago, the groups of Salvesen and Green showed for the first time that this is a major problem while interpreting results, and proved at the same time that in
The next interesting example is that of neutrophil serine proteases, which include neutrophil elastase, cathepsin G, proteinase 3 and NSP4 (Perera et al., 2013; Pham, 2006). These enzymes occur in neutrophils and are responsible for their correct functioning. However, the disturbance of their activity, for instance, in the case of neutrophil elastase may lead to the development of lung cancer and other lung diseases (Moroy et al., 2012). Moreover, these enzymes are involved in the process of creating active neutrophil extracellular traps responsible for combating pathogens (Brinkmann et al., 2004; O’Donoghue et al., 2013). These proteases were very well characterized and described. The substrate specificity towards natural amino acids of all these proteases is also known (Perera et al., 2013; Rawlings et al., 2014; Schilling & Overall, 2008). However, the greatest problem was creating specific chemical tools for their study. Similarly, as in the case of caspases, these enzymes recognized similar sequences, which prevented effective studies of their functions in the biological system. Particularly difficult here were neutrophil elastase and proteinase 3, which showed a very similar profile of substrate specificity (Kasperkiewicz et al., 2014). What is more, the existing substrates and inhibitors based on simple natural amino acids were not sufficiently active in biological systems.To address this issue the solution was to replace simple substrate libraries with much more complex hybrid fluorogenic substrate libraries containing natural amino acids as well as an extensive collection of unnatural amino acids. The performed studies on substrate specificity allowed the selection of a substrate that was several hundred times more selective
Another interesting example of such simplicity and simultaneous complexity is that comprising the whole group of deubiquitinating endoproteases (DUB proteases), whose function is the activation and processing of ubiquitin (Russell & Wilkinson, 2005). The complexity of this system is such that to date over a hundred enzymes belonging to this family have successfully been characterized and identified. Its simplicity, on the other hand, consists in the fact that practically all these enzymes recognize only one substrate, the small protein ubiquitin. This phenomenon is fascinating in that many of these enzymes act at the same time and in the same place, and it is very difficult to understand their co-dependence in the processing of ubiquitin (Eletr & Wilkinson, 2014). What is more, the latest studies prove that many of these enzymes specialize in processing specific chain forms of polyubiquitin (Reyes-Turcu et al., 2009). Analogical to this are desumoylating proteases (SENP s) which process SUMO protein substrates structurally similar to ubiquitin (SUMO-1, 2 and 3) (Mikolajczyk et al., 2007). Also in this case it is not fully known at present which mechanisms direct this whole system. It is certainly known that deubiquitinating proteases as well as desumoylating proteases have substrate specificity determined with the help of combinatorial fluorogenic substrate libraries in the S1-S4 pockets very similar to those occurring in their natural substrates, that is LRGG for ubiquitin and QTGG for SUMO (Drag, Mikolajczyk, Bekes, et al., 2008; Drag, Mikolajczyk, Krishnakumar, et al., 2008). One of the greatest challenges at present is to investigate these systems, particularly taking into consideration the great medical value of these enzymes which participate in the development processes of cancers and neurodegenerative diseases (Lim & Baek, 2013).
3 Conclusions
In summary, it can be concluded that proteolytic enzymes, regardless of their classification based on the site of hydrolysis of peptide bonds, can have either straightforward substrate specificity or, what is more often observed, a highly
References
Berger, A. B., Sexton, K. B., & Bogyo, M. (2006). Commonly used caspase inhibitors designed based on substrate specificity profiles lack selectivity. Cell Research, 16(12), 961–963.
Brinkmann, V., Reichard, U., Goosmann, C., Fauler, B., Uhlemann, Y., Weiss, D. S., Weinrauch, Y., & Zychlinsky, A. (2004). Neutrophil extracellular traps kill bacteria. Science, 303(5663), 1532–1535.
Byzia, A., Haeggström, J. Z., Salvesen, G. S., & Drag, M. (2014). A remarkable activity of human Leukotriene A4 Hydrolase (LTA4H) toward unnatural amino acids. Amino Acids, 46(5), 1313–1320.
Deu, E., Verdoes, M., & Bogyo, M. (2012). New approaches for dissecting protease functions to improve probe development and drug discovery. Nature Structural & Molecular Biology, 19(1), 9–16.
Drag, M., Bogyo, M., Ellman, J. A., & Salvesen, G. S. (2010). Aminopeptidase fingerprints, an integrated approach for identification of good substrates and optimal inhibitors. The Journal of Biological Chemistry, 285(5), 3310–3318.
Drag, M., Mikolajczyk, J., Bekes, M., Reyes-Turcu, F. E., Ellman, J. A., Wilkinson, K. D., & Salvesen, G. S. (2008). Positional-scanning fluorigenic substrate libraries reveal unexpected specificity determinants of DUB s (deubiquitinating enzymes). Biochemical Journal, 415(3), 367–375.
Drag, M., Mikolajczyk, J., Krishnakumar, I. M., Huang, Z., & Salvesen, G. S. (2008). Activity profiling of human deSUMOylating enzymes (SENP s) with synthetic substrates suggests an unexpected specificity of two newly characterized members of the family. Biochemical Journal, 409(2), 461–469.
Drag, M., & Salvesen, G. S. (2010). Emerging principles in protease-based drug discovery. Nature Reviews. Drug Discovery, 9(9), 690–701.
Eletr, Z. M., & Wilkinson, K. D. (2014). Regulation of proteolysis by human deubiquitinating enzymes. Biochimica et Biophysica Acta, 1843(1), 114–128.
Kasperkiewicz, P., Gajda, A. D., & Drąg, M. (2012). Current and prospective applications of non-proteinogenic amino acids in profiling of proteases substrate specificity. Biological Chemistry, 393(9), 843–851.
Kasperkiewicz, P., Poreba, M., Snipas, S. J., Parker, H., Winterbourn, C. C., Salvesen, G. S., & Drag, M. (2014). Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling. Proceedings of the National Academy of Sciences of the United States of America, 111(7), 2518–2523.
Lim, K.-H., & Baek, K.-H. (2013). Deubiquitinating enzymes as therapeutic targets in cancer. Current Pharmaceutical Design, 19(22), 4039–4052.
McStay, G. P., Salvesen, G. S., & Green, D. R. (2008). Overlapping cleavage motif selectivity of caspases: Implications for analysis of apoptotic pathways. Cell Death and Differentiation, 15(2), 322–331.
Mikolajczyk, J., Drag, M., Békés, M., Cao, J. T., Ronai, Z. ’ev, & Salvesen, G. S. (2007). Small Ubiquitin-related Modifier (SUMO)-specific proteases: profiling the specificities and activities of human SENP s. The Journal of Biological Chemistry, 282(36), 26217–26224.
Mohamed, M. M., & Sloane, B. F. (2006). Cysteine cathepsins: multifunctional enzymes in cancer. Nature Reviews. Cancer, 6(10), 764–775.
Moroy, G., Alix, A. J. P., Sapi, J., Hornebeck, W., & Bourguet, E. (2012). Neutrophil elastase as a target in lung cancer. Anti-Cancer Agents in Medicinal Chemistry, 12(6), 565–579.
O’Donoghue, A. J., Jin, Y., Knudsen, G. M., Perera, N. C., Jenne, D. E., Murphy, J. E., Craik, C. S., & Hermiston, T. W. (2013). Global substrate profiling of proteases in human neutrophil extracellular traps reveals consensus motif predominantly contributed by elastase. PLoS One, 8(9), e75141.
Perera, N. C., Wiesmüller, K.-H., Larsen, M. T., Schacher, B., Eickholz, P., Borregaard, N., & Jenne, D. E. (2013). NSP4 is stored in azurophil granules and released by activated neutrophils as active endoprotease with restricted specificity. Journal of Immunology, 191(5), 2700–2707.
Pham, C. T. N. (2006). Neutrophil serine proteases: Specific regulators of inflammation. Nature Reviews. Immunology, 6(7), 541–550.
Pop, C., & Salvesen, G. S. (2009). Human caspases: Activation, specificity, and regulation. The Journal of Biological Chemistry, 284(33), 21777–21781.
Poreba, M., & Drag, M. (2010). Current strategies for probing substrate specificity of proteases. Current Medicinal Chemistry, 17(33), 3968–3995.
Poreba, M., Gajda, A., Picha, J., Jiracek, J., Marschner, A., Klein, C. D., Salvesen, G. S., & Drag, M. (2012). S1 pocket fingerprints of human and bacterial methionine aminopeptidases determined using fluorogenic libraries of substrates and phosphorus based inhibitors. Biochimie, 94(3), 704–710.
Poreba, M., Kasperkiewicz, P., Snipas, S. J., Fasci, D., Salvesen, G. S., & Drag, M. (2014). Unnatural amino acids increase sensitivity and provide for the design of highly selective caspase substrates. Cell Death and Differentiation, 21(9), 1482–1492.
Poreba, M., McGowan, S., Skinner-Adams, T. S., Trenholme, K. R., Gardiner, D. L., Whisstock, J. C., To, J., Salvesen, G. S., Dalton, J. P., & Drag, M. (2012). Fingerprinting the substrate specificity of M1 and M17 aminopeptidases of human malaria, Plasmodium falciparum. PLoS One, 7(2), e31938.
Poreba, M., Mihelic, M., Krai, P., Rajkovic, J., Krezel, A., Pawelczak, M., Klemba, M., Turk, D., Turk, B., Latajka, R., & Drag, M. (2014). Unnatural amino acids increase activity and specificity of synthetic substrates for human and malarial cathepsin C. Amino Acids, 46(4), 931–943.
Rawlings, N. D., Barrett, A. J., & Bateman, A. (2014). Using the MEROPS database for proteolytic enzymes and their inhibitors and substrates. Current Protocols in Bioinformatics/Editoral Board, Andreas D. Baxevanis … [et al.], 48, 1.25.1–1.25.33.
Reyes-Turcu, F. E., Ventii, K. H., & Wilkinson, K. D. (2009). Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annual Review of Biochemistry, 78, 363–397.
Riedl, S. J., & Salvesen, G. S. (2007). The apoptosome: Signalling platform of cell death. Nature Reviews. Molecular Cell Biology, 8(5), 405–413.
Russell, N. S., & Wilkinson, K. D. (2005). Deubiquitinating enzyme purification, assay inhibitors, and characterization. Methods in Molecular Biology, 301, 207–219.
Salvesen, G. S., & Dixit, V. M. (1997). Caspases: Intracellular signaling by proteolysis. Cell, 91(4), 443–446.
Salvesen, G. S., & Riedl, S. J. (2008). Caspase mechanisms. Advances in Experimental Medicine and Biology, 615, 13–23.
Schilling, O., & Overall, C. M. (2008). Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nature Biotechnology, 26(6), 685–694.
Thornberry, N. A., Rano, T. A., Peterson, E. P., Rasper, D. M., Timkey, T., Garcia-Calvo, M., Houtzager, V. M., Nordstrom, P. A., Roy, S., Vaillancourt, J. P., Chapman, K. T., & Nicholson, D. W. (1997). A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis. The Journal of Biological Chemistry, 272(29), 17907–17911.
Turk, B. (2006). Targeting proteases: Successes, failures and future prospects. Nature Reviews. Drug Discovery, 5(9), 785–799.
Wang, F., Krai, P., Deu, E., Bibb, B., Lauritzen, C., Pedersen, J., Bogyo, M., & Klemba, M. (2011). Biochemical characterization of Plasmodium falciparum dipeptidyl aminopeptidase 1. Molecular and Biochemical Parasitology, 175(1), 10–20.
Węglarz-Tomczak, E., Poręba, M., Byzia, A., Berlicki, Ł., Nocek, B., Mulligan, R., Joachimiak, A., Drąg, M., & Mucha, A. (2013). An integrated approach to the ligand binding specificity of Neisseria meningitidis M1 alanine aminopeptidase by fluorogenic substrate profiling, inhibitory studies and molecular modeling. Biochimie, 95(2), 419–428.
Yuan, F., Verhelst, S. H. L., Blum, G., Coussens, L. M., & Bogyo, M. (2006). A selective activity-based probe for the papain family cysteine protease dipeptidyl peptidase I/cathepsin C. Journal of the American Chemical Society, 128(17), 5616–5617.