Cytokine-mediated proteolysis in tissue remodelling

Proteolytic enzymes play a key role in a variety of physiological processes in which the degradation of macromolecules is essential: angiogenesis, embryogenesis, bone and tissue remodelling, blood hemostasis and cell migration. The action of these enzymes is also crucial in the development of many pathological conditions such as wound healing, neoplasia, inflammation and arthritic disorders. The activity of proteases is negatively affected by specific protease-inhibitors. Various growth factors and other cytokines modulate the synthesis and secretion of both proteases and protease-inhibitors. The study of this regulation results in a better insight into (patho)physiology at the molecular level and promises to result in alternative treatment strategies.     

Über die Funktion der Eiweissdrüse vonHelix pomatia

Summary A strong immunological crossreactivity between the extracts of the albumin gland of snails (Helix pomatia) and the content of snail eggs is described, suggesting that the former supplies the eggs with protective substances (agglutinins, protease-inhibitors).     

Proteases in apoptosis

The interleukin-1 β-converting enzyme (ICE)-like family proteases have recently been identified as key enzymes in apoptotic cell death. Among these proteases one can identify specific activities which may be involved in cytokine production or in resident protein cleavage. Several factors influence the constitutive apoptotic mechanism and may provide insight into the role of protease(s) in apoptosis. Although it appears that ICE family members play a most important role in promoting apoptotic cell death, evidence has been advanced that other proteases are also involved in sequential or parallel steps of apoptosis. Activation of a particular protease can lead to processing molecules either of the same or different proteases, leading to an activation of a protease cascade. Here we attempt to summarize the current thinking concerning these proteases and their involvement in apoptosis.     

Proteases and protein degradation in Escherichia coli.

In E. coli, protein degradation plays important roles in regulating the levels of specific proteins and in eliminating damaged or abnormal proteins. E. coli possess a very large number of proteolytic enzymes distributed in the cytoplasm, the inner membrane, and the periplasm, but, with few exceptions, the physiological functions of these proteases are not known. More than 90% of the protein degradation occurring in the cytoplasm is energy-dependent, but the activities of most E. coli proteases in vitro are not energy-dependent. Two ATP-dependent proteases, Lon and Clp, are responsible for 70-80% of the energy-dependent degradation of proteins in vivo. In vitro studies with Lon and Clp indicate that both proteases directly interact with substrates for degradation. ATP functions as an allosteric effector promoting an active conformation of the proteases, and ATP hydrolysis is required for rapid catalytic turnover of peptide bond cleavage in proteins. Lon and Clp show virtually no homology at the amino acid level, and thus it appears that at least two families of ATP-dependent proteases have evolved independently.     

Deciphering cryptic proteases

Proteases are deeply involved in physiology and pathology. For most, the mechanism is well defined but several fail to display typical protease features (as is the case of the four proteases contained in fibronectin, the inhibitor-resistant mesotrypsin and the proteosomal deubiquitinating enzyme) or have unclear physiological function (such as calpain-like proteins, transthyretin and factor seven activating protease). In other cases, such as in peroxisomal processing proteases, although substrates are defined, the enzyme remains undiscovered. Furthermore, several proteases were identified in pathological conditions, namely secretases in Alzheimers disease and gross cystic disease fluid protein 15 kDa in breast cancer, when most likely their physiological substrate is still hidden. Lastly, the evolutionary conservation of proteolytic enzymes raises questions related to the origin of biological events, such as the origin of cystein proteases and cell death responses. In this review we will discuss the above cryptic enzymes, as they will probably be relevant in the future.Received 7 December 2004; received after revision 5 January 2005; accepted 10 January 2005 Available online 09 March 2005     

Proteases and protein degradation inEscherichia coli

InE. coli, protein degradation plays important roles in regulating the levels of specific proteins and in eliminating damaged or abnormal proteins.E. coli possess a very large number of proteolytic enzymes distributed in the cytoplasm, the inner membrane, and the periplasm, but, with few exceptions, the physiological functions of these proteases are not known. More than 90% of the protein degradation occurring in the cytoplasm is energy-dependent, but the activities of mostE. coli proteases in vitro are not energy-dependent. Two ATP-dependent proteases, Lon and Clp, are responsible for 70–80% of the energy-dependent degradation of proteins in vivo. In vitro studies with Lon and Clp indicate that both proteases directly interact with substrates for degradation. ATP functions as an allosteric effector promoting an active conformation of the proteases, and ATP hydrolysis is required for rapid catalytic turnover of peptide bond cleavage in proteins. Lon and Clp show virtually no homology at the amino acid level, and thus it appears that at least two families of ATP-dependent proteases have evolved independently.     

Debriding ability of a novel multi-enzyme preparation isolated from Antarctic krill (Euphausia superba)

Summary The wound-debriding activity of various types of proteolytic enzymes and proteases from Antarctic krill (multi-enzyme system consisting of both endo- and exopeptidases) was evaluated. The results, based on the enzymatically acieved weight reduction of a necrotic animal material (excised rat skin) in vitro, clearly showed that the multi-enzyme system (krill) had a higher degrading activity than the single enzyme preparation, or that with only a few enzymes. The debriding effect of the krill enzymes was markedly related to the enzyme concentration, resulting in 70–100% substrate degradation after 24 h. The digesting capacity of trypsin reached about 50%, but an increase in concentration of this enzyme did not substantially influence its overall activity. The effect of streptokinase-streptodornase, collagenase and plasmin-desoxyribonuclease was weak (10–20% digested).     

Molecular mechanisms of thrombin function

The discovery of thrombin as a Na⁺-dependent allosteric enzyme has revealed a novel strategy for regulating protease activity and specificity. The allosteric nature of this enzyme influences all its physiologically important interactions and rationalizes a large body of structural and functional information. For the first time, a coherent mechanistic framework is available for understanding how thrombin interacts with fibrinogen, thrombomodulin and protein C, and how Na⁺ binding influences the specificity sites of the enzyme. This information can be used for engineering thrombin mutants with selective specificity towards protein C and for the rational design of potent active site inhibitors. Thrombin also serves as a paradigm for allosteric proteases. Elucidation of the molecular basis of the Na⁺-dependent allosteric regulation of catalytic activity, based on the residue present at position 225, provides unprecedented insights into the function and evolution of serine proteases. This mechanism represents one of the simplest and most important structure-function correlations ever reported for enzymes in general. All vitamin K-dependent proteases and some complement factors are subject to the Na⁺-dependent regulation discovered for thrombin. Na⁺ is therefore a key factor in the activation of zymogens in the coagulation and complement systems.     

Resistance of purified cholera toxin to enzymatic treatment with pancreatic elastase and papain

Summary Treatment of Cholera toxin with pancreatic elastase and papain in vitro shoed a high resistance of the toxin molecule to these enzymes, under non-denaturing conditions or in the presence of 2M urea. These experiments support the hypothesis of a particularly stable molecular structure of the toxin, as an explanation of its activity in the intestinal lumen where the pancreatic proteases are active.     

New developments in enzymatic peptide synthesis.

This review article describes new enzymatic methods developed for the efficient and irreversible synthesis of peptides based on native and modified proteases, and for the synthesis of polypeptides containing D- and/or unnatural amino acids. Potential opportunities for future developments in the field based on new enzymes, tailor-made catalytic antibodies, and on the technique of in vitro mutagenesis are also described.     

Strategies for the inhibition of serine proteases

Serine proteases have been shown to play a multifarious role in health and disease. As a result, there has been considerable interest in the design and development of synthetic inhibitors of these enzymes. In view of their diverse roles in biological processing events, one of the great challenges in such endeavours has been the need to produce compounds with exquisite selectivity. Inhibitor design has been broadly guided by the use of either peptide- or heterocyclic-based compounds, designed to exploit the known substrate specificity characteristics of individual enzymes. This review describes the thinking and strategies employed in such efforts. Received 8 August 2000; received after revision 16 November 2000; accepted 17 November 2000     

Snake venom thrombin-like enzymes: from reptilase to now

The snake venom thrombin-like enzymes (SVTLEs) comprise a number of serine proteases functionally and structurally related to thrombin. Until recently, only nine complete sequences of this subgroup of the serine protease family were known. Over the past 5 years, the primary structure of several SVTLEs has been characterized, and now this family includes several members. Of particular interest is their possible use in pathologies such as thrombosis. The aim of the present review is to summarize the state of the art concerning the evolutionary, structural and biological features of the SVTLEs.Received 16 August 2003; received after revision 26 September 2003; accepted 1 October 2003     

New developments in enzymatic peptide synthesis

This review article describes new enzymatic methods developed for the efficient and irreversible synthesis of peptides based on native and modified proteases, and for the synthesis of polypeptides containing D- and/or unnatural amino acids. Potential opportunities for future developments in the field based on new enzymes, tailormade catalytic antibodies, and on the technique of in vitro mutagenesis are also described.     

Protein structure to function: insights from computation

Computation plays an important role in functional genomics. THEMATICS is a computational method that predicts chemical and electrostatic properties of residues in enzymes and utilizes information contained in those predictions to identify active sites. The only input required is the three-dimensional structure of the query protein. The identification of residues involved in catalysis and in recognition is discussed. The two serine proteases Kex2 from Saccharomyces cerevisiae and subtilisin from Bacillus subtilis are used as examples to illustrate how the method finds the catalytic residues for both enzymes. In addition, Kex2 is specific for dibasic sites and THEMATICS finds the recognition residues for both the S1 and S2 sites of Kex2. In contrast, no such recognition sites are found for the non-specific enzyme subtilisin. The ability to identify sites that govern recognition opens the door to better understanding of specificity and to the design of highly specific inhibitors.Received 22 July 2003; received after revision 16 September 2003; accepted 20 October 2003     

Proteases in cutaneous malignant melanoma: relevance as biomarker and therapeutic target

Cutaneous malignant melanoma is the most aggressive skin cancer. It is also the most rapidly spreading cancer in terms of worldwide incidence. Although it is detected by simple inspection and can be relatively easily removed or treated, differential diagnosis to other melanocytic lesions, lack of prognostic markers, and no efficient treatment of advanced melanoma pose problems. Detection and targeting of proteases may represent a useful tool since they play a role in tumor cell metabolism, invasion, angiogenesis and metastasis. This review gives an overview of the role of proteases in development and progression of cutaneous malignant melanoma. In addition, regulation, activation, and interaction of proteases and their inhibitors are explained for tumors in general. The potential use of proteases as differential markers for melanoma mimicking melanocytic lesions, as biomarkers in tissues, and as prognostic serum markers is discussed. Current and future possibilities to target tumor proteases in therapy are presented.     

Timing of action of sperm proteases in ascidian fertilization

Summary The timing of action of three sperm proteases, acrosin, spermosin, and a chymotrypsin-like enzyme, in the fertilization of the ascidian,Halocynthia roretzi, was examined by adding specific protease inhibitors at various times after insemination. The results indicate that the last two enzymes both function at the early stage of the process of sperm penetration through the egg investment, while acrosin functions at the late stage.Acknowledgments. We are indebted to Dr M. Hoshi of Tokyo Institute of Technology for his helpful discussion, and to Dr T. Someno of Nippon Kayaku Kogyo Co. for his generous gifts of Z-Val-Pro-Arg-H and leupeptin. This work was supported by Grants-in-Aid from the Ministry of Education, Science and Culture of Japan, and from Naito Research Foundation.     

ATP-dependent proteases controlling mitochondrial function in the yeast Saccharomyces cerevisiae

Regulated protein degradation by ATP-dependent proteases plays a fundamental role in the biogenesis of mitochondria. Membrane-bound and soluble ATP-dependent proteases have been identified in various subcompartments of this organelle. Subunits composing these proteases are evolutionarily conserved from yeast to humans and, in support of an endosymbiotic origin of mitochondria, evolved from prokaryotic ancestors: the PIM1/Lon protease is active in the matrix of mitochondria, while the i-AAA protease and the m-AAA protease mediate the turnover of inner membrane proteins. Most of the knowledge concerning the biogenesis and the physiological role of ATP-dependent proteases comes from studies in the yeast Saccharomyces cerevisiae. Proteases were found to be required for mitochondrial stasis, for the maintenance of the morphology of the organelle and for mitochondrial genome integrity. ATP-dependent proteolysis is crucial for the expression of mitochondrially encoded subunits of respiratory chain complexes and for the assembly of these complexes. Hence, mitochondrial ATP-dependent proteases exert multiple roles which are essential for the maintenance of cellular respiratory competence.     

Recent progress in understanding the diversity of the human ov-serpin/clade B serpin family

The inhibitory mechanism against proteases is important in the maintenance of homeostasis or health in the body. The human ovalbumin serpin (ovserpin)/ clade B serpin family is one group of the human serpins, a family of serine protease inhibitors. They have acquired diversity in the profiles of target proteases, inhibitory mechanisms, and localization patterns during their evolution. Most serpins target serine proteases, however, some ov-serpins target only cysteine proteases or both serine and cysteine proteases and furthermore, several ov-serpins do not possess inhibitory activities. Although the ov-serpins act primarily as intracellular serpins, some show extracellular and nuclear localizations. Such diversity enables the ov-serpins to play multiple physiological roles in the body. Recent analyses have revealed that the functions of human ov-serpins are more diversified than we previously knew. In this article, we describe recent progress in our understanding of how the human ov-serpin/clade B serpin family demonstrates diversity.     

Theories of enzyme specificity and their application to proteases and aminoacyl-Transfer RNA synthetases

Summary The question of enzyme specificity which is a corollary of the phenomenon of biological recognition is reviewed. The following theories are outlined briefly: non-productive binding, induced fit, transition state binding, the general strain theory and the kinetic proofreading hypothesis. Data on proteolytic enzymes and aminoacyl-tRNA synthetases are discussed in the light of predictions made by the various theories. The specificity of inhibitor and substrate binding to chymotrypsin and subtilisins is revealed at the sub-molecular level as an example of binding specificity. Kinetic specificity is experimentally distinguished from binding specificity. Conformational adaptability of enzyme and substrate, which is crucial in some theories, is documented by data on aminoacyl-tRNA synthetases. Expected and observed specificity of tRNA charging is discussed with regard to a theoretical limit of specificity. Additional means seem necessary beside those contained in the isolated enzyme-substrate system to account for the high specificity of most synthetases. In conclusion, we have arrived at quite good explanations for moderate specificity such as is displayed by many proteases, but there are still ample difficulties in the understanding of highly specific enzyme reactions.Dedicated to the memory of the late ProfessorJosef Rudinger.I acknowledge a fellowship by the Schweizerischer Nationalfonds which I received while doing much of my own work cited in this article.