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Van Elzen R, Konijnenberg A, Van der Veken P, Edgeworth MJ, Scrivens JH, Fülöp V, Sobott F, Lambeir AM. Study of the Conformational Dynamics of Prolyl Oligopeptidase by Mass Spectrometry: Lessons Learned. J Med Chem 2024; 67:10436-10446. [PMID: 38783480 PMCID: PMC11215766 DOI: 10.1021/acs.jmedchem.4c00866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Ion mobility mass spectrometry (IM-MS) can be used to analyze native proteins according to their size and shape. By sampling individual molecules, it allows us to study mixtures of conformations, as long as they have different collision cross sections and maintain their native conformation after dehydration and vaporization in the mass spectrometer. Even though conformational heterogeneity of prolyl oligopeptidase has been demonstrated in solution, it is not detectable in IM-MS. Factors that affect the conformation in solution, binding of an active site ligand, the stabilizing Ser554Ala mutation, and acidification do not qualitatively affect the collision-induced unfolding pattern. However, measuring the protection of accessible cysteines upon ligand binding provides a principle for the development of MS-based ligand screening methods.
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Affiliation(s)
- Roos Van Elzen
- Laboratory
of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Albert Konijnenberg
- Laboratory
of Biomolecular & Analytical Mass Spectrometry, Department of
Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Pieter Van der Veken
- Laboratory
of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Matthew J. Edgeworth
- Waters/Warwick
Centre for BioMedical Mass Spectrometry and Proteomics, School of
Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - James H. Scrivens
- Waters/Warwick
Centre for BioMedical Mass Spectrometry and Proteomics, School of
Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Vilmos Fülöp
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
- Institute
of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Frank Sobott
- Laboratory
of Biomolecular & Analytical Mass Spectrometry, Department of
Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Anne-Marie Lambeir
- Laboratory
of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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2
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Pijning T, Vujičić‐Žagar A, van der Laan J, de Jong RM, Ramirez‐Palacios C, Vente A, Edens L, Dijkstra BW. Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger. Protein Sci 2024; 33:e4856. [PMID: 38059672 PMCID: PMC10731622 DOI: 10.1002/pro.4856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
Proline-specific endoproteases have been successfully used in, for example, the in-situ degradation of gluten, the hydrolysis of bitter peptides, the reduction of haze during beer production, and the generation of peptides for mass spectroscopy and proteomics applications. Here we present the crystal structure of the extracellular proline-specific endoprotease from Aspergillus niger (AnPEP), a member of the S28 peptidase family with rarely observed true proline-specific endoprotease activity. Family S28 proteases have a conventional Ser-Asp-His catalytic triad, but their oxyanion-stabilizing hole shows a glutamic acid, an amino acid not previously observed in this role. Since these enzymes have an acidic pH optimum, the presence of a glutamic acid in the oxyanion hole may confine their activity to an acidic pH. Yet, considering the presence of the conventional catalytic triad, it is remarkable that the A. niger enzyme remains active down to pH 1.5. The determination of the primary cleavage site of cytochrome c along with molecular dynamics-assisted docking studies indicate that the active site pocket of AnPEP can accommodate a reverse turn of approximately 12 amino acids with proline at the S1 specificity pocket. Comparison with the structures of two S28-proline-specific exopeptidases reveals not only a more spacious active site cavity but also the absence of any putative binding sites for amino- and carboxyl-terminal residues as observed in the exopeptidases, explaining AnPEP's observed endoprotease activity.
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Affiliation(s)
- Tjaard Pijning
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Andreja Vujičić‐Žagar
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | | | | | | | - Andre Vente
- Taste, Texture and HealthDSM‐FirmenichDelftThe Netherlands
| | - Luppo Edens
- Taste, Texture and HealthDSM‐FirmenichDelftThe Netherlands
| | - Bauke W. Dijkstra
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
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Baharin A, Ting TY, Goh HH. Post-Proline Cleaving Enzymes (PPCEs): Classification, Structure, Molecular Properties, and Applications. PLANTS (BASEL, SWITZERLAND) 2022; 11:1330. [PMID: 35631755 PMCID: PMC9147577 DOI: 10.3390/plants11101330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Proteases or peptidases are hydrolases that catalyze the breakdown of polypeptide chains into smaller peptide subunits. Proteases exist in all life forms, including archaea, bacteria, protozoa, insects, animals, and plants due to their vital functions in cellular processing and regulation. There are several classes of proteases in the MEROPS database based on their catalytic mechanisms. This review focuses on post-proline cleaving enzymes (PPCEs) from different peptidase families, as well as prolyl endoprotease/oligopeptidase (PEP/POP) from the serine peptidase family. To date, most PPCEs studied are of microbial and animal origins. Recently, there have been reports of plant PPCEs. The most common PEP/POP are members of the S9 family that comprise two conserved domains. The substrate-limiting β-propeller domain prevents unwanted digestion, while the α/β hydrolase catalyzes the reaction at the carboxyl-terminal of proline residues. PPCEs display preferences towards the Pro-X bonds for hydrolysis. This level of selectivity is substantial and has benefited the brewing industry, therapeutics for celiac disease by targeting proline-rich substrates, drug targets for human diseases, and proteomics analysis. Protein engineering via mutagenesis has been performed to improve heat resistance, pepsin-resistant capability, specificity, and protein turnover of PPCEs for pharmacological applications. This review aims to synthesize recent structure-function studies of PPCEs from different families of peptidases to provide insights into the molecular mechanism of prolyl cleaving activity. Despite the non-exhaustive list of PPCEs, this is the first comprehensive review to cover the biochemical properties, biological functions, and biotechnological applications of PPCEs from the diverse taxa.
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Huang P, Lv A, Yan Q, Jiang Z, Yang S. The structure and molecular dynamics of prolyl oligopeptidase from Microbulbifer arenaceous provide insights into catalytic and regulatory mechanisms. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:735-751. [DOI: 10.1107/s2059798322004247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/20/2022] [Indexed: 11/10/2022]
Abstract
Prolyl oligopeptidases (POPs) are atypical serine proteases that are unique in their involvement in the maturation and degradation of prolyl-containing peptide hormones and neuropeptides. They are potential pharmaceutical targets for the treatment of several neurodegenerative disorders, such as Alzheimer's disease. In this study, the catalytic and substrate-regulatory mechanisms of a novel bacterial POP from Microbulbifer arenaceous (MaPOP) were investigated. The crystal structure revealed that the catalytic triad of MaPOP was covered by the central tunnel of an unusual β-propeller domain. The tunnel not only provided the sole access to the active site for oligopeptides, but also protected large structured peptides or proteins from accidental proteolysis. The enzyme was able to cleave angiotensin I specifically at the carboxyl side of the internal proline residue, but could not hydrolyze long-chain bovine insulin B in vitro. Like the ligand-free structure, MaPOP bound to the transition-state analog inhibitor ZPR was also in a closed state, which was not modulated by the common `latching loop' found in other POPs. The substrate-assisted catalytic mechanism of MaPOP reported here may represent a common mechanism for all POPs. These results may facilitate a better understanding of the catalytic behavior of POPs under physiological conditions.
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The decolorization and degradation of azo dyes by two Stenotrophomonas strains isolated from textile effluent (Tepetitla, Mexico). Braz J Microbiol 2021; 52:1755-1767. [PMID: 34494227 DOI: 10.1007/s42770-021-00542-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 06/08/2021] [Indexed: 10/20/2022] Open
Abstract
Stenotrophomonas' metabolic versatility plays important roles in the remediation of contaminated environment and plant growth promotion. We investigated two Stenotrophomonas strains isolated from textile polluted sewage for their ability to decolorize and degrade azo dyes. Two Stenotrophomonas strains (TepeL and TepeS) were isolated from textile effluents (Tepetitla, Mexico) using the selective agar Stenotrophomonas vancomycin, imipenem, amphotericin B agar (SVIA). Isolates' identity was determined by the sequencing of their partial 16S rRNA fragments. Their abilities to decolorize dyes were tested in a Luria broth supplemented with varying concentrations (50 mg/L-1 g/L) of textile dyes (acidic red, methyl orange, reactive green, acidic yellow, and reactive black). Fourier-transform infrared (FTIR) spectroscopy and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) metabolite analyses were used to determine the effect of the isolates' growth on the dyes (acidic red, methyl orange). We also identified the enzymes that may be involved in the degradation process. Phylogenetic analysis based on the 16S rDNA sequences showed that the isolates belong to the genus Stenotrophomonas. Stenotrophomonas sp. TepeL and TepeS respectively decolorize all the azo dyes at the tested concentration except at 1 g/L and degraded the azo dyes. The degradation resulted in the formation of N, N-dimethyl p-phenylenediamine, and sodium 4-amino-1-naphthalenesulfonate from methyl orange and acid red. TepeL and TepeS rapidly decolorized and degraded the azo dyes tested. This result showed that the two isolates have a good potential for the decontamination of textile effluents.
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Zhao Y, Feng Q, Zhou X, Zhang Y, Lukman M, Jiang J, Ruiz-Carrillo D. Mycobacterium tuberculosis puromycin hydrolase displays a prolyl oligopeptidase fold and an acyl aminopeptidase activity. Proteins 2021; 89:614-622. [PMID: 33426726 DOI: 10.1002/prot.26044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/11/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
Abstract
Puromycin-hydrolizing peptidases have been described as members of the prolyl oligopeptidase peptidase family. These enzymes are present across all domains of life but still little is known of the homologs found in the pathogenic bacterium Mycobacterium tuberculosis. The crystal structure of a M. tuberculosis puromycin hydrolase peptidase has been determined at 3 Angstrom resolution, revealing a conserved prolyl oligopeptidase fold, defined by α/β-hydrolase and β-propeller domains with two distinctive loops that occlude access of large substrates to the active site. The enzyme displayed amino peptidase activity with a substrate specificity preference for hydrophobic residues in the decreasing order of phenylalanine, leucine, alanine and proline. The enzyme's active site is lined by residues Glu564 for the coordination of the substrates amino terminal moiety and His561, Val608, Tyr78, Trp306, Phe563 and Ty567 for the accommodation of hydrophobic substrates. The availability of a crystal structure for puromycin hydrolase of M. tuberculosis shall facilitate the development of inhibitors with therapeutic applications.
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Affiliation(s)
- YuanHao Zhao
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Qiaoli Feng
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Xiao Zhou
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Yan Zhang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Maxwell Lukman
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Jie Jiang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - David Ruiz-Carrillo
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
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Da’adoosh B, Kaito K, Miyashita K, Sakaguchi M, Goldblum A. Computational design of substrate selective inhibition. PLoS Comput Biol 2020; 16:e1007713. [PMID: 32196495 PMCID: PMC7112232 DOI: 10.1371/journal.pcbi.1007713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 04/01/2020] [Accepted: 02/04/2020] [Indexed: 12/24/2022] Open
Abstract
Most enzymes act on more than a single substrate. There is frequently a need to block the production of a single pathogenic outcome of enzymatic activity on a substrate but to avoid blocking others of its catalytic actions. Full blocking might cause severe side effects because some products of that catalysis may be vital. Substrate selectivity is required but not possible to achieve by blocking the catalytic residues of an enzyme. That is the basis of the need for "Substrate Selective Inhibitors" (SSI), and there are several molecules characterized as SSI. However, none have yet been designed or discovered by computational methods. We demonstrate a computational approach to the discovery of Substrate Selective Inhibitors for one enzyme, Prolyl Oligopeptidase (POP) (E.C 3.4.21.26), a serine protease which cleaves small peptides between Pro and other amino acids. Among those are Thyrotropin Releasing Hormone (TRH) and Angiotensin-III (Ang-III), differing in both their binding (Km) and in turnover (kcat). We used our in-house "Iterative Stochastic Elimination" (ISE) algorithm and the structure-based "Pharmacophore" approach to construct two models for identifying SSI of POP. A dataset of ~1.8 million commercially available molecules was initially reduced to less than 12,000 which were screened by these models to a final set of 20 molecules which were sent for experimental validation (five random molecules were tested for comparison). Two molecules out of these 20, one with a high score in the ISE model, the other successful in the pharmacophore model, were confirmed by in vitro measurements. One is a competitive inhibitor of Ang-III (increases its Km), but non-competitive towards TRH (decreases its Vmax). Many proteins are enzymes—"catalytic machines" performing chemical reactions on "substrates"–which may be small or large molecules. Evolution optimized the speed of enzyme reactions, but mutations or excessive enzyme production could lead to non-controlled, accelerated activity, which must be blocked to avoid a product that promotes disease. Many inhibitors of enzymatic activity became drugs which can block the production of the aberrant product, due to blocking the enzymatic "machinery", the amino acids involved in catalysis. Most enzymes have several substrates and so, those other substrates are blocked too. Those may be vital to the well-being of cells and life and total inhibition is prone to cause serious side effects. It is therefore essential to solve the need for inhibition of a single substrate without inhibiting others. We have thus developed computational methods to block specifically the "culprit" substrate while allowing the enzyme machine to act on other substrates. By applying these computational methods, we predicted candidates for inhibiting one out of two substrates ("substrate selective inhibition") of a well-known enzyme reaction. In collaboration with a research group that excels in studying that specific enzyme (prolyl oligopeptidase) we found that two candidates out of a set of twenty that we picked out of 1.8 million molecules by filtering through computer models—are indeed selective to one substrate vis-a-vis the other (five random molecules were tested for comparison). This may be the first example of a computational method leading to substrate selective inhibitor drugs which could avoid side effects.
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Affiliation(s)
- Benny Da’adoosh
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kon Kaito
- Laboratory of Cell Biology, Osaka University of Pharmaceutical Sciences, Osaka, Japan
| | - Keishi Miyashita
- Laboratory of Cell Biology, Osaka University of Pharmaceutical Sciences, Osaka, Japan
| | - Minoru Sakaguchi
- Laboratory of Cell Biology, Osaka University of Pharmaceutical Sciences, Osaka, Japan
| | - Amiram Goldblum
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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Elufisan TO, Luna ICR, Oyedara OO, Varela AS, García VB, Oluyide BO, Treviño SF, López MAV, Guo X. Antimicrobial susceptibility pattern of Stenotrophomonas species isolated from Mexico. Afr Health Sci 2020; 20:168-181. [PMID: 33402905 PMCID: PMC7750080 DOI: 10.4314/ahs.v20i1.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Stenotrophomonas species are multi-resistant bacteria with ability to cause opportunistic infections. OBJECTIVE We isolated 45 Stenotrophomonas species from soil, sewage and the clinic with the aim of investigating their susceptibility to commonly used antimicrobial agents. METHODOLOGY The identities of isolates were confirmed with 16S rRNA gene sequence and MALDI-TOF analysis. Anti-microbial resistance, biofilm production and clonal diversity were also evaluated. The minimum inhibitory concentration technique as described by Clinical & Laboratory Standards Institute: CLSI Guidelines (CLSI) was employed for the evaluation of isolate susceptibility to antibiotics. RESULT Forty-five Stenotrophomonas species which include 36 environmental strains and 9 clinical strains of S. maltophilia were considered in this study. 32 (88.9 %) environmental strains were identified to be S. maltophilia, 2 (5.6 %) were Stenotrophomonas nitritireducens, and 2 (5.6 %) cluster as Stenotrophomonas spp. Stenotrophomonas isolates were resistant to at least six of the antibiotics tested, including Trimethoprim/Sulfamethoxazole (SXT). CONCLUSION Environmental isolates from this study were resistant to SXT which is commonly used for the treatment of S. maltophilia infections. This informs the need for good public hygiene as the environment could be a reservoir of multi-resistant bacteria. It also buttresses the importance of surveillance study in the management of bacterial resistance.
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Affiliation(s)
- Temidayo O Elufisan
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa, Tamaulipas 88710, México
- National Center for Technology Management (An agency of the Federal Ministry of Science and Technology (FMST), Nigeria, Obafemi Awolowo University, Ile-Ife)
| | | | - Omotayo O Oyedara
- Department of Biological Sciences, College of Science, Engineering and Technology, Faculty of Basic and Applied Science, Osun State University, Osogbo, Osun State, Nigeria
| | - Alejandro Sanchez Varela
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa, Tamaulipas 88710, México
| | | | - Busayo O Oluyide
- Ekiti State College of Science and Health Technology, Ijero Ekiti, Ekiti State, Nigeria
| | - Samantha Flores Treviño
- Departamento de Medicina, Autonomous University of Nuevo León (UANL), Interna San Nicolás de los Garza, Mexico
| | - Miguel Angel Villalobos López
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tepetitla, Tlaxcala 90700, México
| | - Xianwu Guo
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa, Tamaulipas 88710, México
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Denesyuk A, Dimitriou PS, Johnson MS, Nakayama T, Denessiouk K. The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PLoS One 2020; 15:e0229376. [PMID: 32084230 PMCID: PMC7034887 DOI: 10.1371/journal.pone.0229376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a “structural catalytic tetrad”. Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
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Affiliation(s)
- Alexander Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
- * E-mail:
| | - Polytimi S. Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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10
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Elufisan TO, Rodríguez-Luna IC, Oyedara OO, Sánchez-Varela A, Hernández-Mendoza A, Dantán Gonzalez E, Paz-González AD, Muhammad K, Rivera G, Villalobos-Lopez MA, Guo X. The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico. PeerJ 2020; 8:e8102. [PMID: 31934497 PMCID: PMC6951288 DOI: 10.7717/peerj.8102] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/25/2019] [Indexed: 11/20/2022] Open
Abstract
Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.
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Affiliation(s)
- Temidayo O Elufisan
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico.,Science Policy and Innovation Studies (SPIS), National Center for Technology Management Obafemi Awolowo University campus Ile-Ife, Ile-Ife, Osun, Nigeria
| | - Isabel C Rodríguez-Luna
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | | | - Alejandro Sánchez-Varela
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | - Edgar Dantán Gonzalez
- Laboratorio de Estudios Ecogenómicos (UAEM), Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Alma D Paz-González
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Kashif Muhammad
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | | | - Xianwu Guo
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
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11
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Ellis-Guardiola K, Rui H, Beckner RL, Srivastava P, Sukumar N, Roux B, Lewis JC. Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase. Biochemistry 2019; 58:1616-1626. [PMID: 30786206 PMCID: PMC6714975 DOI: 10.1021/acs.biochem.9b00031] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. The crystal structures of Pyrococcus furiosus ( Pfu) prolyl oligopeptidase (POP) and the corresponding S477C mutant were determined to 1.9 and 2.2 Å resolution, respectively. The wild type enzyme crystallized in an open conformation, indicating that this state is readily accessible, and it contained bound chloride ions and a prolylproline ligand. These structures were used as starting points for molecular dynamics simulations of Pfu POP conformational dynamics. The simulations showed that large-scale domain opening and closing occurred spontaneously, providing facile substrate access to the active site. Movement of the loop containing the catalytically essential histidine into a conformation similar to those found in structures with fully formed catalytic triads also occurred. This movement was modulated by chloride binding, providing a rationale for experimentally observed activation of POP peptidase catalysis by chloride. Thus, the structures and simulations reported in this study, combined with existing biochemical data, provide a number of insights into POP catalysis.
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Affiliation(s)
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ryan L. Beckner
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Poonam Srivastava
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Narayanasami Sukumar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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12
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Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates. Nat Commun 2017; 8:1045. [PMID: 29051530 PMCID: PMC5648786 DOI: 10.1038/s41467-017-00862-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/02/2017] [Indexed: 01/30/2023] Open
Abstract
Peptide macrocycles are promising therapeutic molecules because they are protease resistant, structurally rigid, membrane permeable, and capable of modulating protein-protein interactions. Here, we report the characterization of the dual function macrocyclase-peptidase enzyme involved in the biosynthesis of the highly toxic amanitin toxin family of macrocycles. The enzyme first removes 10 residues from the N-terminus of a 35-residue substrate. Conformational trapping of the 25 amino-acid peptide forces the enzyme to release this intermediate rather than proceed to macrocyclization. The enzyme rebinds the 25 amino-acid peptide in a different conformation and catalyzes macrocyclization of the N-terminal eight residues. Structures of the enzyme bound to both substrates and biophysical analysis characterize the different binding modes rationalizing the mechanism. Using these insights simpler substrates with only five C-terminal residues were designed, allowing the enzyme to be more effectively exploited in biotechnology.
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13
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Bainbridge TW, Dunshee DR, Kljavin NM, Skelton NJ, Sonoda J, Ernst JA. Selective Homogeneous Assay for Circulating Endopeptidase Fibroblast Activation Protein (FAP). Sci Rep 2017; 7:12524. [PMID: 28970566 PMCID: PMC5624913 DOI: 10.1038/s41598-017-12900-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/14/2017] [Indexed: 01/10/2023] Open
Abstract
Fibroblast Activation Protein (FAP) is a membrane-bound serine protease whose expression is often elevated in activated fibroblasts associated with tissue remodeling in various common diseases such as cancer, arthritis and fibrosis. Like the closely related dipeptidyl peptidase DPPIV, the extracellular domain of FAP can be released into circulation as a functional enzyme, and limited studies suggest that the circulating level of FAP correlates with the degree of tissue fibrosis. Here we describe a novel homogeneous fluorescence intensity assay for circulating FAP activity based on a recently identified natural substrate, FGF21. This assay is unique in that it can effectively distinguish endopeptidase activity of FAP from that of other related enzymes such as prolyl endopeptidase (PREP) and was validated using Fap-deficient mice. Structural modeling was used to elucidate the mechanistic basis for the observed specificity in substrate recognition by FAP, but not by DPPIV or PREP. Finally, the assay was used to detect elevated FAP activity in human patients diagnosed with liver cirrhosis and to determine the effectiveness of a chemical inhibitor for FAP in mice. We propose that the assay presented here could thus be utilized for diagnosis of FAP-related pathologies and for the therapeutic development of FAP inhibitors.
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Affiliation(s)
| | | | - Noelyn M Kljavin
- Molecular Oncology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Nicholas J Skelton
- Discovery Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Junichiro Sonoda
- Molecular Biology, Genentech Inc., South San Francisco, CA, 94080, USA. .,Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA.
| | - James A Ernst
- Protein Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA. .,Neuroscience, Genentech Inc., South San Francisco, CA, 94080, USA.
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14
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Van Elzen R, Schoenmakers E, Brandt I, Van Der Veken P, Lambeir AM. Ligand-induced conformational changes in prolyl oligopeptidase: a kinetic approach. Protein Eng Des Sel 2017; 30:217-224. [PMID: 28062644 DOI: 10.1093/protein/gzw079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/17/2016] [Indexed: 11/14/2022] Open
Abstract
Most kinetic studies of prolyl oligopeptidase (PREP) were performed with the porcine enzyme using modified peptide substrates. Yet recent biophysical studies used the human homolog. Therefore, the aim of this study was to compare the kinetic behavior of human and porcine PREP, as well as to find a suitable method to study enzyme kinetics with an unmodified biological substrate. It was found that human PREP behaves identically to the porcine homolog, displaying a double bell-shaped pH profile and a pH-dependent solvent kinetic isotope effect of the kcat/Km, features that set it apart from the related exopeptidase dipeptidyl peptidase IV (DPP IV). However, the empirical temperature coefficient Q10, describing the temperature dependency of the kinetic parameters and the non-linear Arrhenius plot of kcat/Km are common characteristics between PREP and DPP IV. The results also demonstrate the feasibility of microcalorimetry for measuring turn-over of proline containing peptides.
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Affiliation(s)
- R Van Elzen
- Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - E Schoenmakers
- Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - I Brandt
- Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - P Van Der Veken
- Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - A M Lambeir
- Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
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15
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Dynamics and ligand-induced conformational changes in human prolyl oligopeptidase analyzed by hydrogen/deuterium exchange mass spectrometry. Sci Rep 2017; 7:2456. [PMID: 28550305 PMCID: PMC5446394 DOI: 10.1038/s41598-017-02550-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/12/2017] [Indexed: 11/08/2022] Open
Abstract
Prolyl oligopeptidase (PREP) is conserved in many organisms across life. It is involved in numerous processes including brain function and neuropathology, that require more than its strict proteolytic role. It consists of a seven-bladed β-propeller juxtaposed to a catalytic α/β-hydrolase domain. The conformational dynamics of PREP involved in domain motions and the gating mechanism that allows substrate accessibility remain elusive. Here we used Hydrogen Deuterium eXchange Mass Spectrometry (HDX-MS) to derive the first near-residue resolution analysis of global PREP dynamics in the presence or absence of inhibitor bound in the active site. Clear roles are revealed for parts that would be critical for the activation mechanism. In the free state, the inter-domain interface is loose, providing access to the catalytic site. Inhibitor binding "locks" the two domains together exploiting prominent interactions between the loop of the first β-propeller blade and its proximal helix from the α/β-hydrolase domain. Loop A, thought to drive gating, is partially stabilized but remains flexible and dynamic. These findings provide a conformational guide for further dissection of the gating mechanism of PREP, that would impact drug development. Moreover, they offer a structural framework against which to study proteolysis-independent interactions with disordered proteins like α-synuclein involved in neurodegenerative disease.
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16
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Abstract
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Prolyl
oligopeptidase B from Galerina marginata (GmPOPB)
has recently been discovered as a peptidase capable of
breaking and forming peptide bonds to yield a cyclic peptide. Despite
the relevance of prolyl oligopeptidases in human biology and disease,
a kinetic analysis pinpointing rate-limiting steps for a member of
this enzyme family is not available. Macrocyclase enzymes are currently
exploited to produce cyclic peptides with potential therapeutic applications.
Cyclic peptides are promising druglike molecules because of their
stability and conformational rigidity. Here we describe an in-depth
kinetic characterization of a prolyl oligopeptidase acting as a macrocyclase
enzyme. By combining steady-state and pre-steady-state kinetics, we
propose a kinetic sequence in which a step after macrocyclization
limits steady-state turnover. Additionally, product release is ordered,
where the cyclic peptide departs first followed by the peptide tail.
Dissociation of the peptide tail is slow and significantly contributes
to the turnover rate. Furthermore, trapping of the enzyme by the peptide
tail becomes significant beyond initial rate conditions. The presence
of a burst of product formation and a large viscosity effect further
support the rate-limiting nature of a physical step occurring after
macrocyclization. This is the first detailed description of the kinetic
sequence of a macrocyclase enzyme from this class. GmPOPB is among
the fastest macrocyclases described to date, and this work is a necessary
step toward designing broad-specificity efficient macrocyclases.
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Affiliation(s)
- Clarissa M Czekster
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews , North Haugh, St Andrews K16 9ST, U.K
| | - James H Naismith
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews , North Haugh, St Andrews K16 9ST, U.K.,Biotherapy Centre, Sichuan University , Chengdu, China
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17
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Männistö PT, García-Horsman JA. Mechanism of Action of Prolyl Oligopeptidase (PREP) in Degenerative Brain Diseases: Has Peptidase Activity Only a Modulatory Role on the Interactions of PREP with Proteins? Front Aging Neurosci 2017; 9:27. [PMID: 28261087 PMCID: PMC5306367 DOI: 10.3389/fnagi.2017.00027] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/30/2017] [Indexed: 12/14/2022] Open
Abstract
In the aging brain, the correct balance of neural transmission and its regulation is of particular significance, and neuropeptides have a significant role. Prolyl oligopeptidase (PREP) is a protein highly expressed in brain, and evidence indicates that it is related to aging and in neurodegenration. Although PREP is regarded as a peptidase, the physiological substrates in the brain have not been defined, and after intense research, the molecular mechanisms where this protein is involved have not been defined. We propose that PREP functions as a regulator of other proteins though peptide gated direct interaction. We speculate that, at least in some processes where PREP has shown to be relevant, the peptidase activity is only a consequence of the interactions, and not the main physiological activity.
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Affiliation(s)
- Pekka T Männistö
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki Helsinki, Finland
| | - J Arturo García-Horsman
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki Helsinki, Finland
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18
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Bogdanović X, Palm GJ, Schwenteit J, Singh RK, Gudmundsdóttir BK, Hinrichs W. Structural evidence of intramolecular propeptide inhibition of the aspzincin metalloendopeptidase AsaP1. FEBS Lett 2016; 590:3280-94. [DOI: 10.1002/1873-3468.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Xenia Bogdanović
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Biochemistry and Molecular Biology; ZBMZ; Medical Faculty; University of Freiburg; Freiburg im Breisgau Germany
| | - Gottfried J. Palm
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | - Johanna Schwenteit
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Experimental Pathology; University of Iceland, Keldur; Reykjavík Iceland
| | - Rajesh K. Singh
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | | | - Winfried Hinrichs
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
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19
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Rauwerdink A, Kazlauskas RJ. How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes. ACS Catal 2015; 5:6153-6176. [PMID: 28580193 DOI: 10.1021/acscatal.5b01539] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes within a family often catalyze different reactions. In some cases, this variety stems from different catalytic machinery, but in other cases the machinery is identical; nevertheless, the enzymes catalyze different reactions. In this review, we examine the subset of α/β-hydrolase fold enzymes that contain the serine-histidine-aspartate catalytic triad. In spite of having the same protein fold and the same core catalytic machinery, these enzymes catalyze seventeen different reaction mechanisms. The most common reactions are hydrolysis of C-O, C-N and C-C bonds (Enzyme Classification (EC) group 3), but other enzymes are oxidoreductases (EC group 1), acyl transferases (EC group 2), lyases (EC group 4) or isomerases (EC group 5). Hydrolysis reactions often follow the canonical esterase mechanism, but eight variations occur where either the formation or cleavage of the acyl enzyme intermediate differs. The remaining eight mechanisms are lyase-type elimination reactions, which do not have an acyl enzyme intermediate and, in four cases, do not even require the catalytic serine. This diversity of mechanisms from the same catalytic triad stems from the ability of the enzymes to bind different substrates, from the requirements for different chemical steps imposed by these new substrates and, only in about half of the cases, from additional hydrogen bond partners or additional general acids/bases in the active site. This detailed analysis shows that binding differences and non-catalytic residues create new mechanisms and are essential for understanding and designing efficient enzymes.
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Affiliation(s)
- Alissa Rauwerdink
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
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20
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Kotev M, Lecina D, Tarragó T, Giralt E, Guallar V. Unveiling prolyl oligopeptidase ligand migration by comprehensive computational techniques. Biophys J 2015; 108:116-25. [PMID: 25564858 DOI: 10.1016/j.bpj.2014.11.3453] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 01/03/2023] Open
Abstract
Prolyl oligopeptidase (POP) is a large 80 kDa protease, which cleaves oligopeptides at the C-terminal side of proline residues and constitutes an important pharmaceutical target. Despite the existence of several crystallographic structures, there is an open debate about migration (entrance and exit) pathways for ligands, and their coupling with protein dynamics. Recent studies have shown the capabilities of molecular dynamics and classical force fields in describing spontaneous binding events and nonbiased ligand migration pathways. Due to POP's size and to the buried nature of its active site, an exhaustive sampling by means of conventional long enough molecular dynamics trajectories is still a nearly impossible task. Such a level of sampling, however, is possible with the breakthrough protein energy landscape exploration technique. Here, we present an exhaustive sampling of POP with a known inhibitor, Z-pro-prolinal. In >3000 trajectories Z-pro-prolinal explores all the accessible surface area, showing multiple entrance events into the large internal cavity through the pore in the β-propeller domain. Moreover, we modeled a natural substrate binding and product release by predicting the entrance of an undecapeptide substrate, followed by manual active site cleavage and nonbiased exit of one of the products (a dipeptide). The product exit shows preference from a flexible 18-amino acid residues loop, pointing to an overall mechanism where entrance and exit occur in different sites.
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Affiliation(s)
- Martin Kotev
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Daniel Lecina
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Teresa Tarragó
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Department of Organic Chemistry, University of Barcelona (UB), Barcelona, Spain.
| | - Víctor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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21
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Lafarga T, O’Connor P, Hayes M. In silico methods to identify meat-derived prolyl endopeptidase inhibitors. Food Chem 2015; 175:337-43. [DOI: 10.1016/j.foodchem.2014.11.150] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/05/2014] [Accepted: 11/27/2014] [Indexed: 12/13/2022]
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22
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Menyhárd DK, Orgován Z, Szeltner Z, Szamosi I, Harmat V. Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality. ACTA ACUST UNITED AC 2015; 71:461-72. [PMID: 25760596 DOI: 10.1107/s1399004714026819] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/05/2014] [Indexed: 11/10/2022]
Abstract
Acylaminoacyl peptidase (AAP) is an oligopeptidase that only cleaves short peptides or protein segments. In the case of AAP from Aeropyrum pernix (ApAAP), previous studies have led to a model in which the clamshell-like opening and closing of the enzyme provides the means of substrate-size selection. The closed form of the enzyme is catalytically active, while opening deactivates the catalytic triad. The crystallographic results presented here show that the open form of ApAAP is indeed functionally disabled. The obtained crystal structures also reveal that the closed form is penetrable to small ligands: inhibitor added to the pre-formed crystal was able to reach the active site of the rigidified protein, which is only possible through the narrow channel of the propeller domain. Molecular-dynamics simulations investigating the structure of the complexes formed with longer peptide substrates showed that their binding within the large crevice of the closed form of ApAAP leaves the enzyme structure unperturbed; however, their accessing the binding site seems more probable when assisted by opening of the enzyme. Thus, the open form of ApAAP corresponds to a scavenger of possible substrates, the actual cleavage of which only takes place if the enzyme is able to re-close.
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Affiliation(s)
| | - Zoltán Orgován
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Ilona Szamosi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Veronika Harmat
- MTA-ELTE Protein Modelling Research Group, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
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23
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Luo H, Hong SY, Sgambelluri RM, Angelos E, Li X, Walton JD. Peptide macrocyclization catalyzed by a prolyl oligopeptidase involved in α-amanitin biosynthesis. ACTA ACUST UNITED AC 2014; 21:1610-7. [PMID: 25484237 DOI: 10.1016/j.chembiol.2014.10.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/08/2014] [Accepted: 10/22/2014] [Indexed: 11/29/2022]
Abstract
Amatoxins are ribosomally encoded and posttranslationally modified peptides that account for the majority of fatal mushroom poisonings of humans. A representative amatoxin is the bicyclic octapeptide α-amanitin, formed via head-to-tail macrocyclization, which is ribosomally biosynthesized as a 35-amino acid propeptide in Amanita bisporigera and in the distantly related mushroom Galerina marginata. Although members of the prolyl oligopeptidase (POP) family of serine proteases have been proposed to play a role in α-amanitin posttranslational processing, the exact mechanistic details are not known. Here, we show that a specific POP (GmPOPB) is required for toxin maturation in G. marginata. Recombinant GmPOPB catalyzed two nonprocessive reactions: hydrolysis at an internal Pro to release the C-terminal 25-mer from the 35-mer propeptide and transpeptidation at the second Pro to produce the cyclic octamer. On the other hand, we show that GmPOPA, the putative housekeeping POP of G. marginata, behaves like a conventional POP.
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Affiliation(s)
- Hong Luo
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Sung-Yong Hong
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - R Michael Sgambelluri
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Evan Angelos
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Xuan Li
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Jonathan D Walton
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
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24
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Palermo G, Campomanes P, Cavalli A, Rothlisberger U, De Vivo M. Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion. J Phys Chem B 2014; 119:789-801. [DOI: 10.1021/jp5052276] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Giulia Palermo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Andrea Cavalli
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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25
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Syrén PO. The solution of nitrogen inversion in amidases. FEBS J 2013; 280:3069-83. [DOI: 10.1111/febs.12241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Per-Olof Syrén
- Institute of Technical Biochemistry; University of Stuttgart; Germany
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26
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Van der Veken P, Fülöp V, Rea D, Gerard M, Van Elzen R, Joossens J, Cheng JD, Baekelandt V, De Meester I, Lambeir AM, Augustyns K. P2-substituted N-acylprolylpyrrolidine inhibitors of prolyl oligopeptidase: biochemical evaluation, binding mode determination, and assessment in a cellular model of synucleinopathy. J Med Chem 2012; 55:9856-67. [PMID: 23121075 DOI: 10.1021/jm301060g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have investigated the effect of regiospecifically introducing substituents in the P2 part of the typical dipeptide derived basic structure of PREP inhibitors. This hitherto unexplored modification type can be used to improve target affinity, selectivity, and physicochemical parameters in drug discovery programs focusing on PREP inhibitors. Biochemical evaluation of the produced inhibitors identified several substituent types that significantly increase target affinity, thereby reducing the need for an electrophilic "warhead" functionality. Pronounced PREP specificity within the group of Clan SC proteases was generally observed. Omission of the P1 electrophilic function did not affect the overall binding mode of three representative compounds, as studied by X-ray crystallography, while the P2 substituents were demonstrated to be accommodated in a cavity of PREP that, to date, has not been probed by inhibitors. Finally, we report on results of selected inhibitors in a SH-SY5Y cellular model of synucleinopathy and demonstrate a significant antiaggregation effect on α-synuclein.
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Affiliation(s)
- Pieter Van der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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Kaszuba K, Róg T, Danne R, Canning P, Fülöp V, Juhász T, Szeltner Z, St. Pierre JF, García-Horsman A, Männistö PT, Karttunen M, Hokkanen J, Bunker A. Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase. Biochimie 2012; 94:1398-411. [DOI: 10.1016/j.biochi.2012.03.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/13/2012] [Indexed: 01/10/2023]
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28
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Syrén PO, Hendil-Forssell P, Aumailley L, Besenmatter W, Gounine F, Svendsen A, Martinelle M, Hult K. Esterases with an introduced amidase-like hydrogen bond in the transition state have increased amidase specificity. Chembiochem 2012; 13:645-8. [PMID: 22378481 DOI: 10.1002/cbic.201100779] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Per-Olof Syrén
- Department of Biochemistry, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
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Syrén PO, Hult K. Amidases Have a Hydrogen Bond that Facilitates Nitrogen Inversion, but Esterases Have Not. ChemCatChem 2011. [DOI: 10.1002/cctc.201000448] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Harmat V, Domokos K, Menyhárd DK, Palló A, Szeltner Z, Szamosi I, Beke-Somfai T, Náray-Szabó G, Polgár L. Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase. J Biol Chem 2010; 286:1987-98. [PMID: 21084296 DOI: 10.1074/jbc.m110.169862] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acylaminoacyl peptidase from Aeropyrum pernix is a homodimer that belongs to the prolyl oligopeptidase family. The monomer subunit is composed of one hydrolase and one propeller domain. Previous crystal structure determinations revealed that the propeller domain obstructed the access of substrate to the active site of both subunits. Here we investigated the structure and the kinetics of two mutant enzymes in which the aspartic acid of the catalytic triad was changed to alanine or asparagine. Using different substrates, we have determined the pH dependence of specificity rate constants, the rate-limiting step of catalysis, and the binding of substrates and inhibitors. The catalysis considerably depended both on the kind of mutation and on the nature of the substrate. The results were interpreted in terms of alterations in the position of the catalytic histidine side chain as demonstrated with crystal structure determination of the native and two mutant structures (D524N and D524A). Unexpectedly, in the homodimeric structures, only one subunit displayed the closed form of the enzyme. The other subunit exhibited an open gate to the catalytic site, thus revealing the structural basis that controls the oligopeptidase activity. The open form of the native enzyme displayed the catalytic triad in a distorted, inactive state. The mutations affected the closed, active form of the enzyme, disrupting its catalytic triad. We concluded that the two forms are at equilibrium and the substrates bind by the conformational selection mechanism.
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Affiliation(s)
- Veronika Harmat
- Laboratory of Structural Chemistry and Biology and HAS-ELTE Protein Modeling Group, Institute of Chemistry, Eötvös Loránd University, Pázmány P. sétány 1/A, H-1117 Budapest, Hungary
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Tarragó T, Claasen B, Kichik N, Rodriguez-Mias RA, Gairí M, Giralt E. A cost-effective labeling strategy for the NMR study of large proteins: selective 15N-labeling of the tryptophan side chains of prolyl oligopeptidase. Chembiochem 2010; 10:2736-9. [PMID: 19798721 DOI: 10.1002/cbic.200900575] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Teresa Tarragó
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac, 10, 08028 Barcelona, Spain
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Kaszuba K, Rog T, St Pierre JF, Mannisto PT, Karttunen M, Bunker A. Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2009; 20:595-609. [PMID: 20024801 DOI: 10.1080/10629360903438198] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We used the crystal structure of prolyl oligopeptidase (POP) with bound Z-pro-prolinal (ZPP) inhibitor (Protein Data Bank (PDB) structure 1QFS) to perform an intensive molecular dynamics study of the POP-ZPP complex. We performed 100 ns of simulation with the hemiacetal bond, through which the ZPP is bound to the POP, removed in order to better investigate the binding cavity environment. From basic analysis, measuring the radius of gyration, root mean square deviation, solvent accessible surface area and definition of the secondary structure of protein, we determined that the protein structure is highly stable and maintains its structure over the entire simulation time. This demonstrates that such long time simulations can be performed without the protein structure losing stability. We found that water bridges and hydrogen bonds play a negligible role in binding the ZPP thus indicating the importance of the hemiacetal bond. The two domains of the protein are bound by a set of approximately 12 hydrogen bonds, specific to the particular POP protein.
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Affiliation(s)
- K Kaszuba
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
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33
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A new side opening on prolyl oligopeptidase revealed by electron microscopy. FEBS Lett 2009; 583:3344-8. [DOI: 10.1016/j.febslet.2009.09.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 09/16/2009] [Accepted: 09/18/2009] [Indexed: 11/21/2022]
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34
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Szeltner Z, Kiss AL, Domokos K, Harmat V, Náray-Szabó G, Polgár L. Characterization of a novel acylaminoacyl peptidase with hexameric structure and endopeptidase activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1204-10. [DOI: 10.1016/j.bbapap.2009.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/25/2009] [Accepted: 03/09/2009] [Indexed: 10/21/2022]
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35
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Comellas G, Kaczmarska Z, Tarragó T, Teixidó M, Giralt E. Exploration of the one-bead one-compound methodology for the design of prolyl oligopeptidase substrates. PLoS One 2009; 4:e6222. [PMID: 19593439 PMCID: PMC2704865 DOI: 10.1371/journal.pone.0006222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 06/18/2009] [Indexed: 11/18/2022] Open
Abstract
Here we describe the design, synthesis and evaluation of the first solid-phase substrates for prolyl oligopeptidase (POP), a cytosolic serine peptidase associated with schizophrenia, bipolar affective disorder and related neuropsychiatric disorders. This study seeks to contribute to the future design of a one-bead one-compound (OBOC) peptide library of POP substrates, based on an intramolecular energy transfer substrate. Unexpectedly, the enzymatic evaluation of the substrates attached on solid-phase by means of the HMBA linker were cleaved through the ester bond, thereby suggesting an unknown esterase activity of POP, in addition to its known peptidase activity. By performing multiple activity assays, we have confirmed the esterase activity of this enzyme and its capacity to process the substrates on solid-phase. Finally, we tested a new linker, compatible with both the solid-phase peptide-synthesis used and the enzymatic assay, for application in the future design of an OBOC library.
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Affiliation(s)
- Gemma Comellas
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Barcelona, Spain
- Department of Organic Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Zusanna Kaczmarska
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Barcelona, Spain
| | - Teresa Tarragó
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Barcelona, Spain
| | - Meritxell Teixidó
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Barcelona, Spain
| | - Ernest Giralt
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Barcelona, Spain
- Department of Organic Chemistry, Universitat de Barcelona, Barcelona, Spain
- * E-mail:
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36
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Djekic UV, Gaggar A, Weathington NM. Attacking the multi-tiered proteolytic pathology of COPD: new insights from basic and translational studies. Pharmacol Ther 2009; 121:132-46. [PMID: 19026684 PMCID: PMC4465592 DOI: 10.1016/j.pharmthera.2008.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 09/18/2008] [Indexed: 02/06/2023]
Abstract
Protease activity in inflammation is complex. Proteases released by cells in response to infection, cytokines, or environmental triggers like cigarette smoking cause breakdown of the extracellular matrix (ECM). In chronic inflammatory diseases like chronic obstructive pulmonary disease (COPD), current findings indicate that pathology and morbidity are driven by dysregulation of protease activity, either through hyperactivity of proteases or deficiency or dysfunction their antiprotease regulators. Animal studies demonstrate the accuracy of this hypothesis through genetic and pharmacologic tools. New work shows that ECM destruction generates peptide fragments active on leukocytes via neutrophil or macrophage chemotaxis towards collagen and elastin derived peptides respectively. Such fragments now have been isolated and characterized in vivo in each case. Collectively, this describes a biochemical circuit in which protease activity leads to activation of local immunocytes, which in turn release cytokines and more proteases, leading to further leukocyte infiltration and cyclical disease progression that is chronic. This circuit concept is well known, and is intrinsic to the protease-antiprotease hypothesis; recently analytic techniques have become sensitive enough to establish fundamental mechanisms of this hypothesis, and basic and clinical data now implicate protease activity and peptide signaling as pathologically significant pharmacologic targets. This review discusses targeting protease activity for chronic inflammatory disease with special attention to COPD, covering important basic and clinical findings in the field; novel therapeutic strategies in animal or human studies; and a perspective on the successes and failures of agents with a focus on clinical potential in human disease.
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Affiliation(s)
- Uros V Djekic
- University of Alabama at Birmingham, Department of Physiology and Biophysics
| | - Amit Gaggar
- University of Alabama at Birmingham, Department of Physiology and Biophysics
- University of Alabama at Birmingham, Department of Medicine, Division of Pulmonary and Critical Care
| | - Nathaniel M Weathington
- University of Alabama at Birmingham, Department of Physiology and Biophysics
- University of Alabama at Birmingham, Department of Medicine, Internal Medicine Residency Program
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37
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Kánai K, Arányi P, Böcskei Z, Ferenczy G, Harmat V, Simon K, Bátori S, Náray-Szabó G, Hermecz I. Prolyl Oligopeptidase Inhibition by N-Acyl-pro-pyrrolidine-type Molecules. J Med Chem 2008; 51:7514-22. [DOI: 10.1021/jm800944x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Károly Kánai
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - Péter Arányi
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - Zsolt Böcskei
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - György Ferenczy
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - Veronika Harmat
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - Kálmán Simon
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - Sándor Bátori
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - Gábor Náray-Szabó
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
| | - István Hermecz
- CHINOIN, Ltd, H-1045 Budapest, Tó u. 1-5, Hungary, Protein Modeling Group, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117 Budapest, Pázmány Péter u. 1a, Hungary, and Co-operation Research Center for Molecular Design, Semmelweis University, H-1062 Budapest, Rippl-Rónai u. 37, Hungary
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38
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Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue. J Bacteriol 2008; 190:7819-29. [PMID: 18820015 DOI: 10.1128/jb.02010-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The crystal structure of dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia was determined at 2.8-A resolution by the multiple isomorphous replacement method, using platinum and selenomethionine derivatives. The crystals belong to space group P4(3)2(1)2, with unit cell parameters a = b = 105.9 A and c = 161.9 A. Dipeptidyl aminopeptidase IV is a homodimer, and the subunit structure is composed of two domains, namely, N-terminal beta-propeller and C-terminal catalytic domains. At the active site, a hydrophobic pocket to accommodate a proline residue of the substrate is conserved as well as those of mammalian enzymes. Stenotrophomonas dipeptidyl aminopeptidase IV exhibited activity toward a substrate containing a 4-hydroxyproline residue at the second position from the N terminus. In the Stenotrophomonas enzyme, one of the residues composing the hydrophobic pocket at the active site is changed to Asn611 from the corresponding residue of Tyr631 in the porcine enzyme, which showed very low activity against the substrate containing 4-hydroxyproline. The N611Y mutant enzyme was generated by site-directed mutagenesis. The activity of this mutant enzyme toward a substrate containing 4-hydroxyproline decreased to 30.6% of that of the wild-type enzyme. Accordingly, it was considered that Asn611 would be one of the major factors involved in the recognition of substrates containing 4-hydroxyproline.
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39
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Silva CA, Ianzer DA, Portaro FC, Konno K, Faria M, Fernandes BL, Camargo AC. Characterization of urinary metabolites from four synthetic bradykinin potentiating peptides (BPPs) in mice. Toxicon 2008; 52:501-7. [DOI: 10.1016/j.toxicon.2008.06.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 06/20/2008] [Accepted: 06/24/2008] [Indexed: 11/16/2022]
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40
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Novel Inhibitor for Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis and Details of Substrate-recognition Mechanism. J Mol Biol 2008; 375:708-19. [DOI: 10.1016/j.jmb.2007.09.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 09/25/2007] [Accepted: 09/26/2007] [Indexed: 11/19/2022]
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41
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Gorrão SS, Hemerly JP, Lima AR, Melo RL, Szeltner Z, Polgár L, Juliano MA, Juliano L. Fluorescence resonance energy transfer (FRET) peptides and cycloretro-inverso peptides derived from bradykinin as substrates and inhibitors of prolyl oligopeptidase. Peptides 2007; 28:2146-54. [PMID: 17904692 DOI: 10.1016/j.peptides.2007.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 08/17/2007] [Accepted: 08/17/2007] [Indexed: 10/22/2022]
Abstract
Prolyl oligopeptidase (POP, EC 3.4.21.26) is a member of a family of serine peptidases with post-proline cleaving activity towards peptides. It is located in the cytosol in active form but without hydrolytic activity on proteins or peptides higher than 30 amino acids. Its function is not well defined, but it is involved in central nervous system disorders. Here, we studied the substrate specificity of wild type POP (POPwt) and its C255T variant lacking the non-catalytic Cys(255). This residue is located in the seven-bladed beta-propeller domain that regulates the activity of POP. Fluorescence resonance energy transfer (FRET) peptides were used with sequences derived from bradykinin-containing region of human kininogen and flanked by Abz (ortho-aminobenzoic acid) and EDDnp [N-ethylenediamine-(2,4-dinitrophenyl)]. The peptide Abz-GFSPFRQ-EDDnp was taken as leader substrate for the synthesis of five series of peptides modified at the P(3), P(2), P'(1), P'(2) and P'(3) residues. The optimal amino acids in each position for POPwt resulted in the sequence RRPYIR that is very similar to the C-terminal sequence of neurotensin. The cyclic peptides c(G((n))FSPFR) (n=1-4) were hydrolyzed by POP; their cycloretro and cycloretro-inverso analogues were inhibitors in the micromolar range. The differences between POPwt and its C255T mutant in the hydrolysis of the series derived from Abz-GFSPFRQ-EDDnp were restricted to the non-prime site of the substrates. The kinetic data of hydrolysis and inhibition by the cyclic peptides are consistent with the structures of POP-substrate/inhibitor complexes and with the substrate specificity data obtained with linear FRET peptides. All together, these results give information about the POP-substrate/inhibitor interactions that further complete knowledge of this important oligopeptidase.
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Affiliation(s)
- Silvia S Gorrão
- Department of Biophysics, Escola Paulista de Medicina, Rua Três de Maio 100, São Paulo--SP 04044-020, Brazil
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42
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Jarho EM, Venäläinen JI, Poutiainen S, Leskinen H, Vepsäläinen J, Christiaans JAM, Forsberg MM, Männistö PT, Wallén EAA. 2(S)-(Cycloalk-1-enecarbonyl)-1-(4-phenyl-butanoyl)pyrrolidines and 2(S)-(aroyl)-1-(4-phenylbutanoyl)pyrrolidines as prolyl oligopeptidase inhibitors. Bioorg Med Chem 2007; 15:2024-31. [PMID: 17215128 DOI: 10.1016/j.bmc.2006.12.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 12/08/2006] [Accepted: 12/22/2006] [Indexed: 11/19/2022]
Abstract
In order to replace the P2-P1 amide group, different 1-cycloalkenyls and 2-aryls were studied in the place of the P1 pyrrolidine group of a 4-phenylbutanoyl-L-Pro-pyrrolidine structure, which is a well-known prolyl oligopeptidase inhibitor SUAM-1221. The 1-cyclopentenyl and the 2-thienyl groups gave novel compounds, which were equipotent with the corresponding pyrrolidine-analog SUAM-1221. It was shown that the P2-P1 amide group of POP inhibitors can be replaced by an alpha,beta-unsaturated carbonyl group or the aryl conjugated carbonyl group.
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Affiliation(s)
- Elina M Jarho
- Department of Pharmaceutical Chemistry, University of Kuopio, PO Box 1627, FI-70211 Kuopio, Finland.
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43
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Kiss AL, Hornung B, Rádi K, Gengeliczki Z, Sztáray B, Juhász T, Szeltner Z, Harmat V, Polgár L. The acylaminoacyl peptidase from Aeropyrum pernix K1 thought to be an exopeptidase displays endopeptidase activity. J Mol Biol 2007; 368:509-20. [PMID: 17350041 DOI: 10.1016/j.jmb.2007.02.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 01/30/2007] [Accepted: 02/07/2007] [Indexed: 10/23/2022]
Abstract
Mammalian acylaminoacyl peptidase, a member of the prolyl oligopeptidase family of serine peptidases, is an exopeptidase, which removes acylated amino acid residues from the N terminus of oligopeptides. We have investigated the kinetics and inhibitor binding of the orthologous acylaminoacyl peptidase from the thermophile Aeropyrum pernix K1 (ApAAP). Complex pH-rate profiles were found with charged substrates, indicating a strong electrostatic effect in the surroundings of the active site. Unexpectedly, we have found that oligopeptides can be hydrolysed beyond the N-terminal peptide bond, demonstrating that ApAAP exhibits endopeptidase activity. It was thought that the enzyme is specific for hydrophobic amino acids, in particular phenylalanine, in accord with the non-polar S1 subsite of ApAAP. However, cleavage after an Ala residue contradicted this notion and demonstrated that P1 residues of different nature may bind to the S1 subsite depending on the remaining peptide residues. The crystal structures of the complexes formed between the enzyme and product-like inhibitors identified the oxyanion-binding site unambiguously and demonstrated that the phenylalanine ring of the P1 peptide residue assumes a position different from that established in a previous study, using 4-nitrophenylphosphate. We have found that the substrate-binding site extends beyond the S2 subsite, being capable of binding peptides with a longer N terminus. The S2 subsite displays a non-polar character, which is unique among the enzymes of this family. The S3 site was identified as a hydrophobic region that does not form hydrogen bonds with the inhibitor P3 residue. The enzyme-inhibitor complexes revealed that, upon ligand-binding, the S1 subsite undergoes significant conformational changes, demonstrating the plasticity of the specificity site.
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Affiliation(s)
- András L Kiss
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest 112, P.O. Box 7, Hungary
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44
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García-Horsman JA, Männistö PT, Venäläinen JI. On the role of prolyl oligopeptidase in health and disease. Neuropeptides 2007; 41:1-24. [PMID: 17196652 DOI: 10.1016/j.npep.2006.10.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 10/10/2006] [Accepted: 10/17/2006] [Indexed: 11/18/2022]
Abstract
Prolyl oligopeptidase (POP) is a serine peptidase which digests small peptide-like hormones, neuroactive peptides, and various cellular factors. Therefore, this peptidase has been implicated in many physiological processes as well as in some psychiatric disorders, most probably through interference in inositol cycle. Intense research has been performed to elucidate, on the one hand, the basic structure, ligand binding, and kinetic properties of POP, and on the other, the pharmacology of its inhibitors. There is fairly strong evidence of in vivo importance of POP on substance P, arginine vasopressin, thyroliberin and gonadoliberin metabolism. However, information about the biological relevance of POP is not yet conclusive. Evidence regarding the physiological role of POP is lacking, which is surprising considering that peptidase inhibitors have been exploited for drug development, some of which are currently in clinical trials as memory enhancers for the aged and in a variety of neurological disorders. Here we review the recent progress on POP research and evaluate the relevance of the peptidase in the metabolism of various neuropeptides. The recognition of novel forms and relatives of POP may improve our understanding of how this family of proteins functions in normal and in neuropathological conditions.
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Affiliation(s)
- J A García-Horsman
- Centro de Investigación Príncipe Felipe, Neurobiology, Av. Autopista del Saler 16, 46013 Valencia, Spain.
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45
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Abstract
The newest results in the application of various chromatographic methods (gas-liquid chromatography, liquid chromatographic techniques, electrically driven systems) for the separation and quantitative determination of amino acids and short peptides in pure state and in complicated matrices are compiled. The results are concisely described and critically evaluated. The future trends of the chromatographic analysis of amino acids and short peptides are briefly discussed.
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Affiliation(s)
- T Cserháti
- Research Institute of Materials and Environmental Chemistry, Chemical Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
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46
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Wang Q, Yang G, Liu Y, Feng Y. Discrimination of Esterase and Peptidase Activities of Acylaminoacyl Peptidase from Hyperthermophilic Aeropyrum pernix K1 by a Single Mutation. J Biol Chem 2006; 281:18618-25. [PMID: 16670095 DOI: 10.1074/jbc.m601015200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It has been shown that highly conserved residues that form crucial structural elements of the catalytic apparatus may be used to account for the evolutionary history of enzymes. Using saturation mutagenesis, we investigated the role of a conserved residue (Arg(526)) at the active site of acylaminoacyl peptidase from hyperthermophilic Aeropyrum pernix K1 in substrate discrimination and catalytic mechanism. This enzyme has both peptidase and esterase activities. The esterase activity of the wild-type enzyme with p-nitrophenyl caprylate as substrate is approximately 7 times higher than the peptidase activity with Ac-Leu-p-nitroanilide as substrate. However, with the same substrates, this difference was increased to approximately 150-fold for mutant R526V. A more dramatic effect occurred with mutant R526E, which essentially completely abolished the peptidase activity but decreased the esterase activity only by a factor of 2, leading to a 785-fold difference in the enzyme activities. These results provide rare examples that illustrate how enzymes can be evolved to discriminate their substrates by a single mutation. The possible structural and energetic effects of the mutations on k(cat) and K(m) of the enzyme were discussed based on molecular dynamics simulation studies.
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Affiliation(s)
- Qiuyan Wang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, China
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47
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Juhász T, Szeltner Z, Polgár L. Properties of the prolyl oligopeptidase homologue from Pyrococcus furiosus. FEBS Lett 2006; 580:3493-7. [PMID: 16714022 DOI: 10.1016/j.febslet.2006.05.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 05/02/2006] [Accepted: 05/08/2006] [Indexed: 10/24/2022]
Abstract
Prolyl oligopeptidase (POP), the paradigm of a serine peptidase family, hydrolyses peptides, but not proteins. The thermophilic POP from Pyrococcus furiosus (Pfu) appeared to be an exception, since it hydrolysed large proteins. Here we demonstrate that the Pfu POP does not display appreciable activity against azocasein. The autolysis observed earlier was an artefact. We have also found that the pH-rate profile is different from that of the mammalian enzyme and the low pK(a) extracted from the curve represents the ionization of the catalytic histidine. We conclude that some oligopeptidases may be true endopeptidases, cleaving at disordered segments of proteins, but with very low efficacy.
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Affiliation(s)
- Tünde Juhász
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest
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48
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Edosada CY, Quan C, Tran T, Pham V, Wiesmann C, Fairbrother W, Wolf BB. Peptide substrate profiling defines fibroblast activation protein as an endopeptidase of strict Gly(2)-Pro(1)-cleaving specificity. FEBS Lett 2006; 580:1581-6. [PMID: 16480718 DOI: 10.1016/j.febslet.2006.01.087] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 01/24/2006] [Accepted: 01/26/2006] [Indexed: 01/07/2023]
Abstract
Fibroblast activation protein (FAP) is a serine protease of undefined endopeptidase specificity implicated in tumorigenesis. To characterize FAP's P(4)-P(2)(') specificity, we synthesized intramolecularly quenched fluorescent substrate sets based on the FAP cleavage site in alpha(2)-antiplasmin (TSGP-NQ). FAP required substrates with Pro at P(1) and Gly or d-amino acids at P(2) and preferred small, uncharged amino acids at P(3), but tolerated most amino acids at P(4), P(1)(') and P(2)('). These substrate preferences allowed design of peptidyl-chloromethyl ketones that inhibited FAP, but not the related protease, dipeptidyl peptidase-4. Thus, FAP is a narrow specificity endopeptidase and this can be exploited for inhibitor design.
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Affiliation(s)
- Conrad Yap Edosada
- Department of Molecular Oncology, Genentech, Inc., 1 DNA Way - MS42, South San Francisco, CA 94080, USA
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49
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Pripp AH. Quantitative structure-activity relationship of prolyl oligopeptidase inhibitory peptides derived from beta-casein using simple amino acid descriptors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:224-8. [PMID: 16390203 DOI: 10.1021/jf0521303] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Quantitative structure-activity relationship (QSAR) modeling using simple amino acid descriptors was done on a set of prolyl oligopeptidase (POP) inhibitory peptides derived from beta-casein. Using partial least-squares regression, a QSAR model was obtained indicating that increased hydrophobicity and molecular bulkiness of amino acids in positions P3, P2, and P1' of inhibitory sites on peptides resulted in increased inhibition (lower IC50). Proline residues were always assumed to be in position P1. Hydrophobicity and molecular bulkiness have also in other studies been found as important factors for binding between substrates (or inhibitors) and the active site of POP. Prolyl oligopeptidase in blood serum is found to influence the level of hormone and neuropeptides and be related to cognitive and neurological deficiencies, e.g., Alzheimer's disease. Increased knowledge of the relationship between peptides derived from food proteins and their POP inhibition may be important in the development of functional foods as a supplement to pharmaceutical agents.
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Affiliation(s)
- Are Hugo Pripp
- Dairy Technology, Department of Food Science, The Royal Veterinary and Agricultural University, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark.
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50
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Morty RE, Shih AY, Fülöp V, Andrews NW. Identification of the reactive cysteine residues in oligopeptidase B from Trypanosoma brucei. FEBS Lett 2005; 579:2191-6. [PMID: 15811340 DOI: 10.1016/j.febslet.2005.03.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 03/07/2005] [Accepted: 03/07/2005] [Indexed: 11/28/2022]
Abstract
Oligopeptidase B (OpdB) from Trypanosoma brucei is a candidate therapeutic target in African trypanosomiasis. OpdB is an atypical serine peptidase, since activity is inhibited by thiol-blocking reagents and enhanced by reducing agents. We have identified C256 as the reactive cysteine residue that mediates OpdB inhibition by N-ethylmaleimide and iodoacetic acid. Modeling studies suggest that C256 adducts occlude the P(1) substrate-binding site, preventing substrate binding. We further demonstrate that C559 and C597 are responsible for the thiol-enhancement of OpdB activity. These studies may facilitate the development of specific OpdB inhibitors with therapeutic potential, by exploiting these unique properties of this enzyme.
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Affiliation(s)
- Rory E Morty
- Department of Internal Medicine, University of Giessen School of Medicine, Aulweg 123 (Room 6-11), D-35392 Giessen, Germany.
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