1
|
De Meyer F, Carlier A. Ecotin: A versatile protease inhibitor of bacteria and eukaryotes. Front Microbiol 2023; 14:1114690. [PMID: 36760512 PMCID: PMC9904509 DOI: 10.3389/fmicb.2023.1114690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Serine protease inhibitors are a large family of proteins involved in important pathways and processes, such as inflammatory responses and blood clotting. Most are characterized by a precise mode of action, thereby targeting a narrow range of protease substrates. However, the serine-protease inhibitor ecotin is able to inhibit a broad range of serine proteases that display a wide range of specificities. This specificity is driven by special structural features which allow unique flexibility upon binding to targets. Although frequently observed in many human/animal-associated bacteria, ecotin homologs may also be found in plant-associated taxa and environmental species. The purpose of this review is to provide an update on the biological importance, role in host-microbe interactions, and evolutionary relationship between ecotin orthologs isolated from Eukaryotic and Prokaryotic species across the Tree of Life.
Collapse
Affiliation(s)
- Frédéric De Meyer
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Aurélien Carlier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium,LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France,*Correspondence: Aurélien Carlier, ✉
| |
Collapse
|
2
|
Thomas C, Nothaft H, Yadav R, Fodor C, Alemka A, Oni O, Bell M, Rada B, Szymanski CM. Characterization of ecotin homologs from Campylobacter rectus and Campylobacter showae. PLoS One 2020; 15:e0244031. [PMID: 33378351 PMCID: PMC7773321 DOI: 10.1371/journal.pone.0244031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
Ecotin, first described in Escherichia coli, is a potent
inhibitor of a broad range of serine proteases including those typically
released by the innate immune system such as neutrophil elastase (NE). Here we
describe the identification of ecotin orthologs in various
Campylobacter species, including Campylobacter
rectus and Campylobacter showae residing in the
oral cavity and implicated in the development and progression of periodontal
disease in humans. To investigate the function of these ecotins in
vitro, the orthologs from C.
rectus and C. showae were
recombinantly expressed and purified from E.
coli. Using CmeA degradation/protection assays,
fluorescence resonance energy transfer and NE activity assays, we found that
ecotins from C. rectus and C.
showae inhibit NE, factor Xa and trypsin, but not the
Campylobacter jejuni serine protease HtrA or its ortholog
in E. coli, DegP. To further evaluate ecotin
function in vivo, an E. coli
ecotin-deficient mutant was complemented with the C.
rectus and C. showae
homologs. Using a neutrophil killing assay, we demonstrate that the low survival
rate of the E. coli ecotin-deficient mutant
can be rescued upon expression of ecotins from C.
rectus and C. showae. In
addition, the C. rectus and
C. showae ecotins partially compensate for
loss of N-glycosylation and increased protease susceptibility in the related
pathogen, Campylobacter jejuni, thus implicating a similar role
for these proteins in the native host to cope with the protease-rich environment
of the oral cavity.
Collapse
Affiliation(s)
- Cody Thomas
- Department of Microbiology and Complex Carbohydrate Research Center,
University of Georgia, Athens, Georgia, United States of
America
| | - Harald Nothaft
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
| | - Ruchi Yadav
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Christopher Fodor
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
| | - Abofu Alemka
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
| | - Oluwadamilola Oni
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Michael Bell
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Balázs Rada
- Department of Infectious Diseases, University of Georgia, Athens,
Georgia, United States of America
| | - Christine M. Szymanski
- Department of Microbiology and Complex Carbohydrate Research Center,
University of Georgia, Athens, Georgia, United States of
America
- Department of Biological Sciences, University of Alberta, Edmonton,
Alberta, Canada
- * E-mail:
| |
Collapse
|
3
|
Maiti BK, Govil N, Kundu T, Moura JJ. Designed Metal-ATCUN Derivatives: Redox- and Non-redox-Based Applications Relevant for Chemistry, Biology, and Medicine. iScience 2020; 23:101792. [PMID: 33294799 PMCID: PMC7701195 DOI: 10.1016/j.isci.2020.101792] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The designed "ATCUN" motif (amino-terminal copper and nickel binding site) is a replica of naturally occurring ATCUN site found in many proteins/peptides, and an attractive platform for multiple applications, which include nucleases, proteases, spectroscopic probes, imaging, and small molecule activation. ATCUN motifs are engineered at periphery by conjugation to recombinant proteins, peptides, fluorophores, or recognition domains through chemically or genetically, fulfilling the needs of various biological relevance and a wide range of practical usages. This chemistry has witnessed significant growth over the last few decades and several interesting ATCUN derivatives have been described. The redox role of the ATCUN moieties is also an important aspect to be considered. The redox potential of designed M-ATCUN derivatives is modulated by judicious choice of amino acid (including stereochemistry, charge, and position) that ultimately leads to the catalytic efficiency. In this context, a wide range of M-ATCUN derivatives have been designed purposefully for various redox- and non-redox-based applications, including spectroscopic probes, target-based catalytic metallodrugs, inhibition of amyloid-β toxicity, and telomere shortening, enzyme inactivation, biomolecules stitching or modification, next-generation antibiotic, and small molecule activation.
Collapse
Affiliation(s)
- Biplab K. Maiti
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Nidhi Govil
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Taraknath Kundu
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - José J.G. Moura
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| |
Collapse
|
4
|
Factor XII/XIIa inhibitors: Their discovery, development, and potential indications. Eur J Med Chem 2020; 208:112753. [DOI: 10.1016/j.ejmech.2020.112753] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022]
|
5
|
Harish BS, Uppuluri KB. Potential Anticoagulant Activity of Trypsin Inhibitor Purified from an Isolated Marine Bacterium Oceanimonas Sp. BPMS22 and its Kinetics. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:780-791. [PMID: 30121818 DOI: 10.1007/s10126-018-9848-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Protease inhibitors control major biological protease activities to maintain physiological homeostasis. Marine bacteria isolated from oligotrophic conditions could be taxonomically distinct, metabolically unique, and offers a wide variety of biochemicals. In the present investigation, marine sediments were screened for the potential bacteria that can produce trypsin inhibitors. A moderate halotolerant novel marine bacterial strain of Oceanimonas sp. BPMS22 was isolated, identified, and characterized. The effect of various process parameters like salt concentration, temperature, and pH was studied on the growth of the bacteria and production of trypsin inhibitor. Further, the trypsin inhibitor was purified to near homogeneity using anion exchange, size exclusion, and affinity chromatography. The purified trypsin inhibitor was found to competitively inhibit trypsin activity with an inhibition coefficient, Ki, of 3.44 ± 0.13 μM and second-order association rate constant, kass, of 1.08 × 103 M-1 S-1. The proteinaceous trypsin inhibitor had a molecular weight of approximately 30 kDa. The purified trypsin inhibitor showed anticoagulant activity on the human blood samples.
Collapse
Affiliation(s)
- B S Harish
- Bioprospecting Laboratory, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613 401, India
| | - Kiran Babu Uppuluri
- Bioprospecting Laboratory, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613 401, India.
| |
Collapse
|
6
|
Hirose S, Yokota K, Kuroda Y, Wako H, Endo S, Kanai S, Noguchi T. Prediction of protein motions from amino acid sequence and its application to protein-protein interaction. BMC STRUCTURAL BIOLOGY 2010; 10:20. [PMID: 20626880 PMCID: PMC3245509 DOI: 10.1186/1472-6807-10-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Accepted: 07/13/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA) can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. RESULTS In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predict internal and external motions from amino acid sequences based on the Random Forest algorithm. The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. The proposed method exhibited moderate correlation between predicted internal and external motions with those calculated by NMA. It has the highest prediction accuracy compared to a naïve model and three published predictors. CONCLUSIONS Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the predicted high internal motion regions and the observed conformational change regions.
Collapse
Affiliation(s)
- Shuichi Hirose
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST),2-42, Aomi, Koto-ku, Tokyo, 135-0064, Japan.
| | | | | | | | | | | | | |
Collapse
|
7
|
Kantyka T, Rawlings ND, Potempa J. Prokaryote-derived protein inhibitors of peptidases: A sketchy occurrence and mostly unknown function. Biochimie 2010; 92:1644-56. [PMID: 20558234 DOI: 10.1016/j.biochi.2010.06.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/08/2010] [Indexed: 11/28/2022]
Abstract
In metazoan organisms protein inhibitors of peptidases are important factors essential for regulation of proteolytic activity. In vertebrates genes encoding peptidase inhibitors constitute up to 1% of genes reflecting a need for tight and specific control of proteolysis especially in extracellular body fluids. In stark contrast unicellular organisms, both prokaryotic and eukaryotic consistently contain only few, if any, genes coding for putative peptidase inhibitors. This may seem perplexing in the light of the fact that these organisms produce large numbers of proteases of different catalytic classes with the genes constituting up to 6% of the total gene count with the average being about 3%. Apparently, however, a unicellular life-style is fully compatible with other mechanisms of regulation of proteolysis and does not require protein inhibitors to control their intracellular and extracellular proteolytic activity. So in prokaryotes occurrence of genes encoding different types of peptidase inhibitors is infrequent and often scattered among phylogenetically distinct orders or even phyla of microbiota. Genes encoding proteins homologous to alpha-2-macroglobulin (family I39), serine carboxypeptidase Y inhibitor (family I51), alpha-1-peptidase inhibitor (family I4) and ecotin (family I11) are the most frequently represented in Bacteria. Although several of these gene products were shown to possess inhibitory activity, with an exception of ecotin and staphostatins, the biological function of microbial inhibitors is unclear. In this review we present distribution of protein inhibitors from different families among prokaryotes, describe their mode of action and hypothesize on their role in microbial physiology and interactions with hosts and environment.
Collapse
Affiliation(s)
- Tomasz Kantyka
- Department of Microbiology, Jagiellonian University, Krakow, Poland
| | | | | |
Collapse
|
8
|
McCrudden MTC, Ryan LA, Turkington P, Timson DJ. The contribution of key hydrophobic residues in ecotin to enzyme-inhibitor complex stability. J Enzyme Inhib Med Chem 2010; 24:1207-10. [PMID: 19912053 DOI: 10.3109/14756360902779458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Escherichia coli protease inhibitor ecotin is believed to be implicated in the evasion of host defenses during infection. The protein has also attracted attention as a scaffold for the design of novel, specific protease inhibitors. Ecotin interacts with its targets through two sites. Key hydrophobic residues in both sites (Leu-64, Trp-67, Tyr-69, Met-84, and Met-85) were mutated to alanine and the effects on the inhibition of trypsin, chymotrypsin, and elastase were assessed. Each of these mutant ecotin proteins tested in kinetic assays with these enzymes exerted less inhibitory potency compared to wild-type ecotin. However, these effects were relatively small and not additive.
Collapse
|
9
|
Eschenlauer SCP, Faria MS, Morrison LS, Bland N, Ribeiro-Gomes FL, DosReis GA, Coombs GH, Lima APCA, Mottram JC. Influence of parasite encoded inhibitors of serine peptidases in early infection of macrophages with Leishmania major. Cell Microbiol 2009; 11:106-20. [PMID: 19016791 PMCID: PMC2659362 DOI: 10.1111/j.1462-5822.2008.01243.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 09/12/2008] [Accepted: 09/17/2008] [Indexed: 12/11/2022]
Abstract
Ecotin is a potent inhibitor of family S1A serine peptidases, enzymes lacking in the protozoan parasite Leishmania major. Nevertheless, L. major has three ecotin-like genes, termed inhibitor of serine peptidase (ISP). ISP1 is expressed in vector-borne procyclic and metacyclic promastigotes, whereas ISP2 is also expressed in the mammalian amastigote stage. Recombinant ISP2 inhibited neutrophil elastase, trypsin and chymotrypsin with K(i)s between 7.7 and 83 nM. L. major ISP2-ISP3 double null mutants (Deltaisp2/3) were created. These grew normally as promastigotes, but were internalized by macrophages more efficiently than wild-type parasites due to the upregulation of phagocytosis by a mechanism dependent on serine peptidase activity. Deltaisp2/3 promastigotes transformed to amastigotes, but failed to divide for 48 h. Intracellular multiplication of Deltaisp2/3 was similar to wild-type parasites when serine peptidase inhibitors were present, suggesting that defective intracellular growth results from the lack of serine peptidase inhibition during promastigote uptake. Deltaisp2/3 mutants were more infective than wild-type parasites to BALB/c mice at the early stages of infection, but became equivalent as the infection progressed. These data support the hypothesis that ISPs of L. major target host serine peptidases and influence the early stages of infection of the mammalian host.
Collapse
Affiliation(s)
- Sylvain C P Eschenlauer
- Glasgow Biomedical Research Centre, Wellcome Centre for Molecular Parasitology and Division of Infection and Immunity, Faculty of Biomedical and Life Sciences, University of GlasgowGlasgow G12 8TA, UK
| | - Marilia S Faria
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de JaneiroRio de Janeiro, RJ 21949-900, Brazil
| | - Lesley S Morrison
- Glasgow Biomedical Research Centre, Wellcome Centre for Molecular Parasitology and Division of Infection and Immunity, Faculty of Biomedical and Life Sciences, University of GlasgowGlasgow G12 8TA, UK
| | - Nicolas Bland
- Glasgow Biomedical Research Centre, Wellcome Centre for Molecular Parasitology and Division of Infection and Immunity, Faculty of Biomedical and Life Sciences, University of GlasgowGlasgow G12 8TA, UK
| | - Flavia L Ribeiro-Gomes
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de JaneiroRio de Janeiro, RJ 21949-900, Brazil
| | - George A DosReis
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de JaneiroRio de Janeiro, RJ 21949-900, Brazil
| | - Graham H Coombs
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of StrathclydeGlasgow G4 0NR, UK
| | - Ana Paula C A Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de JaneiroRio de Janeiro, RJ 21949-900, Brazil
| | - Jeremy C Mottram
- Glasgow Biomedical Research Centre, Wellcome Centre for Molecular Parasitology and Division of Infection and Immunity, Faculty of Biomedical and Life Sciences, University of GlasgowGlasgow G12 8TA, UK
| |
Collapse
|
10
|
Inestrosa NC, Sagal JP, Colombres M. Acetylcholinesterase interaction with Alzheimer amyloid beta. Subcell Biochem 2005; 38:299-317. [PMID: 15709485 DOI: 10.1007/0-387-23226-5_15] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Acetylcholinesterase (AChE) is an enzyme involved in cholinergic and non-cholinergic functions in both the central and peripheral nervous system, most of the AChE is found as a tetrameric form bound to neuronal membranes. Early cytochemical studies have demonstrated that the AChE associated with senile plaques differs enzymatically from the AChE associated with neurons in several respects. Biochemical studies indicated that AChE induces amyloid fibril formation and form highly toxic AChE-Abeta complexes. A 3.5 kDa peptide containing a tryptophan of the enzyme peripheral binding site (PAS) mimics the effect of the whole enzyme on amyloid formation. The neurotoxicity induced by AChE-Abeta complexes indicated that they trigger more neurodegeneration than those of the Abeta peptide alone, both in vitro (hippocampal neurons) and in vivo (rats injected in the dorsal hippocampus as a model of Alzheimer). The fact that AChE is able to accelerate amyloid formation and that such effect is sensitive to drugs that block PAS of the enzyme, suggests that specific and new AChE inhibitors may well provide an attractive possibility for treating Alzheimer's disease.
Collapse
|
11
|
Eggers CT, Murray IA, Delmar VA, Day AG, Craik CS. The periplasmic serine protease inhibitor ecotin protects bacteria against neutrophil elastase. Biochem J 2004; 379:107-18. [PMID: 14705961 PMCID: PMC1224055 DOI: 10.1042/bj20031790] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Accepted: 01/06/2004] [Indexed: 11/17/2022]
Abstract
Ecotin is a dimeric periplasmic protein from Escherichia coli that has been shown to inhibit potently many trypsin-fold serine proteases of widely varying substrate specificity. To help elucidate the physiological function of ecotin, we examined the family of ecotin orthologues, which are present in a subset of Gram-negative bacteria. Phylogenetic analysis suggested that ecotin has an exogenous target, possibly neutrophil elastase. Recombinant protein was expressed and purified from E. coli, Yersinia pestis and Pseudomonas aeruginosa, all species that encounter the mammalian immune system, and also from the plant pathogen Pantoea citrea. Notably, the Pa. citrea variant inhibits neutrophil elastase 1000-fold less potently than the other orthologues. All four orthologues are dimeric proteins that potently inhibit (<10 pM) the pancreatic digestive proteases trypsin and chymotrypsin, while showing more variable inhibition (5 pM to 24 microM) of the blood proteases Factor Xa, thrombin and urokinase-type plasminogen activator. To test whether ecotin does, in fact, protect bacteria from neutrophil elastase, an ecotin-deficient strain was generated in E. coli. This strain is significantly more sensitive in cell-killing assays to human neutrophil elastase, which causes increased permeability of the outer membrane that persists even during renewed bacterial growth. Ecotin affects primarily the ability of E. coli to recover and grow following treatment with neutrophil elastase, rather than the actual rate of killing. This suggests that an important part of the antimicrobial mechanism of neutrophil elastase may be a periplasmic bacteriostatic effect of protease that has translocated across the damaged outer membrane.
Collapse
Affiliation(s)
- Christopher T Eggers
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143-92280, USA
| | | | | | | | | |
Collapse
|
12
|
Felitsyn N, Kitova EN, Klassen JS. Thermal dissociation of the protein homodimer ecotin in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:1432-42. [PMID: 12484463 DOI: 10.1016/s1044-0305(02)00647-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The influence of charge on the thermal dissociation of gaseous, protonated, homodimeric, protein ecotin ions produced by nanoflow electrospray ionization (nanoES) was investigated using the blackbody infrared radiative dissociation technique. Dissociation of the protonated dimer, (E2 + nH)(n+) congruent to E2(n+) where n = 14-17, into pairs of monomer ions is the dominant reaction at temperatures from 126 to 175 degrees C. The monomer pair corresponding to the most symmetric charge distribution is preferred, although 50-60% of the monomer product ions correspond to an asymmetric partitioning of charge. The relative abundance of the different monomer ion pairs produced from E2(14+), E2(15+), and E2(16+) depends on reaction time, with the more symmetric charge distribution pair dominating at longer times. The relative yield of monomer ions observed late in the reaction is independent of temperature indicating that proton transfer between the monomers does not occur during dissociation and that the different monomer ion pairs are formed from dimer ions which differ in the distribution of charge between the monomers. For E2(17+), the yield of monomer ions is independent of reaction time but does exhibit slight temperature dependence, with higher temperatures favoring the monomers corresponding to most symmetric charge distribution. The charge distribution in the E2(15+) and E2(16+) dimer ions influences the dissociation kinetics, with the more asymmetric distribution resulting in greater reactivity. In contrast, the charge distribution has no measurable effect on the dissociation kinetics and energetics of the E2(17+) dimer.
Collapse
Affiliation(s)
- Natalia Felitsyn
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | | |
Collapse
|
13
|
Person MD, Brown KC, Mahrus S, Craik CS, Burlingame AL. Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer. Protein Sci 2001; 10:1549-62. [PMID: 11468352 PMCID: PMC2374083 DOI: 10.1110/ps.ps.46601] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In the presence of a suitable oxidizing agent, the Ni(II) complex of glycyl-glycyl-histidine (GGH) mediates efficient and specific oxidative protein cross-linking. The fusion of GGH to the N terminus of a protein allows for the cross-linking reagent to be delivered in a site-specific fashion, making this system extremely useful for analyzing protein-protein contacts in complicated mixtures of biomolecules. Tyrosine residues have been postulated to be the primary amino acid target of this reaction, and using the dimeric serine protease inhibitor ecotin, we previously demonstrated that engineering a tyrosine at the protein interface of a dimer dramatically increased cross-linking efficiency. Cross-linking increased four-fold for GGH-ecotin D137Y in comparison to wild-type GGH-ecotin, presumably through bityrosine formation at the dimer interface. Here we report the first complete structural analysis of the cross-linked GGH-ecotin D137Y dimer. Using a combination of mass spectrometric and chemical derivatization methods, a sole novel cross-link between the N-terminal glycine residues and the engineered tyrosine at position 137 has been characterized. The dimer cross-link is localized to a single site without other protein modifications, but different reaction pathways produce structurally related products. We propose a mechanism that involves covalent bond formation between the protein backbone and a dopaquinone moiety derived from a specific tyrosine residue. This finding establishes that it is not necessary to have two tyrosine residues within close proximity in the protein interface to obtain high protein cross-linking yields, and suggests that the cross-linking reagent may be of more general utility than previously thought.
Collapse
Affiliation(s)
- M D Person
- Department of Pharmaceutical Chemistry, University of California at San Francisco, 94143-0446, USA
| | | | | | | | | |
Collapse
|
14
|
Eggers CT, Wang SX, Fletterick RJ, Craik CS. The role of ecotin dimerization in protease inhibition. J Mol Biol 2001; 308:975-91. [PMID: 11352586 DOI: 10.1006/jmbi.2001.4754] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ecotin is a homodimeric protein from Escherichia coli that inhibits many serine proteases of the chymotrypsin fold, often with little effect from the character or extent of enzyme substrate specificity. This pan-specificity of inhibition is believed to derive from formation of a heterotetrameric complex with target proteases involving three types of interface: the dimerization interface, a primary substrate-like interaction, and a smaller secondary interaction between the partner ecotin subunit and the protease. A monomeric ecotin variant (mEcotin) and a single-chain ecotin dimer (scEcotin) were constructed to study the effect of a network of protein interactions on binding affinity and the role of dimerization in broad inhibitor specificity. mEcotin was produced by inserting a beta-turn into the C-terminal arm, which normally exchanges with the other subunit. While the dimerization constant (K(dim)) of wild-type (WT) ecotin was found to be picomolar by subunit exchange experiments using FRET and by association kinetics, mEcotin was monomeric up to 1 mM as judged by gel filtration and analytical centrifugation. A crystal structure of uncomplexed mEcotin to 2.0 A resolution verifies the design, showing a monomeric protein in which the C-terminal arm folds back onto itself to form a beta-barrel structure nearly identical to its dimeric counterpart. The kinetic rate constants and equilibrium dissociation constants for monomeric and dimeric ecotin variants were determined with both trypsin and chymotrypsin. The effect of the secondary binding site on affinity was found to vary inversely with the strength of the interaction at the primary site. This compensatory effect yields a nonadditivity of up to 5 kcal/mol and can be explained in terms of the optimization of binding orientation. Such a mechanism of adaptability allows femtomolar affinities for two proteases with very different specificities.
Collapse
Affiliation(s)
- C T Eggers
- Departments of Biochemistry and Biophysics, University of California at San Francisco 94143-0446, USA
| | | | | | | |
Collapse
|
15
|
Castro HC, Silva DM, Craik C, Zingali RB. Structural features of a snake venom thrombin-like enzyme: thrombin and trypsin on a single catalytic platform? BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1547:183-95. [PMID: 11410274 DOI: 10.1016/s0167-4838(01)00177-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Lachesis muta thrombin-like enzyme (LM-TL) is a single chain serine protease that shares 38% sequence identity with the serine protease domain of thrombin and also displays similar fibrinogen-clotting activity. In addition, the 228 amino acid residue LM-TL is 52% identical to trypsin, and cleaves chromogenic substrates with similar specificity. Herein we report a three-dimensional (3D) model validated experimentally for LM-TL based on these two homologous proteins of known 3D structure. Spatial modeling of LM-TL reveals a serine protease with a chymotrypsin fold presenting a hydrophobic pocket on its surface, involved in substrate recognition, and an important 90's loop, involved in restricting the LM-TL catalytic site cleft. Docking analysis showed that LM-TL would not form a stable complex with basic pancreatic trypsin inhibitor and wild-type ecotin since its 90's loop would restrict the access to the catalytic site. LM-TL formed acceptable interactions with fibrinopeptide A and a variant of ecotin; ecotin-TSRR/R in which both the primary and secondary binding sites are mutated Val81Thr, Thr83Ser, Met84Arg, Met85Arg and Asp70Arg. Furthermore, analysis of the primary structures of LM-TL and of the seven snake venom thrombin-like enzymes (SVTLEs) family reveals a subgroup formed by LM-TL, crotalase, and bilineobin, both closely related to thrombin. Therefore, LM-TL provides an initial point to compare SVTLEs with their counterparts, e.g. the mammalian serine proteases, and a basis for the localization of important residues within the little known SVTLEs family.
Collapse
Affiliation(s)
- H C Castro
- Departamento de Bioquímica Médica-ICB, Universidade Federal do Rio de Janeiro, Brazil.
| | | | | | | |
Collapse
|
16
|
Gillmor SA, Takeuchi T, Yang SQ, Craik CS, Fletterick RJ. Compromise and accommodation in ecotin, a dimeric macromolecular inhibitor of serine proteases. J Mol Biol 2000; 299:993-1003. [PMID: 10843853 DOI: 10.1006/jmbi.2000.3812] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ecotin is a dimeric serine protease inhibitor from Escherichia coli which binds proteases to form a hetero-tetramer with three distinct interfaces: an ecotin-ecotin dimer interface, a larger primary ecotin-protease interface, and a smaller secondary ecotin-protease interface. The contributions of these interfaces to binding and inhibition are unequal. To investigate the contribution and adaptability of each interface, we have solved the structure of two mutant ecotin-trypsin complexes and compared them to the structure of the previously determined wild-type ecotin-trypsin complex. Wild-type ecotin has an affinity of 1 nM for trypsin, while the optimized mutant, ecotin Y69F, D70P, which was found using phage display technologies, inhibits rat trypsin with a K(i) value of 0.08 nM. Ecotin 67-70A, M84R which has four alanine substitutions in the ecotin-trypsin secondary binding site, along with the M84R mutation at the primary site, has a K(i) value against rat trypsin of 0.2 nM. The structure of the ecotin Y69F, D70P-trypsin complex shows minor structural changes in the ecotin-trypsin tetramer. The structure of the ecotin 67-70A, M84R mutant bound to trypsin shows large deviations in the tertiary and quaternary structure of the complex. The trypsin structure shows no significant changes, but the conformation of several loop regions of ecotin are altered, resulting in the secondary site releasing its hold on trypsin. The structure of several regions previously considered to be rigid is also significantly modified. The inherent flexibility of ecotin allows it to accommodate these mutations and still maintain tight binding through the compromises of the protein-protein interfaces in the ecotin-trypsin tetramer. A comparison with two recently described ecotin-like genes from other bacteria suggests that these structural and functional features are conserved in otherwise distant bacterial lineages.
Collapse
Affiliation(s)
- S A Gillmor
- Graduate Group in Biophysics, University of California, San Francisco, CA, 94143-0448, USA
| | | | | | | | | |
Collapse
|
17
|
Chang C, Park BC, Lee DS, Suh SW. Crystal structures of thermostable xylose isomerases from Thermus caldophilus and Thermus thermophilus: possible structural determinants of thermostability. J Mol Biol 1999; 288:623-34. [PMID: 10329168 DOI: 10.1006/jmbi.1999.2696] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structures of highly thermostable xylose isomerases from Thermus thermophilus (TthXI) and Thermus caldophilus (TcaXI), both with the optimum reaction temperature of 90 degrees C, have been determined by X-ray crystallography. The model of TcaXI has been refined to an R-factor of 17.8 % for data extending to 2.3 A and that of TthXI to 17.1 % for data extending to 2.2 A. The tetrameric arrangement of subunits characterized by the 222-symmetry and the tertiary fold of each subunit in both TcaXI and TthXI are basically the same as in other xylose isomerases. Each monomer is composed of two domains. Domain I (residues 1 to 321) folds into the (beta/alpha)8-barrel. Domain II (residues 322 to 387), lacking beta-strands, makes extensive contacts with domain I of an adjacent subunit. Each monomer of TcaXI contains ten beta-strands, 15 alpha-helices, and six 310-helices, while that of TthXI contains ten beta-strands, 16 alpha-helices, and five 310-helices. Although the electron density does not indicate the presence of bound metal ions in the present models of both TcaXI and TthXI, the active site residues show the conserved structural features. In order to understand the structural basis for thermostability of these enzymes, their structures have been compared with less thermostable XIs from Arthrobacter B3728 and Actinoplanes missouriensis (AXI and AmiXI), with the optimum reaction temperatures of 80 degrees C and 75 degrees C, respectively. Analyses of various factors that may affect protein thermostability indicate that the possible structural determinants of the enhanced thermostability of TcaXI/TthXI over AXI/AmiXI are (i) an increase in ion pairs and ion-pair networks, (ii) a decrease in the large inter-subunit cavities, (iii) a removal of potential deamidation/isoaspartate formation sites, and (iv) a shortened loop.
Collapse
Affiliation(s)
- C Chang
- College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea
| | | | | | | |
Collapse
|