1
|
Ali MY, Bar-Peled L. Chemical proteomics to study metabolism, a reductionist approach applied at the systems level. Cell Chem Biol 2024; 31:446-451. [PMID: 38518745 DOI: 10.1016/j.chembiol.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/02/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
Cellular metabolism encompasses a complex array of interconnected biochemical pathways that are required for cellular homeostasis. When dysregulated, metabolism underlies multiple human pathologies. At the heart of metabolic networks are enzymes that have been historically studied through a reductionist lens, and more recently, using high throughput approaches including genomics and proteomics. Merging these two divergent viewpoints are chemical proteomic technologies, including activity-based protein profiling, which combines chemical probes specific to distinct enzyme families or amino acid residues with proteomic analysis. This enables the study of metabolism at the network level with the precision of powerful biochemical approaches. Herein, we provide a primer on how chemical proteomic technologies custom-built for studying metabolism have unearthed fundamental principles in metabolic control. In parallel, these technologies have leap-frogged drug discovery through identification of novel targets and drug specificity. Collectively, chemical proteomics technologies appear to do the impossible: uniting systematic analysis with a reductionist approach.
Collapse
Affiliation(s)
- Md Yousuf Ali
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
| |
Collapse
|
2
|
Chugunov AO, Dvoryakova EA, Dyuzheva MA, Simonyan TR, Tereshchenkova VF, Filippova IY, Efremov RG, Elpidina EN. Fighting Celiac Disease: Improvement of pH Stability of Cathepsin L In Vitro by Computational Design. Int J Mol Sci 2023; 24:12369. [PMID: 37569743 PMCID: PMC10418366 DOI: 10.3390/ijms241512369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Roughly 1% of the global population is susceptible to celiac disease (CD)-inheritable autoimmune inflammation of the small intestine caused by intolerance to gliadin proteins present in wheat, rye, and barley grains, and called gluten in wheat. Classical treatment is a life-long gluten-free diet, which is constraining and costly. An alternative approach is based upon the development and oral reception of effective peptidases that degrade in the stomach immunogenic proline- and glutamine-rich gliadin peptides, which are the cause of the severe reaction in the intestine. In previous research, we have established that the major digestive peptidase of an insect Tribolium castaneum-cathepsin L-hydrolyzes immunogenic prolamins after Gln residues but is unstable in the extremely acidic environment (pH 2-4) of the human stomach and cannot be used as a digestive aid. In this work, using molecular dynamics simulations, we discover the probable cause of the pH instability of cathepsin L-loss of the catalytically competent rotameric state of one of the active site residues, His 275. To "fix" the correct orientation of this residue, we designed a V277A mutant variant, which extends the range of stability of the peptidase in the acidic environment while retaining most of its activity. We suggest this protein as a lead glutenase for the development of oral medical preparation that fights CD and gluten intolerance in susceptible people.
Collapse
Affiliation(s)
- Anton O. Chugunov
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.D.); (R.G.E.)
- L.D. Landau School of Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Elena A. Dvoryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (E.A.D.); (E.N.E.)
| | - Maria A. Dyuzheva
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.D.); (R.G.E.)
- Higher Chemical College of the Russian Academy of Sciences, D. Mendeleev University of Chemical Technology, 125047 Moscow, Russia
| | - Tatyana R. Simonyan
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (T.R.S.); (V.F.T.); (I.Y.F.)
| | - Valeria F. Tereshchenkova
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (T.R.S.); (V.F.T.); (I.Y.F.)
| | - Irina Yu. Filippova
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (T.R.S.); (V.F.T.); (I.Y.F.)
| | - Roman G. Efremov
- M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.D.); (R.G.E.)
- L.D. Landau School of Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Elena N. Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (E.A.D.); (E.N.E.)
| |
Collapse
|
3
|
Awoonor-Williams E, Golosov AA, Hornak V. Benchmarking In Silico Tools for Cysteine p Ka Prediction. J Chem Inf Model 2023; 63:2170-2180. [PMID: 36996330 DOI: 10.1021/acs.jcim.3c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Accurate estimation of the pKa's of cysteine residues in proteins could inform targeted approaches in hit discovery. The pKa of a targetable cysteine residue in a disease-related protein is an important physiochemical parameter in covalent drug discovery, as it influences the fraction of nucleophilic thiolate amenable to chemical protein modification. Traditional structure-based in silico tools are limited in their predictive accuracy of cysteine pKa's relative to other titratable residues. Additionally, there are limited comprehensive benchmark assessments for cysteine pKa predictive tools. This raises the need for extensive assessment and evaluation of methods for cysteine pKa prediction. Here, we report the performance of several computational pKa methods, including single-structure and ensemble-based approaches, on a diverse test set of experimental cysteine pKa's retrieved from the PKAD database. The dataset consisted of 16 wildtype and 10 mutant proteins with experimentally measured cysteine pKa values. Our results highlight that these methods are varied in their overall predictive accuracies. Among the test set of wildtype proteins evaluated, the best method (MOE) yielded a mean absolute error of 2.3 pK units, highlighting the need for improvement of existing pKa methods for accurate cysteine pKa estimation. Given the limited accuracy of these methods, further development is needed before these approaches can be routinely employed to drive design decisions in early drug discovery efforts.
Collapse
Affiliation(s)
- Ernest Awoonor-Williams
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei A Golosov
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
4
|
Pedron FN, Messias A, Zeida A, Roitberg AE, Estrin DA. Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field. J Chem Inf Model 2023; 63:595-604. [PMID: 36630702 DOI: 10.1021/acs.jcim.2c01104] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cysteine is a common amino acid with a thiol group that plays a pivotal role in a variety of scenarios in redox biochemistry. In contrast, selenocysteine, the 21st amino acid, is only present in 25 human proteins. Classical force-field parameters for cysteine and selenocysteine are still scarce. In this context, we present a methodology to obtain Lennard-Jones parameters for cysteine and selenocysteine in different physiologically relevant oxidation and protonation states. The new force field parameters obtained in this work are available at https://github.com/MALBECC/AMBER-parameters-database. The parameters were adjusted to reproduce water radial distribution functions obtained by density functional theory ab initio molecular dynamics. We validated the results by evaluating the impact of the choice of parameters on the structure and dynamics in classical molecular dynamics simulations of representative proteins containing catalytic cysteine/selenocysteine residues. There are significant changes in protein structure and dynamics depending on the parameters choice, specifically affecting the residues close to the catalytic sites.
Collapse
Affiliation(s)
- Federico N Pedron
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Ari Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, 11800 Montevideo, Uruguay
| | - Adrián E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| |
Collapse
|
5
|
Zanetti-Polzi L, Charchar P, Yarovsky I, Corni S. Origins of the pH-Responsive Photoluminescence of Peptide-Functionalized Au Nanoclusters. ACS NANO 2022; 16:20129-20140. [PMID: 36300936 DOI: 10.1021/acsnano.2c04335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with the aim of enhancing the rational design of gold nanoclusters for bioapplications. Employing a hybrid quantum/classical computational methodology, we systematically calculate deprotonation free energies of N-terminal cysteine amine groups in proximity to the inherently fluorescent core of Au25(Peptide)18 nanoclusters. We find that subtle changes in hexapeptide sequence alter the electrostatic environment and significantly shift the conventional N-terminal amine pKa expected for amino acids free-in-solution. Our findings provide an insight into how the deprotonation equilibrium of N-terminal amine and side chain carboxyl groups cooperatively respond to solution pH changes, explaining the experimentally observed, yet elusive, pH-responsive fluorescence of peptide-functionalized Au25 clusters.
Collapse
Affiliation(s)
- Laura Zanetti-Polzi
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125Modena, Italy
| | | | - Irene Yarovsky
- School of Engineering, RMIT University, Victoria3001, Australia
| | - Stefano Corni
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125Modena, Italy
- Dipartimento di Scienze Chimiche, Università di Padova, 35131Padova, Italy
| |
Collapse
|
6
|
Alfarhan S, Brown J, Liu B, Long T, Jin K. Chemically recyclable crosslinked thiol‐ene photopolymers via thiol‐disulfide exchange reactions. JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1002/pol.20220131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Saleh Alfarhan
- Chemical Engineering, School for Engineering of Matter, Transport and Energy Arizona State University Tempe Arizona USA
| | - James Brown
- Chemistry, School of Molecular Sciences Arizona State University Tempe Arizona USA
- Biodesign Center for Sustainable Macromolecular Materials and Manufacturing Arizona State University Tempe Arizona USA
| | - Boer Liu
- Chemistry, School of Molecular Sciences Arizona State University Tempe Arizona USA
- Biodesign Center for Sustainable Macromolecular Materials and Manufacturing Arizona State University Tempe Arizona USA
| | - Timothy Long
- Chemical Engineering, School for Engineering of Matter, Transport and Energy Arizona State University Tempe Arizona USA
- Chemistry, School of Molecular Sciences Arizona State University Tempe Arizona USA
- Biodesign Center for Sustainable Macromolecular Materials and Manufacturing Arizona State University Tempe Arizona USA
| | - Kailong Jin
- Chemical Engineering, School for Engineering of Matter, Transport and Energy Arizona State University Tempe Arizona USA
- Biodesign Center for Sustainable Macromolecular Materials and Manufacturing Arizona State University Tempe Arizona USA
| |
Collapse
|
7
|
Norton-Baker B, Mehrabi P, Kwok AO, Roskamp KW, Rocha MA, Sprague-Piercy MA, von Stetten D, Miller RJD, Martin RW. Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging. Structure 2022; 30:763-776.e4. [PMID: 35338852 PMCID: PMC9081212 DOI: 10.1016/j.str.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022]
Abstract
Cataract, a clouding of the eye lens from protein precipitation, affects millions of people every year. The lens proteins, the crystallins, show extensive post-translational modifications (PTMs) in cataractous lenses. The most common PTMs, deamidation and oxidation, promote crystallin aggregation; however, it is not clear precisely how these PTMs contribute to crystallin insolubilization. Here, we report six crystal structures of the lens protein γS-crystallin (γS): one of the wild-type and five of deamidated γS variants, from three to nine deamidation sites, after sample aging. The deamidation mutations do not change the overall fold of γS; however, increasing deamidation leads to accelerated disulfide-bond formation. Addition of deamidated sites progressively destabilized protein structure, and the deamidated variants display an increased propensity for aggregation. These results suggest that the deamidated variants are useful as models for accelerated aging; the structural changes observed provide support for redox activity of γS-crystallin in the lens.
Collapse
Affiliation(s)
- Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA; Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany; Institute for Nanostructure and Solid-State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ashley O Kwok
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Kyle W Roskamp
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Megan A Rocha
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Marc A Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit C/O Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Rachel W Martin
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.
| |
Collapse
|
8
|
Orosz F, Vértessy BG. What's in a name? From "fluctuation fit" to "conformational selection": rediscovery of a concept. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:88. [PMID: 34244885 PMCID: PMC8270835 DOI: 10.1007/s40656-021-00442-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Rediscoveries are not rare in biology. A recent example is the re-birth of the "fluctuation fit" concept developed by F. B. Straub and G. Szabolcsi in the sixties of the last century, under various names, the most popular of which is the "conformational selection". This theory offers an alternative to the "induced fit" concept by Koshland for the interpretation of the mechanism of protein-ligand interactions. A central question is whether the ligand induces a conformational change (as described by the induced fit model) or rather selects and stabilizes a complementary conformation from a pre-existing equilibrium of various states of the protein (according to the fluctuation fit/conformational selection model). Straub and Szabolcsi's role and the factors hindering the spread of the fluctuation fit theory are discussed in the context of the history of the Hungarian biology in the 1950s and 1960s.
Collapse
Affiliation(s)
- Ferenc Orosz
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117 Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117 Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111 Hungary
| |
Collapse
|
9
|
The β 2 subunit E155 residue as a proton sensor at the binding site on GABA type A receptors. Eur J Pharmacol 2021; 906:174293. [PMID: 34214584 DOI: 10.1016/j.ejphar.2021.174293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022]
Abstract
GABA type A receptor plays a key role in inhibitory signaling in the adult central nervous system. This receptor can be modulated by protons but the underlying molecular mechanisms have not been fully explored. To find possible pH-sensor residues, a comparative study for proton-activated GLIC channel and α1β2γ2 GABA receptor was performed and pK 's of respective residues were estimated by numerical algorithms which consider local interactions. β E155, located at the GABA binding site, showed pKa values close to physiological values and dependence on the receptor state and ligation, suggesting a role in modulation by pH. To validate this prediction, pH sensitivity of current responses to GABA was investigated using patch-clamp technique for WT and mutated (β2E155[C, S, Q, L]) GABA receptors. Cysteine mutation preserved pH sensitivity. However, for remaining mutants, the sensitivity to acidification (pH = 6.0) was reduced becoming not statistically significant. The effect of alkaline pH (8.0) was maintained for all mutants with exception for β2E155L for which it was nearly abolished. To further explore the impact of considered mutations, molecular docking was performed which indicated that pH modulation is probably affected by interplay between binding site residues, zwitterion GABA and protons. These data, altogether, indicate that mutation of β2E155 to hydrophobic residue (L) maximally impaired pH modulation while for polar substitutions the effect was smaller. In conclusion, our data provide evidence that a key binding site residue β2E155 plays an important role in proton sensitivity of GABA receptor.
Collapse
|
10
|
Sheedlo MJ, Kenny S, Podkorytov IS, Brown K, Ma J, Iyer S, Hewitt CS, Arbough T, Mikhailovskii O, Flaherty DP, Wilson MA, Skrynnikov NR, Das C. Insights into Ubiquitin Product Release in Hydrolysis Catalyzed by the Bacterial Deubiquitinase SdeA. Biochemistry 2021; 60:584-596. [PMID: 33583181 DOI: 10.1021/acs.biochem.0c00760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the co-crystal structure of the (catalytic Cys)-to-Ala mutant of the deubiquitinase domain of the Legionella pneumophila effector SdeA (SdeADUB) with its ubiquitin (Ub) product. Most of the intermolecular interactions are preserved in this product-bound structure compared to that of the previously characterized complex of SdeADUB with the suicide inhibitor ubiquitin vinylmethyl ester (Ub-VME), whose structure models the acyl-enzyme thioester intermediate. Nuclear magnetic resonance (NMR) titration studies show a chemical shift perturbation pattern that suggests that the same interactions also exist in solution. Isothermal titration calorimetry and NMR titration data reveal that the affinity of wild-type (WT) SdeADUB for Ub is significantly lower than that of the Cys-to-Ala mutant. This is potentially due to repulsive interaction between the thiolate ion of the catalytic Cys residue in WT SdeADUB and the carboxylate group of the C-terminal Gly76 residue in Ub. In the context of SdeADUB catalysis, this electrostatic repulsion arises after the hydrolysis of the scissile isopeptide bond in the acyl-enzyme intermediate and the consequent formation of the C-terminal carboxylic group in the Ub fragment. We hypothesize that this electrostatic repulsion may expedite the release of the Ub product by SdeADUB. We note that similar repulsive interactions may also occur in other deubiquitinases and hydrolases of ubiquitin-like protein modifiers and may constitute a fairly general mechanism of product release within this family. This is a potentially important feature for a family of enzymes that form extensive protein-protein interactions during enzyme-substrate engagement.
Collapse
Affiliation(s)
- Michael J Sheedlo
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sebastian Kenny
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Kwame Brown
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jia Ma
- Bindley Bioscience Center, West Lafayette, Indiana 47906, United States
| | - Shalini Iyer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
| | - Trent Arbough
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Oleg Mikhailovskii
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Nikolai R Skrynnikov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
11
|
Perinelli M, Tegoni M, Freisinger E. Different Behavior of the Histidine Residue toward Cadmium and Zinc in a Cadmium-Specific Metallothionein from an Aquatic Fungus. Inorg Chem 2020; 59:16988-16997. [DOI: 10.1021/acs.inorgchem.0c02171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monica Perinelli
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matteo Tegoni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| |
Collapse
|
12
|
Harris RC, Liu R, Shen J. Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber. J Chem Theory Comput 2020; 16:3689-3698. [PMID: 32330035 PMCID: PMC7772776 DOI: 10.1021/acs.jctc.0c00258] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cysteines existing in the deprotonated thiolate form or having a tendency to become deprotonated are important players in enzymatic and cellular redox functions and frequently exploited in covalent drug design; however, most computational studies assume cysteines as protonated. Thus, developing an efficient tool that can make accurate and reliable predictions of cysteine protonation states is timely needed. We recently implemented a generalized Born (GB) based continuous constant pH molecular dynamics (CpHMD) method in Amber for protein pKa calculations on CPUs and GPUs. Here we benchmark the performance of GB-CpHMD for predictions of cysteine pKa's and reactivities using a data set of 24 proteins with both down- and upshifted cysteine pKa's. We found that 10 ns single-pH or 4 ns replica-exchange CpHMD titrations gave root-mean-square errors of 1.2-1.3 and correlation coefficients of 0.8-0.9 with respect to experiment. The accuracy of predicting thiolates or reactive cysteines at physiological pH with single-pH titrations is 86 or 81% with a precision of 100 or 90%, respectively. This performance well surpasses the traditional structure-based methods, particularly a widely used empirical pKa tool that gives an accuracy less than 50%. We discuss simulation convergence, dependence on starting structures, common determinants of the pKa downshifts and upshifts, and the origin of the discrepancies from the structure-based calculations. Our work suggests that CpHMD titrations can be performed on a desktop computer equipped with a single GPU card to predict cysteine protonation states for a variety of applications, from understanding biological functions to covalent drug design.
Collapse
Affiliation(s)
- Robert C Harris
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Ruibin Liu
- ComputChem LLC, Baltimore, Maryland 21202, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| |
Collapse
|
13
|
Hofer F, Kraml J, Kahler U, Kamenik AS, Liedl KR. Catalytic Site p Ka Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. J Chem Inf Model 2020; 60:3030-3042. [PMID: 32348143 PMCID: PMC7312390 DOI: 10.1021/acs.jcim.0c00190] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Enzymatic function and activity of
proteases is closely controlled
by the pH value. The protonation states of titratable residues in
the active site react to changes in the pH value, according to their
pKa, and thereby determine the functionality
of the enzyme. Knowledge of the titration behavior of these residues
is crucial for the development of drugs targeting the active site
residues. However, experimental pKa data
are scarce, since the systems’ size and complexity make determination
of these pKa values inherently difficult.
In this study, we use single pH constant pH MD simulations as a fast
and robust tool to estimate the active site pKa values of a set of aspartic, cysteine, and serine proteases.
We capture characteristic pKa shifts of
the active site residues, which dictate the experimentally determined
activity profiles of the respective protease family. We find clear
differences of active site pKa values
within the respective families, which closely match the experimentally
determined pH preferences of the respective proteases. These shifts
are caused by a distinct network of electrostatic interactions characteristic
for each protease family. While we find convincing agreement with
experimental data for serine and aspartic proteases, we observe clear
deficiencies in the description of the titration behavior of cysteines
within the constant pH MD framework and highlight opportunities for
improvement. Consequently, with this work, we provide a concise set
of active site pKa values of aspartic
and serine proteases, which could serve as reference for future theoretical
as well as experimental studies.
Collapse
Affiliation(s)
- Florian Hofer
- Institute for General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes Kraml
- Institute for General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Ursula Kahler
- Institute for General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S Kamenik
- Institute for General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute for General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| |
Collapse
|
14
|
Pahari S, Sun L, Alexov E. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5359213. [PMID: 30805645 PMCID: PMC6389863 DOI: 10.1093/database/baz024] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/11/2019] [Accepted: 01/30/2019] [Indexed: 11/14/2022]
Abstract
Ionizable residues play key roles in many biological phenomena including protein folding, enzyme catalysis and binding. We present PKAD, a database of experimentally measured pKas of protein residues reported in the literature or taken from existing databases. The database contains pKa data for 1350 residues in 157 wild-type proteins and for 232 residues in 45 mutant proteins. Most of these values are for Asp, Glu, His and Lys amino acids. The database is available as downloadable file as well as a web server (http://compbio.clemson.edu/pkad). The PKAD database can be used as a benchmarking source for development and improvement of pKa's prediction methods. The web server provides additional information taken from the corresponding structures and amino acid sequences, which allows for easy search and grouping of the experimental pKas according to various biophysical characteristics, amino acid type and others.
Collapse
Affiliation(s)
- Swagata Pahari
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Lexuan Sun
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| |
Collapse
|
15
|
Bak DW, Bechtel TJ, Falco JA, Weerapana E. Cysteine reactivity across the subcellular universe. Curr Opin Chem Biol 2018; 48:96-105. [PMID: 30508703 DOI: 10.1016/j.cbpa.2018.11.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/25/2018] [Accepted: 11/02/2018] [Indexed: 01/01/2023]
Abstract
Cysteine residues are concentrated at key functional sites within proteins, performing diverse roles in metal binding, catalysis, and redox chemistry. Chemoproteomic platforms to interrogate the reactive cysteinome have developed significantly over the past 10 years, resulting in a greater understanding of cysteine functionality, modification, and druggability. Recently, chemoproteomic methods to examine reactive cysteine residues from specific subcellular organelles have provided significantly improved proteome coverage and highlights the unique functionalities of cysteine residues mediated by cellular localization. Here, the diverse physicochemical properties of the mammalian subcellular organelles are explored in the context of their effects on cysteine reactivity. The unique functions of cysteine residues found in the mitochondria and endoplasmic reticulum are highlighted, together with an overview into chemoproteomic platforms employed to investigate cysteine reactivity in subcellular organelles.
Collapse
Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States.
| | - Tyler J Bechtel
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States
| | - Julia A Falco
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States.
| |
Collapse
|
16
|
Pahari S, Sun L, Basu S, Alexov E. DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate. Proteins 2018; 86:1277-1283. [PMID: 30252159 DOI: 10.1002/prot.25608] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/05/2018] [Accepted: 09/14/2018] [Indexed: 11/08/2022]
Abstract
DelPhiPKa is a widely used and unique approach to compute pKa 's of ionizable groups that does not require molecular surface to be defined. Instead, it uses smooth Gaussian-based dielectric function to treat computational space via Poisson-Boltzmann equation (PBE). Here, we report an expansion of DelPhiPKa functionality to enable inclusion of salt in the modeling protocol. The method considers the salt mobile ions in solvent phase without defining solute-solvent boundary. Instead, the ions are penalized to enter solute interior via a desolvation penalty term in the Boltzmann factor in the framework of PBE. Hence, the concentration of ions near the protein is balanced by the desolvation penalty and electrostatic interactions. The study reveals that correlation between experimental and calculated pKa 's is improved significantly by taking into consideration the presence of salt. Furthermore, it is demonstrated that DelphiPKa reproduces the salt sensitivity of experimentally measured pKa 's. Another new development of DelPhiPKa allows for computing the pKa 's of polar residues such as cysteine, serine, threonine and tyrosine. With this regard, DelPhiPKa is benchmarked against experimentally measured cysteine and tyrosine pKa 's and for cysteine it is shown to outperform other existing methods (DelPhiPKa RMSD of 1.73 vs RMSD between 2.40 and 4.72 obtained by other existing pKa prediction methods).
Collapse
Affiliation(s)
- Swagata Pahari
- Department of Physics and Astronomy, Computational Biophysics and Bioinformatics, Clemson University, Clemson, South Carolina
| | - Lexuan Sun
- Department of Physics and Astronomy, Computational Biophysics and Bioinformatics, Clemson University, Clemson, South Carolina
| | - Sankar Basu
- Department of Physics and Astronomy, Computational Biophysics and Bioinformatics, Clemson University, Clemson, South Carolina
| | - Emil Alexov
- Department of Physics and Astronomy, Computational Biophysics and Bioinformatics, Clemson University, Clemson, South Carolina
| |
Collapse
|
17
|
Abstract
Covalent inhibition is a rapidly growing discipline within drug discovery. Many historical covalent inhibitors were discovered by serendipity, with such a mechanism of action often regarded as undesirable due to potential toxicity issues. Recent progress has seen a major shift in this outlook, as covalent inhibition shows promise for targets where previous efforts to identify non-covalent small molecule inhibitors have failed. Targeted covalent inhibitors (TCIs) can offer drug discovery scientists the ability to increase the potency and/or selectivity of small molecule inhibitors, by attachment of reactive functional groups designed to covalently bind to specific sites in a target. In this tutorial review we introduce the broader concept of covalent inhibition, discuss the potential benefits and challenges of such an approach, and provide an overview of the current status of the field. We also describe some strategies and computational tools to enable successful covalent drug discovery.
Collapse
Affiliation(s)
- Richard Lonsdale
- Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK.
| | | |
Collapse
|
18
|
O'Keefe JP, Dustin CM, Barber D, Snider GW, Hondal RJ. A "Seleno Effect" Differentiates the Roles of Redox Active Cysteine Residues in Plasmodium falciparum Thioredoxin Reductase. Biochemistry 2018; 57:1767-1778. [PMID: 29485860 DOI: 10.1021/acs.biochem.8b00004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we introduce the concept of the "seleno effect" in the study of oxidoreductases that catalyze thiol/disulfide exchange reactions. In these reactions, selenium can replace sulfur as a nucleophile, electrophile, or leaving group, and the resulting change in rate (the seleno effect) is defined as kS/ kSe. In solution, selenium accelerates the rate of thiol/disulfide exchange regardless of its chemical role (e.g., nucleophile or electrophile). Here we show that this is not the case for enzyme catalyzed reactions and that the magnitude of the seleno effect can differentiate the role of each sulfur atom of a disulfide bond between that of an electrophile or leaving group. We used selenium for sulfur substitution to study the thiol/disulfide exchange step that occurs between the N-terminal redox center and the C-terminal disulfide-containing β-hairpin motif of Plasmodium falciparum thioredoxin reductase (PfTrxR), which has the sequence Gly-Cys535-Gly-Gly-Gly-Lys-Cys540-Gly. We assayed a truncated PfTrxR enzyme missing this C-terminal tail for disulfide-reductase activity using synthetic peptide substrates in which either Cys535 or Cys540 was replaced with selenocysteine (Sec). The results show that substitution of Cys535 with Sec resulted in a nearly 9-fold decrease in the rate of reduction, while substitution of Cys540 resulted in a 1.5-fold increase in the rate of reduction. We also produced full-length, semisynthetic enzymes in which Sec replaced either of these two Cys residues and observed similar results using E. coli thioredoxin as the substrate. In this assay, the observed seleno effect ( kS/ kSe) for the C535U mutant was 7.4, and that for the C540U mutant was 0.2.
Collapse
Affiliation(s)
- John P O'Keefe
- Department of Biochemistry , University of Vermont , 89 Beaumont Ave, Given Building Room B413 , Burlington , Vermont 05405 , United States
| | - Christopher M Dustin
- Department of Biochemistry , University of Vermont , 89 Beaumont Ave, Given Building Room B413 , Burlington , Vermont 05405 , United States
| | - Drew Barber
- Department of Biochemistry , University of Vermont , 89 Beaumont Ave, Given Building Room B413 , Burlington , Vermont 05405 , United States
| | - Gregg W Snider
- Department of Biochemistry , University of Vermont , 89 Beaumont Ave, Given Building Room B413 , Burlington , Vermont 05405 , United States
| | - Robert J Hondal
- Department of Biochemistry , University of Vermont , 89 Beaumont Ave, Given Building Room B413 , Burlington , Vermont 05405 , United States
| |
Collapse
|
19
|
Frankel EA, Bevilacqua PC. Complexity in pH-Dependent Ribozyme Kinetics: Dark pK a Shifts and Wavy Rate-pH Profiles. Biochemistry 2017; 57:483-488. [PMID: 29271644 DOI: 10.1021/acs.biochem.7b00784] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Charged bases occur in RNA enzymes, or ribozymes, where they play key roles in catalysis. Cationic bases donate protons and perform electrostatic catalysis, while anionic bases accept protons. We previously published simulations of rate-pH profiles for ribozymes in terms of species plots for the general acid and general base that have been useful for understanding how ribozymes respond to pH. In that study, we did not consider interaction between the general acid and general base or interaction with other species on the RNA. Since that report, diverse small ribozyme classes have been discovered, many of which have charged nucleobases or metal ions in the active site that can either directly interact and participate in catalysis or indirectly interact as "influencers". Herein, we simulate experimental rate-pH profiles in terms of species plots in which reverse protonated charged nucleobases interact. These analyses uncover two surprising features of pH-dependent enzyme kinetics. (1) Cooperativity between the general acid and general base enhances population of the functional forms of a ribozyme and manifests itself as hidden or "dark" pKa shifts, real pKa shifts that accelerate the reaction but are not readily observed by standard experimental approaches, and (2) influencers favorably shift the pKas of proton-transferring nucleobases and manifest themselves as "wavy" rate-pH profiles. We identify parallels with the protein enzyme literature, including reverse protonation and wavelike behavior, while pointing out that RNA is more prone to reverse protonation. The complexities uncovered, which arise from simple pairwise interactions, should aid deconvolution of complex rate-pH profiles for RNA and protein enzymes and suggest veiled catalytic devices for promoting catalysis that can be tested by experiment and calculation.
Collapse
Affiliation(s)
- Erica A Frankel
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| |
Collapse
|
20
|
Modeling covalent-modifier drugs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1664-1675. [PMID: 28528876 DOI: 10.1016/j.bbapap.2017.05.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 11/21/2022]
Abstract
In this review, we present a summary of how computer modeling has been used in the development of covalent-modifier drugs. Covalent-modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein-ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent-modifier drugs. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
Collapse
|
21
|
Awoonor-Williams E, Rowley CN. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins. J Chem Theory Comput 2016; 12:4662-73. [DOI: 10.1021/acs.jctc.6b00631] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| |
Collapse
|
22
|
Abstract
The authors were asked by the Editors of ACS Chemical Biology to write an article titled "Why Nature Chose Selenium" for the occasion of the upcoming bicentennial of the discovery of selenium by the Swedish chemist Jöns Jacob Berzelius in 1817 and styled after the famous work of Frank Westheimer on the biological chemistry of phosphate [Westheimer, F. H. (1987) Why Nature Chose Phosphates, Science 235, 1173-1178]. This work gives a history of the important discoveries of the biological processes that selenium participates in, and a point-by-point comparison of the chemistry of selenium with the atom it replaces in biology, sulfur. This analysis shows that redox chemistry is the largest chemical difference between the two chalcogens. This difference is very large for both one-electron and two-electron redox reactions. Much of this difference is due to the inability of selenium to form π bonds of all types. The outer valence electrons of selenium are also more loosely held than those of sulfur. As a result, selenium is a better nucleophile and will react with reactive oxygen species faster than sulfur, but the resulting lack of π-bond character in the Se-O bond means that the Se-oxide can be much more readily reduced in comparison to S-oxides. The combination of these properties means that replacement of sulfur with selenium in nature results in a selenium-containing biomolecule that resists permanent oxidation. Multiple examples of this gain of function behavior from the literature are discussed.
Collapse
Affiliation(s)
- Hans J. Reich
- University of Wisconsin—Madison, Department of Chemistry, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Robert J. Hondal
- University of Vermont, Department of Biochemistry, 89 Beaumont Ave, Given Laboratory, Room B413, Burlington, Vermont 05405, United States
| |
Collapse
|
23
|
Risør MW, Thomsen LR, Sanggaard KW, Nielsen TA, Thøgersen IB, Lukassen MV, Rossen L, Garcia-Ferrer I, Guevara T, Scavenius C, Meinjohanns E, Gomis-Rüth FX, Enghild JJ. Enzymatic and Structural Characterization of the Major Endopeptidase in the Venus Flytrap Digestion Fluid. J Biol Chem 2015; 291:2271-87. [PMID: 26627834 DOI: 10.1074/jbc.m115.672550] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Indexed: 11/06/2022] Open
Abstract
Carnivorous plants primarily use aspartic proteases during digestion of captured prey. In contrast, the major endopeptidases in the digestive fluid of the Venus flytrap (Dionaea muscipula) are cysteine proteases (dionain-1 to -4). Here, we present the crystal structure of mature dionain-1 in covalent complex with inhibitor E-64 at 1.5 Å resolution. The enzyme exhibits an overall protein fold reminiscent of other plant cysteine proteases. The inactive glycosylated pro-form undergoes autoprocessing and self-activation, optimally at the physiologically relevant pH value of 3.6, at which the protective effect of the pro-domain is lost. The mature enzyme was able to efficiently degrade a Drosophila fly protein extract at pH 4 showing high activity against the abundant Lys- and Arg-rich protein, myosin. The substrate specificity of dionain-1 was largely similar to that of papain with a preference for hydrophobic and aliphatic residues in subsite S2 and for positively charged residues in S1. A tentative structure of the pro-domain was obtained by homology modeling and suggested that a pro-peptide Lys residue intrudes into the S2 pocket, which is more spacious than in papain. This study provides the first analysis of a cysteine protease from the digestive fluid of a carnivorous plant and confirms the close relationship between carnivorous action and plant defense mechanisms.
Collapse
Affiliation(s)
- Michael W Risør
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark, the Interdisciplinary Nanoscience Center (iNANO), DK-8000 Aarhus, Denmark
| | - Line R Thomsen
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark, the Interdisciplinary Nanoscience Center (iNANO), DK-8000 Aarhus, Denmark
| | - Kristian W Sanggaard
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark, the Interdisciplinary Nanoscience Center (iNANO), DK-8000 Aarhus, Denmark
| | - Tania A Nielsen
- the Interdisciplinary Nanoscience Center (iNANO), DK-8000 Aarhus, Denmark
| | - Ida B Thøgersen
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Marie V Lukassen
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Litten Rossen
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Irene Garcia-Ferrer
- the Proteolysis Laboratory, Department of Structural Biology ("María de Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain, and
| | - Tibisay Guevara
- the Proteolysis Laboratory, Department of Structural Biology ("María de Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain, and
| | - Carsten Scavenius
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - F Xavier Gomis-Rüth
- the Proteolysis Laboratory, Department of Structural Biology ("María de Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain, and
| | - Jan J Enghild
- From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark, the Interdisciplinary Nanoscience Center (iNANO), DK-8000 Aarhus, Denmark,
| |
Collapse
|
24
|
Dunican BF, Hiller DA, Strobel SA. Transition State Charge Stabilization and Acid-Base Catalysis of mRNA Cleavage by the Endoribonuclease RelE. Biochemistry 2015; 54:7048-57. [PMID: 26535789 DOI: 10.1021/acs.biochem.5b00866] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The bacterial toxin RelE is a ribosome-dependent endoribonuclease. It is part of a type II toxin-antitoxin system that contributes to antibiotic resistance and biofilm formation. During amino acid starvation, RelE cleaves mRNA in the ribosomal A-site, globally inhibiting protein translation. RelE is structurally similar to microbial RNases that employ general acid-base catalysis to facilitate RNA cleavage. The RelE active site is atypical for acid-base catalysis, in that it is enriched with positively charged residues and lacks the prototypical histidine-glutamate catalytic pair, making the mechanism of mRNA cleavage unclear. In this study, we use a single-turnover kinetic analysis to measure the effect of pH and phosphorothioate substitution on the rate constant for cleavage of mRNA by wild-type RelE and seven active-site mutants. Mutation and thio effects indicate a major role for stabilization of increased negative change in the transition state by arginine 61. The wild-type RelE cleavage rate constant is pH-independent, but the reaction catalyzed by many of the mutants is strongly dependent on pH, suggestive of general acid-base catalysis. pH-rate curves indicate that wild-type RelE operates with the pK(a) of at least one catalytic residue significantly downshifted by the local environment. Mutation of any single active-site residue is sufficient to disrupt this microenvironment and revert the shifted pK(a) back above neutrality. pH-rate curves are consistent with K54 functioning as a general base and R81 as a general acid. The capacity of RelE to effect a large pK(a) shift and facilitate a common catalytic mechanism by uncommon means furthers our understanding of other atypical enzymatic active sites.
Collapse
Affiliation(s)
- Brian F Dunican
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06511, United States
| | - David A Hiller
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06511, United States
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06511, United States
| |
Collapse
|
25
|
Quantification of thiols and disulfides. Biochim Biophys Acta Gen Subj 2013; 1840:838-46. [PMID: 23567800 DOI: 10.1016/j.bbagen.2013.03.031] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/25/2013] [Accepted: 03/28/2013] [Indexed: 11/23/2022]
Abstract
BACKGROUND Disulfide bond formation is a key posttranslational modification, with implications for structure, function and stability of numerous proteins. While disulfide bond formation is a necessary and essential process for many proteins, it is deleterious and disruptive for others. Cells go to great lengths to regulate thiol-disulfide bond homeostasis, typically with several, apparently redundant, systems working in parallel. Dissecting the extent of oxidation and reduction of disulfides is an ongoing challenge due, in part, to the facility of thiol/disulfide exchange reactions. SCOPE OF REVIEW In the present account, we briefly survey the toolbox available to the experimentalist for the chemical determination of thiols and disulfides. We have chosen to focus on the key chemical aspects of current methodology, together with identifying potential difficulties inherent in their experimental implementation. MAJOR CONCLUSIONS While many reagents have been described for the measurement and manipulation of the redox status of thiols and disulfides, a number of these methods remain underutilized. The ability to effectively quantify changes in redox conditions in living cells presents a continuing challenge. GENERAL SIGNIFICANCE Many unresolved questions in the metabolic interconversion of thiols and disulfides remain. For example, while pool sizes of redox pairs and their intracellular distribution are being uncovered, very little is known about the flux in thiol-disulfide exchange pathways. New tools are needed to address this important aspect of cellular metabolism. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.
Collapse
|
26
|
Abstract
Cysteine residues on proteins play key roles in catalysis and regulation. These functional cysteines serve as active sites for nucleophilic and redox catalysis, sites of allosteric regulation, and metal-binding ligands on proteins from diverse classes including proteases, kinases, metabolic enzymes, and transcription factors. In this review, we focus on a few select examples that serve to highlight the multiple functions performed by cysteines, with an emphasis on cysteine-mediated protein activities implicated in cancer. The enhanced reactivity of functional cysteines renders them susceptible to modification by electrophilic species. Toward this end, we discuss recent advancements and future prospects for utilizing cysteine-reactive small molecules as drugs and imaging agents for the treatment and diagnosis of cancer.
Collapse
Affiliation(s)
- Nicholas J. Pace
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
27
|
Brocklehurst K, Philpott MP. Cysteine proteases: mode of action and role in epidermal differentiation. Cell Tissue Res 2013; 351:237-44. [PMID: 23344364 DOI: 10.1007/s00441-013-1557-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/03/2013] [Indexed: 12/31/2022]
Abstract
Desquamation or cell shedding in mammalian skin is known to involve serine proteases, aspartic proteases and glycosidases. In addition, evidence continues to accumulate that papain-like cysteine proteases and an inhibitor cystatin M/E largely confined to the cutaneous epithelia also play key roles in the process. This involves the complete proteolysis of cell adhesive structures of the stratum corneum, the corneodesmosomes and notably of the desmogleins. Continual cell replacement in the epidermis is the result of the balance between the loss of the outer squames and mitosis of the cells in the basal cell layer. This article provides a brief account of the salient features of the characteristics and catalytic mechanism of cysteine proteases, followed by a discussion of the relevant epidermal biology. The proteases include the asparaginyl endopeptidase legumain, which exerts a strict specificity for the hydrolysis of asparaginyl bonds, cathepsin-V and cathepsin-L. The control of these enzymes by cystatin M/E regulates the processing of transglutaminases and is crucial in the biochemical pathway responsible for regulating the cross-linking and desquamation of the stratum corneum. In addition, caspase-14 has now been shown to play a major part in epidermal maturation. Uncontrolled proteolytic activity leads to abnormal hair follicle formation and deleterious effects on the skin barrier function.
Collapse
Affiliation(s)
- Keith Brocklehurst
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | |
Collapse
|
28
|
Aghera N, Dasgupta I, Udgaonkar JB. A Buried Ionizable Residue Destabilizes the Native State and the Transition State in the Folding of Monellin. Biochemistry 2012; 51:9058-66. [DOI: 10.1021/bi3008017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nilesh Aghera
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Ishita Dasgupta
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| |
Collapse
|
29
|
Hussain S, Khan A, Gul S, Resmini M, Verma CS, Thomas EW, Brocklehurst K. Identification of interactions involved in the generation of nucleophilic reactivity and of catalytic competence in the catalytic site Cys/His ion pair of papain. Biochemistry 2011; 50:10732-42. [PMID: 22044167 DOI: 10.1021/bi201207z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the roles of noncovalent interactions within the enzyme molecule and between enzyme and substrate or inhibitor is an essential goal of the investigation of active center chemistry and catalytic mechanism. Studies on members of the papain family of cysteine proteinases, particularly papain (EC 3.4.22.2) itself, continue to contribute to this goal. The historic role of the catalytic site Cys/His ion pair now needs to be understood within the context of multiple dynamic phenomena. Movement of Trp177 may be necessary to expose His159 to solvent with consequent decrease in its degree of electrostatic solvation of (Cys25)-S(-). Here we report an investigation of this possibility using computer modeling of quasi-transition states and pH-dependent kinetics using 3,3'-dipyridazinyl disulfide, its n-propyl and phenyl derivatives, and 4,4'-dipyrimidyl disulfide as reactivity probes that differ in the location of potential hydrogen-bonding acceptor atoms. Those interactions that influence ion pair geometry and thereby catalytic competence, including by transmission of the modulatory effect of a remote ionization with pK(a) 4, were identified. A key result is the correlation between the kinetic influence of the modulatory trigger of pK(a) 4 and disruption of the hydrogen bond donated by the indole N-H of Trp177, the hydrophobic shield of the initial "intimate" ion pair. This hydrogen bond is accepted by the amide O of Gln19-a component of the oxyanion hole that binds the tetrahedral species formed from the substrate during the catalytic act. The disruption would be expected to contribute to the mobility of Trp177 and possibly to the effectiveness of the binding of the developing oxyanion.
Collapse
Affiliation(s)
- Syeed Hussain
- Laboratory of Structural and Mechanistic Enzymology, School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | | | | | | | | | | | | |
Collapse
|
30
|
Mirković B, Sosič I, Gobec S, Kos J. Redox-based inactivation of cysteine cathepsins by compounds containing the 4-aminophenol moiety. PLoS One 2011; 6:e27197. [PMID: 22073285 PMCID: PMC3208577 DOI: 10.1371/journal.pone.0027197] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 10/12/2011] [Indexed: 01/06/2023] Open
Abstract
Background Redox cycling compounds have been reported to cause false positive inhibition of proteases in drug discovery studies. This kind of false positives can lead to unusually high hit rates in high-throughput screening campaigns and require further analysis to distinguish true from false positive hits. Such follow-up studies are both time and resource consuming. Methods and Findings In this study we show that 5-aminoquinoline-8-ol is a time-dependent inactivator of cathepsin B with a kinact/KI of 36.7±13.6 M−1s−1 using enzyme kinetics. 5-Aminoquinoline-8-ol inhibited cathepsins H, L and B in the same concentration range, implying a non-specific mechanism of inhibition. Further analogues, 4-aminonaphthalene-1-ol and 4-aminophenol, also displayed time-dependent inhibition of cathepsin B with kinact/KI values of 406.4±10.8 and 36.5±1.3 M−1s−1. No inactivation occurred in the absence of either the amino or the hydroxyl group, suggesting that the 4-aminophenol moiety is a prerequisite for enzyme inactivation. Induction of redox oxygen species (ROS) by 4-aminophenols in various redox environments was determined by the fluorescent probe 2′,7′-dichlorodihydrofluorescein diacetate. Addition of catalase to the assay buffer significantly abrogated the ROS signal, indicating that H2O2 is a component of the ROS induced by 4-aminophenols. Furthermore, using mass spectrometry, active site probe DCG-04 and isoelectric focusing we show that redox inactivation of cysteine cathepsins by 5-aminoquinoline-8-ol is active site directed and leads to the formation of sulfinic acid. Conclusions In this study we report that compounds containing the 4-aminophenol moiety inactivate cysteine cathepsins through a redox-based mechanism and are thus likely to cause false positive hits in the screening assays for cysteine proteases.
Collapse
Affiliation(s)
- Bojana Mirković
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.
| | | | | | | |
Collapse
|
31
|
Linsky T, Wang Y, Fast W. Screening for dimethylarginine dimethylaminohydrolase inhibitors reveals ebselen as a bioavailable inactivator. ACS Med Chem Lett 2011; 2:592-596. [PMID: 21927644 DOI: 10.1021/ml2000824] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Dimethylarginine dimethylaminohydrolase (DDAH) is an endogenous regulator of nitric oxide production and represents a potential therapeutic target. However, only a small number of biologically useful inhibitors have been reported, and many of these are substrate analogs. To seek more diverse scaffolds, we developed a high-throughput screening (HTS) assay and queried two small libraries totaling 2446 compounds. The HTS assay proved to be robust, reproducible and scalable, with Z' factors ≥ 0.78. One inhibitor, ebselen, is structurally divergent from substrate and was characterized in detail. This selenazole covalently inactivates DDAH in vitro and in cultured cells. The rate constant for inactivation of DDAH (44,000 ± 2,400 M(-1)s(-1)) is greater than those reported for any other target, suggesting this pathway is an important aspect of ebselen's total pharmacological effects.
Collapse
Affiliation(s)
- Thomas Linsky
- Graduate Program in Biochemistry and ‡Medicinal Chemistry Division, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Yun Wang
- Graduate Program in Biochemistry and ‡Medicinal Chemistry Division, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Walter Fast
- Graduate Program in Biochemistry and ‡Medicinal Chemistry Division, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| |
Collapse
|
32
|
Ferrer-Sueta G, Manta B, Botti H, Radi R, Trujillo M, Denicola A. Factors affecting protein thiol reactivity and specificity in peroxide reduction. Chem Res Toxicol 2011; 24:434-50. [PMID: 21391663 DOI: 10.1021/tx100413v] [Citation(s) in RCA: 213] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein thiol reactivity generally involves the nucleophilic attack of the thiolate on an electrophile. A low pK(a) means higher availability of the thiolate at neutral pH but often a lower nucleophilicity. Protein structural factors contribute to increasing the reactivity of the thiol in very specific reactions, but these factors do not provide an indiscriminate augmentation in general reactivity. Notably, reduction of hydroperoxides by the catalytic cysteine of peroxiredoxins can achieve extraordinary reaction rates relative to free cysteine. The discussion of this catalytic efficiency has centered in the stabilization of the thiolate as a way to increase nucleophilicity. Such stabilization originates from electrostatic and polar interactions of the catalytic cysteine with the protein environment. We propose that the set of interactions is better described as a means of stabilizing the anionic transition state of the reaction. The enhanced acidity of the critical cysteine is concurrent but not the cause of catalytic efficiency. Protein stabilization of the transition state is achieved by (a) a relatively static charge distribution around the cysteine that includes a conserved arginine and the N-terminus of an α-helix providing a cationic environment that stabilizes the reacting thiolate, the transition state, and also the anionic leaving group; (b) a dynamic set of polar interactions that stabilize the thiolate in the resting enzyme and contribute to restraining its reactivity in the absence of substrate; but upon peroxide binding these active/binding site groups switch interactions from thiolate to peroxide oxygens, simultaneously increasing the nucleophilicity of the attacking sulfur and facilitating the correct positioning of the substrate. The switching of polar interaction provides further acceleration and, importantly, confers specificity to the thiol reactivity. The extraordinary thiol reactivity and specificity toward H(2)O(2) combined with their ubiquity and abundance place peroxiredoxins, along with glutathione peroxidases, as obligate hydroperoxide cellular sensors.
Collapse
Affiliation(s)
- Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | | | | | | | | | | |
Collapse
|
33
|
Johnson CM, Linsky TW, Yoon DW, Person MD, Fast W. Discovery of halopyridines as quiescent affinity labels: inactivation of dimethylarginine dimethylaminohydrolase. J Am Chem Soc 2011; 133:1553-62. [PMID: 21222447 DOI: 10.1021/ja109207m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an effort to develop novel covalent modifiers of dimethylarginine dimethylaminohydrolase (DDAH) that are useful for biological applications, a set of "fragment"-sized inhibitors that were identified using a high-throughput screen are tested for time-dependent inhibition. One structural class of inactivators, 4-halopyridines, show time- and concentration-dependent inactivation of DDAH, and the inactivation mechanism of one example, 4-bromo-2-methylpyridine (1), is characterized in detail. The neutral form of halopyridines is not very reactive with excess glutathione. However, 1 readily reacts, with loss of its halide, in a selective, covalent, and irreversible manner with the active-site Cys249 of DDAH. This active-site Cys is not particularly reactive (pK(a) ca. 8.8), and 1 does not inactivate papain (Cys pK(a) ca. ≤4), suggesting that, unlike many reagents, Cys nucleophilicity is not a predominating factor in selectivity. Rather, binding and stabilization of the more reactive pyridinium form of the inactivator by a second moiety, Asp66, is required for facile reaction. This constraint imparts a unique selectivity profile to these inactivators. To our knowledge, halopyridines have not previously been reported as protein modifiers, and therefore they represent a first-in-class example of a novel type of quiescent affinity label.
Collapse
Affiliation(s)
- Corey M Johnson
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | | | | | | | | |
Collapse
|
34
|
Costa MGS, Batista PR, Shida CS, Robert CH, Bisch PM, Pascutti PG. How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. BMC Genomics 2010; 11 Suppl 5:S5. [PMID: 21210971 PMCID: PMC3045798 DOI: 10.1186/1471-2164-11-s5-s5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Cathepsin B (catB) is a promising target for anti-cancer drug design due to its implication in several steps of tumorigenesis. catB activity and inhibition are pH-dependent, making it difficult to identify efficient inhibitor candidates for clinical trials. In addition it is known that heparin binding stabilizes the enzyme in alkaline conditions. However, the molecular mechanism of stabilization is not well understood, indicating the need for more detailed structural and dynamic studies in order to clarify the influence of pH and heparin binding on catB stability. Results Our pKa calculations of catB titratable residues revealed distinct protonation states under different pH conditions for six key residues, of which four lie in the crucial interdomain interface. This implies changes in the overall charge distribution at the catB surface, as revealed by calculation of the electrostatic potential. We identified two basic surface regions as possible heparin binding sites, which were confirmed by docking calculations. Molecular dynamics (MD) of both apo catB and catB-heparin complexes were performed using protonation states for catB residues corresponding to the relevant acidic or alkaline conditions. The MD of apo catB at pH 5.5 was very stable, and presented the highest number and occupancy of hydrogen bonds within the inter-domain interface. In contrast, under alkaline conditions the enzyme's overall flexibility was increased: interactions between active site residues were lost, helical content decreased, and domain separation was observed as well as high-amplitude motions of the occluding loop – a main target of drug design studies. Essential dynamics analysis revealed that heparin binding modulates large amplitude motions promoting rearrangement of contacts between catB domains, thus favoring the maintenance of helical content as well as active site stability. Conclusions The results of our study contribute to unraveling the molecular events involved in catB inactivation in alkaline pH, highlighting the fact that protonation changes of few residues can alter the overall dynamics of an enzyme. Moreover, we propose an allosteric role for heparin in the regulation of catB stability in such a manner that the restriction of enzyme flexibility would allow the establishment of stronger contacts and thus the maintenance of overall structure.
Collapse
Affiliation(s)
- Mauricio G S Costa
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21949-901, Rio de Janeiro, Brasil.
| | | | | | | | | | | |
Collapse
|
35
|
Takanishi CL, Ma LH, Wood MJ. The role of active site residues in the oxidant specificity of the Orp1 thiol peroxidase. Biochem Biophys Res Commun 2010; 403:46-51. [PMID: 21036150 DOI: 10.1016/j.bbrc.2010.10.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/22/2010] [Indexed: 11/19/2022]
Abstract
In this study we investigated the role of active site residues in the peroxidase activity of Orp1 (GPx3) using three different peroxide substrates. Using a structural homology model of the reduced form of Orp1, we identified Asn126 and Phe127 as evolutionarily conserved residues that line the back of the Orp1 active site and which are likely to affect the peroxidase activity of Orp1. Additionally, we identified Phe38 as a surface residue that could influence substrate specificity as it is located adjacent to Cys36, in the same position occupied by similar hydrophobic amino acids in many Orp1 homologs. We individually mutated these residues to alanine and examined the effect of each mutation in vitro and in vivo. Chloro-4-nitrobenzo-2-oxa-1,3-diazole was used to identify Cys-SOH modification of Cys36 in response to H(2)O(2), tert-butyl-hydroperoxide (tert-BHP), and cumene hydroperoxide (CHP) in Orp1(WT). Mutation of Asn126 and Phe127 eliminate Cys-SOH formation and peroxidase activity in response to H(2)O(2), tert-BHP and CHP. Furthermore, the pK(a) of Cys36 is elevated closer to that of free cysteine compared to Orp1(WT). Mutation of Phe38 does not affect the peroxidase activity of Orp1 upon exposure to H(2)O(2). The Phe38 mutation decreases Orp1 peroxidase activities in response to either tert-BHP or CHP. The in vivo sensitivity of the Phe38 mutant to both tert-BHP and CHP is increased, while the H(2)O(2) sensitivity is unchanged. The pK(a) of Cys36 in the Phe38 mutant is 5.0, which is the same as Orp1(WT). Taken together, these results suggest that Phe38 does not play a role in the reactivity of Cys36, but does modulate the affinity of Orp1 for alkyl hydroperoxides.
Collapse
Affiliation(s)
- Christina L Takanishi
- Department of Environmental Toxicology, University of California, Davis, One Shields Ave, 4138 Meyer Hall, CA 95616, USA
| | | | | |
Collapse
|
36
|
Avila RL, D'Antonio M, Bachi A, Inouye H, Feltri ML, Wrabetz L, Kirschner DA. P0 (protein zero) mutation S34C underlies instability of internodal myelin in S63C mice. J Biol Chem 2010; 285:42001-12. [PMID: 20937820 DOI: 10.1074/jbc.m110.166967] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
P0 constitutes 50-60% of protein in peripheral nerve myelin and is essential for its structure and stability. Mutations within the P0 gene (MPZ) underlie a variety of hereditary neuropathies. MpzS63C transgenic mice encode a P0 with a serine to cysteine substitution at position 34 in the extracellular domain of mature P0 (P0S34C), associated with the hypomyelinating Déjérine-Sottas syndrome in human. S63C mice develop a dysmyelinating neuropathy, with packing defects in peripheral myelin. Here, we used x-ray diffraction to examine time-dependent packing defects in unfixed myelin. At ∼7 h post-dissection, WT and S63C(+/+) myelin showed native periods (175 Å) with the latter developing at most a few percent swollen myelin, whereas up to ∼50% of S63C(+/-) (mutant P0 on heterozygous P0 null background) or P0(+/-) myelin swelled to periods of ∼205 Å. In the same time frame, S63C(-/-) myelin was stable, remaining swollen at ∼210 Å. Surprisingly, treatment of whole S63C(-/-) nerves with a reducing agent completely reverted swollen arrays to native spacing and also normalized the swollen arrays that had formed in S63C(+/-) myelin, the genotype most closely related to the human disorder. Western blot revealed P0-positive bands at ∼27 and ∼50 kDa, and MALDI-TOF mass spectrometry showed these bands consisted of Ser(34)-containing peptides or P0 dimers having oxidized Cys(34) residues. We propose that P0S34C forms ectopic disulfide bonds in trans between apposed Cys(34) side chains that retard wrapping during myelin formation causing hypomyelination. Moreover, the new bonds create a packing defect by stabilizing swollen membrane arrays that leads to demyelination.
Collapse
Affiliation(s)
- Robin L Avila
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467-3811, USA
| | | | | | | | | | | | | |
Collapse
|
37
|
Shokhen M, Khazanov N, Albeck A. Challenging a paradigm: theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain. Proteins 2010; 77:916-26. [PMID: 19688822 DOI: 10.1002/prot.22516] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A central mechanistic paradigm of cysteine proteases is that the His-Cys catalytic diad forms an ion-pair NH(+)/S(-) already in the catalytically active free enzyme. Most molecular modeling studies of cysteine proteases refer to this paradigm as their starting point. Nevertheless, several recent kinetics and X-ray crystallography studies of viral and bacterial cysteine proteases depart from the ion-pair mechanism, suggesting general base catalysis. We challenge the postulate of the ion-pair formation in free papain. Applying our QM/SCRF(VS) molecular modeling approach, we analyzed all protonation states of the catalytic diad in free papain and its SMe derivative, comparing the predicted and experimental pK(a) data. We conclude that the His-Cys catalytic diad in free papain is fully protonated, NH(+)/SH. The experimental pK(a) = 8.62 of His159 imidazole in free papain, obtained by NMR-controlled titration and originally interpreted as the NH(+)/S(-) <==> N/S(-) NH(+)/S(-) <==> N/S(-) equilibrium, is now assigned to the NH(+)/SH <==> N/SH NH(+)/SH <==> N/SH equilibrium.
Collapse
Affiliation(s)
- Michael Shokhen
- Department of Chemistry, The Julius Spokojny Bioorganic Chemistry Laboratory, Bar Ilan University, Ramat Gan 52900, Israel.
| | | | | |
Collapse
|
38
|
Grimsley GR, Scholtz JM, Pace CN. A summary of the measured pK values of the ionizable groups in folded proteins. Protein Sci 2009; 18:247-51. [PMID: 19177368 DOI: 10.1002/pro.19] [Citation(s) in RCA: 235] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We tabulated 541 measured pK values reported in the literature for the Asp, Glu, His, Cys, Tyr, and Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are for the Asp, Glu, and His side chains. The average pK values are Asp 3.5 +/- 1.2 (139); Glu 4.2 +/- 0.9 (153); His 6.6 +/- 1.0 (131); Cys 6.8 +/- 2.7 (25); Tyr 10.3 +/- 1.2 (20); Lys 10.5 +/- 1.1 (35); C-terminus 3.3 +/- 0.8 (22) and N-terminus 7.7 +/- 0.5 (16). We compare these results with the measured pK values of these groups in alanine pentapeptides, and comment on our overall findings.
Collapse
Affiliation(s)
- Gerald R Grimsley
- Department of Molecular and Cellular Medicine, Texas A&M University System Health Science Center, College Station, Texas 77843, USA
| | | | | |
Collapse
|
39
|
Huang HH, Arscott LD, Ballou DP, Williams CH. Function of Glu-469' in the acid-base catalysis of thioredoxin reductase from Drosophila melanogaster. Biochemistry 2009; 47:12769-76. [PMID: 18991392 DOI: 10.1021/bi801449h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thioredoxin reductase (TrxR) catalyzes the reduction of thioredoxin (Trx) by NADPH. Because dipteran insects such as Drosophila melanogaster lack glutathione reductase, their TrxRs are particularly important for antioxidant protection; reduced Trx reacts nonenzymatically with oxidized glutathione to maintain a high glutathione/glutathione disulfide ratio. Like other members of the pyridine nucleotide-disulfide oxidoreductase family, TrxR is a homodimer; in the enzyme from D. melanogaster (DmTrxR), each catalytically active unit consists of three redox centers: FAD and an N-terminal Cys-57-Cys-62 redox-active disulfide from one monomer and a Cys-489'-Cys-490' C-terminal redox-active disulfide from the second monomer. A dyad of His-464' and Glu-469' in TrxR acts as the acid-base catalyst of the dithiol-disulfide interchange reactions required in catalysis [Huang, H.-H., et al. (2008) Biochemistry 47, 1721-1731]. In this investigation, the role of Glu-469' in catalysis by DmTrxR has been studied. The E469'A and E469'Q DmTrxR variants retain 28 and 35% of the wild-type activity, respectively, indicating that this glutamate residue is important but not critical to catalysis. The pH dependence of V(max) for both glutamate variants yields pK(a) values of 6.0 and 8.7, compared to those in the wild-type enzyme of 6.4 and 9.3, respectively, indicating that the basicity of His-464' in TrxR in complex with its substrate, DmTrx-2, is significantly lower in the glutamate variants than in wild-type enzyme. The rates of some steps in the reductive half-reactions in both glutamate variants are much slower than those of the wild-type enzyme. On the basis of our observations, it is proposed that the function of Glu-469' is to facilitate the positioning of His-464' toward the interchange thiol, Cys-57, as suggested for the analogous residue in glutathione reductase.
Collapse
Affiliation(s)
- Hsin-Hung Huang
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA
| | | | | | | |
Collapse
|
40
|
Takeuchi Y, Fujiwara T, Shimone Y, Miyataka H, Satoh T, Kirk KL, Hori H. Possible involvement of radical intermediates in the inhibition of cysteine proteases by allenyl esters and amides. Bioorg Med Chem Lett 2008; 18:6202-5. [PMID: 18951789 PMCID: PMC2607570 DOI: 10.1016/j.bmcl.2008.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 09/08/2008] [Accepted: 10/01/2008] [Indexed: 11/30/2022]
Abstract
In order to investigate crystallographically the mechanism of inhibition of cysteine protease by alpha-methyl-gamma,gamma-diphenylallenecarboxylic acid ethyl ester 3, a cysteine protease inhibitor having in vivo stability, we synthesized N-(alpha-methyl-gamma,gamma-diphenylallenecarbonyl)-L-phenylalanine ethyl ester 4. Reaction of 4 with thiophenol, the SH group of which has similar pK(a) value to that of cysteine protease, produced oxygen-mediated radical adducts 6 and 7 in ambient air but did not proceed under oxygen-free conditions. Catalytic activities of two thiol enzymes including cathepsin B were also lowered in the absence of oxygen. These results suggest that cysteine protease can act through an oxygen-dependent radical mechanism.
Collapse
Affiliation(s)
- Yoshio Takeuchi
- Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
| | | | | | | | | | | | | |
Collapse
|
41
|
Schneck JL, Villa JP, McDevitt P, McQueney MS, Thrall SH, Meek TD. Chemical mechanism of a cysteine protease, cathepsin C, as revealed by integration of both steady-state and pre-steady-state solvent kinetic isotope effects. Biochemistry 2008; 47:8697-710. [PMID: 18656960 DOI: 10.1021/bi8007627] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cathepsin C, or dipeptidyl peptidase I, is a lysosomal cysteine protease of the papain family that catalyzes the sequential removal of dipeptides from the free N-termini of proteins and peptides. Using the dipeptide substrate Ser-Tyr-AMC, cathepsin C was characterized in both steady-state and pre-steady-state kinetic modes. The pH(D) rate profiles for both log k cat/ K m and log k cat conformed to bell-shaped curves for which an inverse solvent kinetic isotope effect (sKIE) of 0.71 +/- 0.14 for (D)( k cat/ K a) and a normal sKIE of 2.76 +/- 0.03 for (D) k cat were obtained. Pre-steady-state kinetics exhibited a single-exponential burst of AMC formation in which the maximal acylation rate ( k ac = 397 +/- 5 s (-1)) was found to be nearly 30-fold greater than the rate-limiting deacylation rate ( k dac = 13.95 +/- 0.013 s (-1)) and turnover number ( k cat = 13.92 +/- 0.001 s (-1)). Analysis of pre-steady-state burst kinetics in D 2O allowed abstraction of a normal sKIE for the acylation half-reaction that was not observed in steady-state kinetics. Since normal sKIEs were obtained for all measurable acylation steps in the presteady state [ (D) k ac = 1.31 +/- 0.04, and the transient kinetic isotope effect at time zero (tKIE (0)) = 2.3 +/- 0.2], the kinetic step(s) contributing to the inverse sKIE of (D)( k cat/ K a) must occur more rapidly than the experimental time frame of the transient kinetics. Results are consistent with a chemical mechanism in which acylation occurs via a two-step process: the thiolate form of Cys-234, which is enriched in D 2O and gives rise to the inverse value of (D)( k cat/ K a), attacks the substrate to form a tetrahedral intermediate that proceeds to form an acyl-enzyme intermediate during a proton transfer step expressing a normal sKIE. The subsequent deacylation half-reaction is rate-limiting, with proton transfers exhibiting normal sKIEs. Through derivation of 12 equations describing all kinetic parameters and sKIEs for the proposed cathepsin C mechanism, integration of both steady-state and pre-steady-state kinetics with sKIEs allowed the provision of at least one self-consistent set of values for all 13 rate constants in this cysteine protease's chemical mechanism. Simulation of the resulting kinetic profile showed that at steady state approximately 80% of the enzyme exists in an active-site cysteine-acylated form in the mechanistic pathway. The chemical and kinetic details deduced from this work provide a potential roadmap to help steer drug discovery efforts for this and other disease-relevant cysteine proteases.
Collapse
Affiliation(s)
- Jessica L Schneck
- Department of Biological Reagents and Assay Development and Discovery Technology Group, GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, USA
| | | | | | | | | | | |
Collapse
|
42
|
Schaschke N. (2S,3S)-Oxirane-2,3-dicarboxylic acid: A privileged platform for probing human cysteine cathepsins. J Biotechnol 2007; 129:308-15. [PMID: 17339064 DOI: 10.1016/j.jbiotec.2007.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 01/14/2007] [Accepted: 01/26/2007] [Indexed: 01/03/2023]
Abstract
The notion that human cysteine cathepsins contribute only to general protein turnover within the lysosomes has changed in the last decade in a substantial manner. A continuously growing number of data accumulated in different fields of life sciences revealed that these enzymes are involved in a variety of pivotal physiological processes. To investigate these particular fraction of proteolytical activity of the human degradome even in a complex cellular environment, chemical probes that covalently label the corresponding proteases proved to be versatile tools. (2S,3S)-Oxirane-2,3-dicarboxylic acid provides an ideal platform for the design of such probing systems. Depending on the complexity of the attached recognition elements, either the activity of the entire group of human cysteine cathepsins or individual members can be detected.
Collapse
Affiliation(s)
- Norbert Schaschke
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.
| |
Collapse
|
43
|
Graham C, Brocklehurst K, Pickersgill R, Warren M. Characterization of retinaldehyde dehydrogenase 3. Biochem J 2006; 394:67-75. [PMID: 16241904 PMCID: PMC1386004 DOI: 10.1042/bj20050918] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RALDH3 (retinal dehydrogenase 3) was characterized by kinetic and binding studies, protein engineering, homology modelling, ligand docking and electrostatic-potential calculations. The major recognition determinant of an RALDH3 substrate was shown to be an eight-carbon chain bonded to the aldehyde group whose kinetic influence (kcat/Km at pH 8.5) decreases when shortened or lengthened. Surprisingly, the b-ionone ring of all-trans-retinal is not a major recognition site. The dissociation constants (Kd) of the complexes of RALDH3 with octanal, NAD+ and NADH were determined by intrinsic tryptophan fluorescence. The similarity of the Kd values for the complexes with NAD+ and with octanal suggests a random kinetic mechanism for RALDH3, in contrast with the ordered sequential mechanism often associated with aldehyde dehydrogenase enzymes. Inhibition of RALDH3 by tri-iodothyronine binding in competition with NAD+, predicted by the modelling, was established kinetically and by immunoprecipitation. Mechanistic implications of the kinetically influential ionizations with macroscopic pKa values of 5.0 and 7.5 revealed by the pH-dependence of kcat are discussed. Analogies with data for non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans, together with the present modelled structure of the thioacyl RALDH3, suggest (a) that kcat characterizes deacylation of this intermediate for specific substrates and (b) the assignment of the pKa of the major ionization (approximating to 7.5) to the perturbed carboxy group of Glu280 whose conjugate base is envisaged as supplying general base catalysis to attack of a water molecule. The macroscopic pKa of the minor ionization (5.0) is considered to approximate to that of the carboxy group of Glu488.
Collapse
Affiliation(s)
- Caroline E. Graham
- *School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
| | - Keith Brocklehurst
- *School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
- To whom correspondence should be addressed (email )
| | - Richard W. Pickersgill
- *School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
| | - Martin J. Warren
- *School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, U.K
| |
Collapse
|
44
|
Vivares D, Arnoux P, Pignol D. A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. Proc Natl Acad Sci U S A 2005; 102:18848-53. [PMID: 16339904 PMCID: PMC1310510 DOI: 10.1073/pnas.0505833102] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Indexed: 11/18/2022] Open
Abstract
Phytochelatin synthase (PCS) is a key enzyme for heavy-metal detoxification in plants. PCS catalyzes the production of glutathione (GSH)-derived peptides (called phytochelatins or PCs) that bind heavy-metal ions before vacuolar sequestration. The enzyme can also hydrolyze GSH and GS-conjugated xenobiotics. In the cyanobacterium Nostoc, the enzyme (NsPCS) contains only the catalytic domain of the eukaryotic synthase and can act as a GSH hydrolase and weakly as a peptide ligase. The crystal structure of NsPCS in its native form solved at a 2.0-A resolution shows that NsPCS is a dimer that belongs to the papain superfamily of cysteine proteases, with a conserved catalytic machinery. Moreover, the structure of the protein solved as a complex with GSH at a 1.4-A resolution reveals a gamma-glutamyl cysteine acyl-enzyme intermediate stabilized in a cavity of the protein adjacent to a second putative GSH binding site. GSH hydrolase and PCS activities of the enzyme are discussed in the light of both structures.
Collapse
Affiliation(s)
- Denis Vivares
- Département d'Ecophysiologie Végétale et de Microbiologie, Direction des Sciences du Vivant, Laboratoire de Bioénergétique Cellulaire, Commissariat á l'Energie Atomique/Cadarache, 13108 St Paul lez Durance Cedex, France
| | | | | |
Collapse
|
45
|
Gul S, Brown R, May E, Mazzulla M, Smyth MG, Berry C, Morby A, Powell DJ. Staphylococcus aureus DNA ligase: characterization of its kinetics of catalysis and development of a high-throughput screening compatible chemiluminescent hybridization protection assay. Biochem J 2005; 383:551-9. [PMID: 15283677 PMCID: PMC1133749 DOI: 10.1042/bj20040054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA ligases are key enzymes involved in the repair and replication of DNA. Prokaryotic DNA ligases uniquely use NAD+ as the adenylate donor during catalysis, whereas eukaryotic enzymes use ATP. This difference in substrate specificity makes the bacterial enzymes potential targets for therapeutic intervention. We have developed a homogeneous chemiluminescence-based hybridization protection assay for Staphylococcus aureus DNA ligase that uses novel acridinium ester technology and demonstrate that it is an alternative to the commonly used radiometric assays for ligases. The assay has been used to determine a number of kinetic constants for S. aureus DNA ligase catalysis. These included the K(m) values for NAD+ (2.75+/-0.1 microM) and the acridinium-ester-labelled DNA substrate (2.5+/-0.2 nM). A study of the pH-dependencies of kcat, K(m) and kcat/K(m) has revealed values of kinetically influential ionizations within the enzyme-substrate complexes (kcat) and free enzyme (kcat/K(m)). In each case, the curves were shown to be composed of one kinetically influential ionization, for k(cat), pK(a)=6.6+/-0.1 and kcat/K(m), pK(a)=7.1+/-0.1. Inhibition characteristics of the enzyme against two Escherichia coli DNA ligase inhibitors have also been determined with IC50 values for these being 3.30+/-0.86 microM for doxorubicin and 1.40+/-0.07 microM for chloroquine diphosphate. The assay has also been successfully miniaturized to a sufficiently low volume to allow it to be utilized in a high-throughput screen (384-well format; 20 microl reaction volume), enabling the assay to be used in screening campaigns against libraries of compounds to discover leads for further drug development.
Collapse
Affiliation(s)
- Sheraz Gul
- Assay Development and Compound Profiling, GlaxoSmithKline Pharmaceuticals, New Frontiers Science Park (North), Third Avenue, Harlow, Essex CM19 4AW, UK.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Reid JD, Hussain S, Bailey TSF, Sonkaria S, Sreedharan SK, Thomas EW, Resmini M, Brocklehurst K. Isomerization of the uncomplexed actinidin molecule: kinetic accessibility of additional steps in enzyme catalysis provided by solvent perturbation. Biochem J 2004; 378:699-703. [PMID: 14640975 PMCID: PMC1223986 DOI: 10.1042/bj20031318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2003] [Revised: 11/14/2003] [Accepted: 11/25/2003] [Indexed: 11/17/2022]
Abstract
The effects of increasing the content of the aprotic dipolar organic co-solvent acetonitrile on the observed first-order rate constant (k(obs)) of the pre-steady state acylation phases of the hydrolysis of N-acetyl-Phe-Gly methyl thionester catalysed by the cysteine proteinase variants actinidin and papain in sodium acetate buffer, pH 5.3, were investigated by stopped-flow spectral analysis. With low acetonitrile content, plots of k(obs) against [S]0 for the actinidin reaction are linear with an ordinate intercept of magnitude consistent with a five-step mechanism involving a post-acylation conformational change. Increasing the acetonitrile content results in marked deviations of the plots from linearity with a rate minimum around [S]0=150 microM. The unusual negative dependence of k(obs) on [S]0 in the range 25-150 microM is characteristic of a rate-determining isomerization of the free enzyme before substrate binding, additional to the five-step mechanism. There was no evidence for this phenomenon nor for the post-acylation conformational change in the analogous reaction with papain. For this enzyme, however, acetonitrile acts as an inhibitor with approximately uncompetitive characteristics. Possible mechanistic consequences of the differential solvent-perturbed kinetics are indicated. The free enzyme isomerization of actinidin may provide an explanation for the marked difference in sensitivity between this enzyme and papain of binding site-catalytic site signalling in reactions of substrate-derived 2-pyridyl disulphide reactivity probes.
Collapse
Affiliation(s)
- James D Reid
- Laboratory of Structural and Mechanistic Enzymology, School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Zong Y, Bice TW, Ton-That H, Schneewind O, Narayana SVL. Crystal structures of Staphylococcus aureus sortase A and its substrate complex. J Biol Chem 2004; 279:31383-9. [PMID: 15117963 DOI: 10.1074/jbc.m401374200] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The cell wall envelope of staphylococci and other Gram-positive pathogens is coated with surface proteins that interact with human host tissues. Surface proteins of Staphylococcus aureus are covalently linked to the cell wall envelope by a mechanism requiring C-terminal sorting signals with an LPXTG motif. Sortase (SrtA) cleaves surface proteins between the threonine (T) and the glycine (G) of the LPXTG motif and catalyzes the formation of an amide bond between threonine at the C-terminal end of polypeptides and cell wall cross-bridges. The active site architecture and catalytic mechanism of sortase A has hitherto not been revealed. Here we present the crystal structures of native SrtA, of an active site mutant of SrtA, and of the mutant SrtA complexed with its substrate LPETG peptide and describe the substrate binding pocket of the enzyme. Highly conserved proline (P) and threonine (T) residues of the LPXTG motif are held in position by hydrophobic contacts, whereas the glutamic acid residue (E) at the X position points out into the solvent. The scissile T-G peptide bond is positioned between the active site Cys(184) and Arg(197) residues and at a greater distance from the imidazolium side chain of His(120). All three residues, His(120), Cys(184), and Arg(197), are conserved in sortase enzymes from Gram-positive bacteria. Comparison of the active sites of S. aureus sortase A and sortase B provides insight into substrate specificity and suggests a universal sortase-catalyzed mechanism of bacterial surface protein anchoring in Gram-positive bacteria.
Collapse
Affiliation(s)
- Yinong Zong
- Center for Biophysical Sciences and Engineering, School of Optometry, University of Alabama, Birmingham, Alabama 35294, USA
| | | | | | | | | |
Collapse
|
48
|
Deaton DN, Kumar S. Cathepsin K Inhibitors: Their Potential as Anti-Osteoporosis Agents. PROGRESS IN MEDICINAL CHEMISTRY 2004; 42:245-375. [PMID: 15003723 DOI: 10.1016/s0079-6468(04)42006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- David N Deaton
- Medicinal Chemistry Department, GlaxoSmithKline Inc., 5 Moore Drive, Research Triangle Park, NC 27709, USA
| | | |
Collapse
|
49
|
Gul S, Sonkaria S, Pinitglang S, Florez-Alvarez J, Hussain S, Thomas EW, Ostler EL, Gallacher G, Resmini M, Brocklehurst K. Improvement in hydrolytic antibody activity by change in haptenic structure from phosphate to phosphonate with retention of a common leaving-group determinant: evidence for the 'flexibility' hypothesis. Biochem J 2003; 376:813-21. [PMID: 12946271 PMCID: PMC1223799 DOI: 10.1042/bj20030716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Revised: 07/15/2003] [Accepted: 08/28/2003] [Indexed: 11/17/2022]
Abstract
To investigate the hypothesis that decreased hapten flexibility may lead to increased catalytic antibody activity, we used two closely related immunogens differing only in the flexibility of the atomic framework around the structural motif of the haptens, analogous to the reaction centre of the corresponding substrates. Identical leaving-group determinants in the haptens and identical leaving groups in the substrates removed the ambiguity inherent in some data reported in the literature. Anti-phosphate and anti-phosphonate kinetically homogeneous polyclonal catalytic antibody preparations were compared by using carbonate and ester substrates respectively, each containing a 4-nitrophenolate leaving group. Synthetic routes to a new phosphonate hapten and new ester substrate were developed. The kinetic advantage of the more rigid anti-phosphonate/ester system was demonstrated at pH 8.0 by a 13-fold advantage in k(cat)/k(non-cat) and a 100-fold advantage in the proficiency constant, k(cat)/k (non-cat) x K(m). Despite these differences, the pH-dependences of the kinetic and binding characteristics and the results of chemical modification studies suggest closely similar catalytic mechanisms. The possible origin of the kinetic advantage of the more rigid hapten/substrate system is discussed.
Collapse
Affiliation(s)
- Sheraz Gul
- Laboratory of Structural and Mechanistic Enzymology, School of Biological Sciences, Queen Mary, University of London, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Connolly KM, Smith BT, Pilpa R, Ilangovan U, Jung ME, Clubb RT. Sortase from Staphylococcus aureus does not contain a thiolate-imidazolium ion pair in its active site. J Biol Chem 2003; 278:34061-5. [PMID: 12824164 DOI: 10.1074/jbc.m305245200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many surface proteins are anchored to the cell wall by the action of sortase enzymes, a recently discovered family of cysteine transpeptidases. As the surface proteins of human pathogens are frequently required for virulence, the sortase-mediated anchoring reaction represents a potential target for new anti-infective agents. It has been suggested that the sortase from Staphylococcus aureus (SrtA), may use a similar catalytic strategy as the papain cysteine proteases, holding its Cys184 side chain in an active configuration through a thiolate-imidazolium ion interaction with residue His120. To investigate the mechanism of transpeptidation, we have synthesized a peptidyl-vinyl sulfone substrate mimic that irreversibly inhibits SrtA. Through the study of the pH dependence of SrtA inhibition and NMR, we have estimated the pKas of the active site thiol (Cys184) and imidazole (His120) to be approximately 9.4 and 7.0, respectively. These measurements are inconsistent with the existence of a thiolate-imidazolium ion pair and suggest a general base catalysis mechanism during transpeptidation.
Collapse
Affiliation(s)
- Kevin M Connolly
- Department of Chemistry and Biochemistry, Molecular Biology Institute and UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570, USA
| | | | | | | | | | | |
Collapse
|