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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA 97403-1252
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2
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Prandi B, Varani M, Faccini A, Lambertini F, Suman M, Leporati A, Tedeschi T, Sforza S. Species specific marker peptides for meat authenticity assessment: A multispecies quantitative approach applied to Bolognese sauce. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.10.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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3
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Nagar M, Kumar H, Bearne SL. A platform for chemical modification of mandelate racemase: characterization of the C92S/C264S and γ-thialysine 166 variants. Protein Eng Des Sel 2018; 31:135-145. [PMID: 29850884 DOI: 10.1093/protein/gzy011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/03/2018] [Indexed: 11/14/2022] Open
Abstract
Mandelate racemase (MR) serves as a paradigm for our understanding of enzyme-catalyzed deprotonation of a carbon acid substrate. To facilitate structure-function studies on MR using non-natural amino acid substitutions, we engineered the Cys92Ser/Cys264Ser variant (dmMR) as a platform for introducing Cys residues at specific locations for subsequent covalent modification. While the highly reactive thiol of Cys furnishes a site for chemical modification, site-specificity requires that other Cys residues be non-reactive or replaced by a non-reactive amino acid, especially if chemical modification is conducted under denaturing conditions. The catalytic efficiency of dmMR is reduced only ~2-fold relative to wild-type MR, making dmMR a viable platform for the site-specific introduction of Cys. As an example, the inactive Lys166Cys variant of dmMR was treated with ethylenimine under denaturing conditions to replace the Brønsted acid-base catalyst Lys 166 with the non-natural amino acid γ-thialysine. Comparison of the pH-activity profiles of dmMR and the active γ-thialysine variant revealed a reduction in the pKa for the side chain amino group of ~0.4 units for the latter variant. Unlike wild-type MR for which diffusion is partially rate-limiting, dmMR and the γ-thialysine variant showed no dependence on the solvent viscosity suggesting that the chemical step is fully rate-limiting.
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Affiliation(s)
- Mitesh Nagar
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Himank Kumar
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Chemistry, Dalhousie University, Halifax, NS, Canada
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4
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Dadová J, Wu KJ, Isenegger PG, Errey JC, Bernardes GL, Chalker JM, Raich L, Rovira C, Davis BG. Precise Probing of Residue Roles by Post-Translational β,γ-C,N Aza-Michael Mutagenesis in Enzyme Active Sites. ACS CENTRAL SCIENCE 2017; 3:1168-1173. [PMID: 29202018 PMCID: PMC5704290 DOI: 10.1021/acscentsci.7b00341] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 06/07/2023]
Abstract
Biomimicry valuably allows the understanding of the essential chemical components required to recapitulate biological function, yet direct strategies for evaluating the roles of amino acids in proteins can be limited by access to suitable, subtly-altered unnatural variants. Here we describe a strategy for dissecting the role of histidine residues in enzyme active sites using unprecedented, chemical, post-translational side-chain-β,γ C-N bond formation. Installation of dehydroalanine (as a "tag") allowed the testing of nitrogen conjugate nucleophiles in "aza-Michael"-1,4-additions (to "modify"). This allowed the creation of a regioisomer of His (iso-His, Hisiso) linked instead through its pros-Nπ atom rather than naturally linked via C4, as well as an aza-altered variant aza-Hisiso. The site-selective generation of these unnatural amino acids was successfully applied to probe the contributing roles (e.g., size, H-bonding) of His residues toward activity in the model enzymes subtilisin protease from Bacillus lentus and Mycobacterium tuberculosis pantothenate synthetase.
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Affiliation(s)
- Jitka Dadová
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kuan-Jung Wu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Patrick G. Isenegger
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - James C. Errey
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Gonçalo
J. L. Bernardes
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Justin M. Chalker
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| | - Benjamin G. Davis
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
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5
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Wright TH, Vallée MRJ, Davis BG. Von der chemischen Mutagenese zur Postexpressions‐Mutagenese: eine 50 Jahre währende Odyssee. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tom H. Wright
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road OX1 3TA Vereinigtes Königreich
| | - M. Robert J. Vallée
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road OX1 3TA Vereinigtes Königreich
| | - Benjamin G. Davis
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road OX1 3TA Vereinigtes Königreich
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6
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Wright TH, Vallée MRJ, Davis BG. From Chemical Mutagenesis to Post-Expression Mutagenesis: A 50 Year Odyssey. Angew Chem Int Ed Engl 2016; 55:5896-903. [PMID: 27119221 PMCID: PMC5074284 DOI: 10.1002/anie.201509310] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/02/2016] [Indexed: 01/06/2023]
Abstract
Site‐directed (gene) mutagenesis has been the most useful method available for the conversion of one amino acid residue of a given protein into another. Until relatively recently, this strategy was limited to the twenty standard amino acids. The ongoing maturation of stop codon suppression and related technologies for unnatural amino acid incorporation has greatly expanded access to nonstandard amino acids by expanding the scope of the translational apparatus. However, the necessity for translation of genetic changes restricts the diversity of residues that may be incorporated. Herein we highlight an alternative approach, termed post‐expression mutagenesis, which operates at the level of the very functional biomolecules themselves. Using the lens of retrosynthesis, we highlight prospects for new strategies in protein modification, alteration, and construction which will enable protein science to move beyond the constraints of the “translational filter” and lead to a true synthetic biology.
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Affiliation(s)
- Tom H Wright
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, UK
| | - M Robert J Vallée
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, UK.
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7
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Nadler C, Nadler A, Hansen C, Diederichsen U. A Photocleavable Auxiliary for Extended Native Chemical Ligation. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Junkova P, Vermachova M, Prchal J, Kuckova S, Hrabal R, Hynek R. IMPROVED APPROACH FOR THE LABELING OF ARGININE, GLUTAMIC, AND ASPARTIC ACID SIDE CHAINS IN PROTEINS USING CHROMATOGRAPHIC TECHNIQUES. J LIQ CHROMATOGR R T 2013. [DOI: 10.1080/10826076.2012.685918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Petra Junkova
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Prague , Czech Republic
| | - Martina Vermachova
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Prague , Czech Republic
| | - Jan Prchal
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Prague , Czech Republic
| | - Stepanka Kuckova
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Prague , Czech Republic
| | - Richard Hrabal
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Prague , Czech Republic
| | - Radovan Hynek
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Prague , Czech Republic
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9
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Timms N, Windle CL, Polyakova A, Ault JR, Trinh CH, Pearson AR, Nelson A, Berry A. Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with γ-thialysine by using a chemical mutagenesis strategy. Chembiochem 2013; 14:474-81. [PMID: 23418011 PMCID: PMC3792637 DOI: 10.1002/cbic.201200714] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/29/2022]
Abstract
Chemical modification has been used to introduce the unnatural amino acid γ-thialysine in place of the catalytically important Lys165 in the enzyme N-acetylneuraminic acid lyase (NAL). The Staphylococcus aureus nanA gene, encoding NAL, was cloned and expressed in E. coli. The protein, purified in high yield, has all the properties expected of a class I NAL. The S. aureus NAL which contains no natural cysteine residues was subjected to site-directed mutagenesis to introduce a cysteine in place of Lys165 in the enzyme active site. Subsequently chemical mutagenesis completely converted the cysteine into γ-thialysine through dehydroalanine (Dha) as demonstrated by ESI-MS. Initial kinetic characterisation showed that the protein containing γ-thialysine regained 17 % of the wild-type activity. To understand the reason for this lower activity, we solved X-ray crystal structures of the wild-type S. aureus NAL, both in the absence of, and in complex with, pyruvate. We also report the structures of the K165C variant, and the K165-γ-thialysine enzyme in the presence, or absence, of pyruvate. These structures reveal that γ-thialysine in NAL is an excellent structural mimic of lysine. Measurement of the pH-activity profile of the thialysine modified enzyme revealed that its pH optimum is shifted from 7.4 to 6.8. At its optimum pH, the thialysine-containing enzyme showed almost 30 % of the activity of the wild-type enzyme at its pH optimum. The lowered activity and altered pH profile of the unnatural amino acid-containing enzyme can be rationalised by imbalances of the ionisation states of residues within the active site when the pK(a) of the residue at position 165 is perturbed by replacement with γ-thialysine. The results reveal the utility of chemical mutagenesis for the modification of enzyme active sites and the exquisite sensitivity of catalysis to the local structural and electrostatic environment in NAL.
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Affiliation(s)
- Nicole Timms
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Claire L Windle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Anna Polyakova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Arwen R Pearson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Chemistry, University of LeedsLeeds, LS2 9JT (UK)
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
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10
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Yakovleva L, Shuman S. Chemical mutagenesis of vaccinia DNA topoisomerase lysine 167 provides insights to the catalysis of DNA transesterification. Biochemistry 2013; 52:984-91. [PMID: 23317114 DOI: 10.1021/bi301643h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vaccinia DNA topoisomerase IB (TopIB) relaxes supercoils by forming and resealing a covalent DNA-(3'-phosphotyrosyl(274))-enzyme intermediate. Conserved active site side chains promote the attack of Tyr274 on the scissile phosphodiester via transition state stabilization and general acid catalysis. Two essential side chains, Lys167 and Arg130, act in concert to protonate and expel the 5'-O leaving group. Here we gained new insights to catalysis through chemical mutagenesis of Lys167. Changing Lys167 to cysteine crippled the DNA cleavage and religation transesterification steps (k(cl) = 4.3 × 10(-4) s(-1); k(rel) = 9 × 10(-4) s(-1)). The transesterification activities of the K167C enzyme were revived by in vitro alkylation with 2-bromoethylamine (k(cl) = 0.031 s(-1); k(rel) ≥ 0.4 s(-1)) and 3-bromopropylamine (k(cl) = 0.013 s(-1); k(rel) = 0.22 s(-1)), which convert the cysteines to γ-thialysine and γ-thiahomolysine, respectively. These chemically installed lysine analogues were more effective than a genetically programmed arginine 167 substitution characterized previously. The modest differences in the transesterification rates of the 2-bromoethylamine- and 3-bromopropylamine-treated enzymes highlight that TopIB is tolerant of a longer homolysine side chain for assembly of the active site and formation of the transition state.
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Affiliation(s)
- Lyudmila Yakovleva
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, United States
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11
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Olucha J, Meneely KM, Lamb AL. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB. Biochemistry 2012; 51:7525-32. [PMID: 22970849 DOI: 10.1021/bi300472n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PchB is an isochorismate-pyruvate lyase from Pseudomonas aeruginosa. A positively charged lysine residue is located in a flexible loop that behaves as a lid to the active site, and the lysine residue is required for efficient production of salicylate. A variant of PchB that lacks the lysine at residue 42 has a reduced catalytic free energy of activation of up to 4.4 kcal/mol. Construction of a lysine isosteric residue bearing a positive charge at the appropriate position leads to the recovery of 2.5-2.7 kcal/mol (about 60%) of the 4.4 kcal/mol by chemical rescue. Exogenous addition of ethylamine to the K42A variant leads to a neglible recovery of activity (0.180 kcal/mol, roughly 7% rescue), whereas addition of propylamine caused an additional modest loss in catalytic power (0.056 kcal/mol, or 2% loss). This is consistent with the view that (a) the lysine-42 residue is required in a specific conformation to stabilize the transition state and (b) the correct conformation is achieved for a lysine-mimetic side chain at site 42 in the course of loop closure, as expected for transition-state stabilization by the side chain ammonio function. That the positive charge is the main effector of transition state stabilization is shown by the construction of a lysine-isosteric residue capable of exerting steric effects and hydrogen bonding but not electrostatic effects, leading to a modest increase of catalytic power (0.267-0.505 kcal/mol of catalytic free energy, or roughly 6-11% rescue).
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Affiliation(s)
- José Olucha
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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12
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Marincean S, Rabago Smith M, Beltz L, Borhan B. Selectivity of labeled bromoethylamine for protein alkylation. J Mol Model 2012; 18:4547-56. [PMID: 22643979 DOI: 10.1007/s00894-012-1461-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 05/04/2012] [Indexed: 11/25/2022]
Abstract
Alkylation of cysteine residues has been used extensively for characterization of proteins and their mode of action in biological systems, research endeavors that are at the core of proteomics. Treatment with a simple alkylating agent such as [2-(13)C] bromoethylamine would result in labeled thialysine at the ε-position. This chemical modification of proteins would allow investigations via both (13)C NMR spectroscopy and mass spectrometry. However [2-(13)C] labeled bromoethylamine is not available commercially. We investigated its synthesis at acid pH with the goal of obtaining singly labeled bromoethylamine and understanding the mechanistic details of the reaction. Based on our experimental and theoretical results, bromination of [2-(13)C] labeled ethanolamine in acidic conditions takes place via exclusive attack of the nucleophile (HBr) at the hydroxyl bearing C. Moreover, hydrogen bonding guides the nucleophilic attack, resulting in no label scrambling of the bromoethylamine product. Protein alkylation at cysteine residue with the synthesized Br(13)CH(2)CH(2)NH(2)-HBr is successful. Ab initio calculations in which CH(3)SH serves as a model for the cysteine residue suggest that in gas phase intermolecular attack by the sulfur bearing nucleophile is favored over the intramolecular substitution by the amino group by 15.4 kJ mol(-1). Solution modeling shows that the trend is preserved at basic pH, which is the experimental one, but is reversed at neutral pH.
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Affiliation(s)
- Simona Marincean
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Rd., Dearborn, MI 48128, USA.
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Maity AN, Shaikh AC, Srimurugan S, Wu CJ, Chen C, Ke SC. Synthesis of 4-thia-[6-(13)C]lysine from [2- (13)C]glycine: access to site-directed isotopomers of 2-aminoethanol, 2-bromoethylamine and 4-thialysine. Amino Acids 2010; 42:309-15. [PMID: 21103898 DOI: 10.1007/s00726-010-0808-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/02/2010] [Indexed: 11/28/2022]
Abstract
4-Thialysine (S-(2-aminoethyl)-L: -cysteine) is an analog of lysine. It has been used as an alternative substrate for lysine in enzymatic reactions. Site-directed isotopomers are often needed for elucidation of mechanism of reactions. 4-Thialysine can be synthesized by reacting cysteine with 2-bromoethylamine, an important reagent in chemical-modification rescue (CMR) of proteins. Here, we present the synthesis of 4-thia-[6-(13)C]lysine, one of the isotopomers of 4-thialysine, from commercially available starting material [2-(13)C]glycine via formation of five intermediates including 2-amino[2-(13)C]ethanol and 2-bromo[1-(13)C]ethylamine. The compounds were characterized using various spectroscopic techniques. Moreover, we discuss that our strategy would provide access to site-directed isotopomers of 2-aminoethanol, 2-bromoethylamine and 4-thialysine. Biological activity of 4-thia-[6-(13)C]lysine was tested in the enzymatic reaction of lysine 5,6-aminomutase.
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14
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Andres-Hernando A, Lanaspa MA, Li N, Cicerchi C, Roncal-Jimenez C, Cantor GH, Sorribas V, Rivard CJ, Berl T. Effects of 2-bromoethanamine on TonEBP expression and its possible role in induction of renal papillary necrosis in mice. Toxicol Sci 2010; 118:510-20. [PMID: 20823374 DOI: 10.1093/toxsci/kfq261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chronic analgesic abuse has been shown to induce severe renal injury characterized by renal papillary necrosis (RPN), an injury detectable at late stage. While direct toxicity of the drug may exist, the molecular mechanisms underlying analgesics induction of RPN remain unknown. A major limitation to study the pathogenesis of RPN is the required chronic exposure before detection of injury. Here, we employed 2-bromoethanamine (BEA) to simulate rapid papillary toxicity using inner medullary collecting duct (IMCD3) cells. Although exposure to 10μM BEA had no effect on cellular viability under isotonic conditions, a 50% loss in cell viability was observed in the first 24 h when cells were subjected to sublethal hypertonic stress and nearly complete cell death after 48 h suggesting that BEA exerts cytotoxicity only under hypertonic conditions. Because TonEBP is a transcription factor critical for cell survival during hypertonic conditions, we undertook experiments to examine the effect of BEA on TonEBP expression and activity. Exposure of cells to 10μM BEA resulted in a substantial reduction in TonEBP protein expression after 24 h. In addition, TonEBP was not translocated to the nucleus in BEA-treated IMCD3 cells under acute hypertonic stress for transcription of target genes essential for osmolyte accumulation. Finally, we found a substantial decrease in TonEBP expression in medullary kidney tissues of mice injected with a single ip dose of BEA. Our data suggest that TonEBP is a potential target for BEA leading to the process of papillary necrosis in the settings of hypertonic stress.
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Affiliation(s)
- Ana Andres-Hernando
- Division of Renal Diseases and Hypertension, School of Medicine, University of Colorado Denver, Aurora, Colorado 80045, USA
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15
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Gonzalez DJ, Lee SW, Hensler ME, Markley AL, Dahesh S, Mitchell DA, Bandeira N, Nizet V, Dixon JE, Dorrestein PC. Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum. J Biol Chem 2010; 285:28220-8. [PMID: 20581111 DOI: 10.1074/jbc.m110.118554] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Through elaboration of its botulinum toxins, Clostridium botulinum produces clinical syndromes of infant botulism, wound botulism, and other invasive infections. Using comparative genomic analysis, an orphan nine-gene cluster was identified in C. botulinum and the related foodborne pathogen Clostridium sporogenes that resembled the biosynthetic machinery for streptolysin S, a key virulence factor from group A Streptococcus responsible for its hallmark beta-hemolytic phenotype. Genetic complementation, in vitro reconstitution, mass spectral analysis, and plasmid intergrational mutagenesis demonstrate that the streptolysin S-like gene cluster from Clostridium sp. is responsible for the biogenesis of a novel post-translationally modified hemolytic toxin, clostridiolysin S.
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Affiliation(s)
- David J Gonzalez
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
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16
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Rehulková H, Marchetti-Deschmann M, Pittenauer E, Allmaier G, Rehulka P. Improved identification of hordeins by cysteine alkylation with 2-bromoethylamine, SDS-PAGE and subsequent in-gel tryptic digestion. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:1613-1621. [PMID: 19787686 DOI: 10.1002/jms.1675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Proteomic-based description of varieties of barley (Hordeum vulgare L.) is a very important task especially in the food and brewing industry. This study is focused on major storage proteins in barley--hordeins--as a group of proteins soluble in alcohol/water mixtures that shows up significant changes in proteomic profiles for different varieties of barley. Unusual amino acid composition of hordeins with low numbers of lysine and arginine in combination with high content of proline and glutamine complicates their identification in a common proteomic workflow, because tryptic digestion produces just a few peptides amenable for successful mass spectrometric analysis. To increase the number of cleavage sites, in this work, cysteines in hordeins were chemically modified with 2-bromoethylamine (BEA) for their conversion into aminoethylcysteines. These mimic lysine residues and are recognized by trypsin as potential cleavage sites (if not followed by a proline residue) on the C-terminal side of the modified cysteine. Small extent of side reactions (towards histidine, N-terminus of the peptide, methionine, and also here the newly discovered reaction towards aminoethylcysteine) during modification with BEA could be observed after a longer period of reaction but this did not hinder the analysis when optimal conditions were used. Application of trypsin for in-gel digestion of hordeins, previously modified chemically with BEA, provided a higher number of short peptides and their subsequent mass spectrometric analysis resulted in an improved identification of hordeins. This approach can also be used for the analysis of other similar protein groups (e.g. gliadins in wheat) or other cysteines containing proteins having a low number of lysine and arginine residues in their primary structure.
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Affiliation(s)
- Helena Rehulková
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Veverí 97, 602 00 Brno, Czech Republic
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17
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Hackenberger C, Schwarzer D. Chemoselektive Ligations- und Modifikationsstrategien für Peptide und Proteine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801313] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Hackenberger C, Schwarzer D. Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed Engl 2008; 47:10030-74. [DOI: 10.1002/anie.200801313] [Citation(s) in RCA: 651] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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19
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Pezza JA, Stopa JD, Brunyak EM, Allen KN, Tolan DR. Thermodynamic analysis shows conformational coupling and dynamics confer substrate specificity in fructose-1,6-bisphosphate aldolase. Biochemistry 2007; 46:13010-8. [PMID: 17935305 DOI: 10.1021/bi700713s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational flexibility is emerging as a central theme in enzyme catalysis. Thus, identifying and characterizing enzyme dynamics are critical for understanding catalytic mechanisms. Herein, coupling analysis, which uses thermodynamic analysis to assess cooperativity and coupling between distal regions on an enzyme, is used to interrogate substrate specificity among fructose-1,6-(bis)phosphate aldolase (aldolase) isozymes. Aldolase exists as three isozymes, A, B, and C, distinguished by their unique substrate preferences despite the fact that the structures of the active sites of the three isozymes are nearly identical. While conformational flexibility has been observed in aldolase A, its function in the catalytic reaction of aldolase has not been demonstrated. To explore the role of conformational dynamics in substrate specificity, those residues associated with isozyme specificity (ISRs) were swapped and the resulting chimeras were subjected to steady-state kinetics. Thermodynamic analyses suggest cooperativity between a terminal surface patch (TSP) and a distal surface patch (DSP) of ISRs that are separated by >8.9 A. Notably, the coupling energy (DeltaGI) is anticorrelated with respect to the two substrates, fructose 1,6-bisphosphate and fructose 1-phosphate. The difference in coupling energy with respect to these two substrates accounts for approximately 70% of the energy difference for the ratio of kcat/Km for the two substrates between aldolase A and aldolase B. These nonadditive mutational effects between the TSP and DSP provide functional evidence that coupling interactions arising from conformational flexibility during catalysis are a major determinant of substrate specificity.
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Affiliation(s)
- John A Pezza
- Department of Biology, Boston University, 5 Cummington Street, Boston, Massachusetts 02215, USA
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20
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Antonkine ML, Maes EM, Czernuszewicz RS, Breitenstein C, Bill E, Falzone CJ, Balasubramanian R, Lubner C, Bryant DA, Golbeck JH. Chemical rescue of a site-modified ligand to a [4Fe–4S] cluster in PsaC, a bacterial-like dicluster ferredoxin bound to Photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:712-24. [PMID: 17434441 DOI: 10.1016/j.bbabio.2007.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 01/21/2007] [Accepted: 02/02/2007] [Indexed: 10/23/2022]
Abstract
Chemical rescue of site-modified amino acids using externally supplied organic molecules represents a powerful method to investigate structure-function relationships in proteins. Here we provide definitive evidence that aryl and alkyl thiolates, reagents typically used for in vitro iron-sulfur cluster reconstitutions, serve as rescue ligands to a site-specifically modified [4Fe-4S](1+,2+) cluster in PsaC, a bacterial dicluster ferredoxin-like subunit of Photosystem I. PsaC binds two low-potential [4Fe-4S](1+,2+) clusters termed F(A) and F(B). In the C13G/C33S variant of PsaC, glycine has replaced cysteine at position 13 creating a protein that is missing one of the ligating amino acids to iron-sulfur cluster F(B). Using a variety of analytical techniques, including non-heme iron and acid-labile sulfur assays, and EPR, resonance Raman, and Mössbauer spectroscopies, we showed that the C13G/C33S variant of PsaC binds two [4Fe-4S](1+,2+) clusters, despite the absence of one of the biological ligands. (19)F NMR spectroscopy indicated that the external thiolate replaces cysteine 13 as a substitute ligand to the F(B) cluster. The finding that site-modified [4Fe-4S](1+,2+) clusters can be chemically rescued with external thiolates opens new opportunities for modulating their properties in proteins. In particular, it provides a mechanism to attach an additional electron transfer cofactor to the protein via a bound, external ligand.
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Affiliation(s)
- Mikhail L Antonkine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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21
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Atsriku C, Benz CC, Scott GK, Gibson BW, Baldwin MA. Quantification of cysteine oxidation in human estrogen receptor by mass spectrometry. Anal Chem 2007; 79:3083-90. [PMID: 17373775 PMCID: PMC2536661 DOI: 10.1021/ac062154o] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Redox-dependent modifications of sulfhydryl groups within the two Cys4 zinc fingers of the estrogen receptor DNA-binding domain (ER-DBD) result in structural damage and loss of ER DNA-binding function, which parallels the situation observed in many ER-positive breast cancers. Quantitation of the redox status of cysteinyl thiols within ER-DBD employed cysteine-specific oxidants to induce varying degrees of oxidation in recombinant ER, followed by differential alkylation with the stable isotopic labeling reagents [12C2]-iodoacetic acid and [13C2]-bromoacetic acid. Subsequent proteolysis with LysC/Asp-N generated diagnostic peptides of which the C-terminal peptide of the second zinc finger is most strongly detected by mass spectrometry (MS) and serves as a suitable marker of ER-DBD redox status. Data were collected from two different MALDI-MS instruments: a time-of-flight and a linear ion trap (vMALDI-LIT). An analogous but larger synthetic peptide treated with three isotopic variants of the alkylating reagent modeled isotopic overlaps that might complicate the relative quantitation of cysteine oxidation. Despite the isotopic overlaps, excellent relative quantitation was achieved from MS data obtained from both instruments. This was also true of tandem MS/MS data from the vMALDI-LIT, which should facilitate selected reaction monitoring. Relative quantitation by MS also closely matched data from immunochemical methods.
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22
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Jebanathirajah JA, Pittman JL, Thomson BA, Budnik BA, Kaur P, Rape M, Kirschner M, Costello CE, O'Connor PB. Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1985-99. [PMID: 16271296 DOI: 10.1016/j.jasms.2005.08.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 08/08/2005] [Accepted: 08/16/2005] [Indexed: 05/05/2023]
Abstract
The use of a new electrospray qQq Fourier transform ion cyclotron mass spectrometer (qQq-FTICR MS) instrument for biologic applications is described. This qQq-FTICR mass spectrometer was designed for the study of post-translationally modified proteins and for top-down analysis of biologically relevant protein samples. The utility of the instrument for the analysis of phosphorylation, a common and important post-translational modification, was investigated. Phosphorylation was chosen as an example because it is ubiquitous and challenging to analyze. In addition, the use of the instrument for top-down sequencing of proteins was explored since this instrument offers particular advantages to this approach. Top-down sequencing was performed on different proteins, including commercially available proteins and biologically derived samples such as the human E2 ubiquitin conjugating enzyme, UbCH10. A good sequence tag was obtained for the human UbCH10, allowing the unambiguous identification of the protein. The instrument was built with a commercially produced front end: a focusing rf-only quadrupole (Q0), followed by a resolving quadrupole (Q1), and a LINAC quadrupole collision cell (Q2), in combination with an FTICR mass analyzer. It has utility in the analysis of samples found in substoichiometric concentrations, as ions can be isolated in the mass resolving Q1 and accumulated in Q2 before analysis in the ICR cell. The speed and efficacy of the Q2 cooling and fragmentation was demonstrated on an LCMS-compatible time scale, and detection limits for phosphopeptides in the 10 amol/muL range (pM) were demonstrated. The instrument was designed to make several fragmentation methods available, including nozzle-skimmer fragmentation, Q2 collisionally activated dissociation (Q2 CAD), multipole storage assisted dissociation (MSAD), electron capture dissociation (ECD), infrared multiphoton induced dissociation (IRMPD), and sustained off resonance irradiation (SORI) CAD, thus allowing a variety of MS(n) experiments. A particularly useful aspect of the system was the use of Q1 to isolate ions from complex mixtures with narrow windows of isolation less than 1 m/z. These features enable top-down protein analysis experiments as well structural characterization of minor components of complex mixtures.
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Affiliation(s)
- Judith A Jebanathirajah
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, MA 02115, USA
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23
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Hopkins CE, Hernandez G, Lee JP, Tolan DR. Aminoethylation in model peptides reveals conditions for maximizing thiol specificity. Arch Biochem Biophys 2005; 443:1-10. [PMID: 16229814 DOI: 10.1016/j.abb.2005.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 08/29/2005] [Accepted: 08/29/2005] [Indexed: 10/25/2022]
Abstract
Control of pH in aminoethylation reactions is critical for maintaining high selectivity towards cysteine modification. Measurement of aminoethylation rate constants by liquid chromatography mass spectrometry demonstrates reaction selectivity of cysteine>>amino-terminus>>histidine. Lysine and methionine were not reactive at the conditions used. For thiol modification, the acid/base property of the gamma-thialysine residue measured by NMR results in a 1.15 decrease in pK(a) (relative to a lysine residue). NMR confirms ethylene imine is the reactive intermediate for alkylation of peptide nucleophiles with bromoethylamine. Conversion of bromoethylamine into ethylene imine prior to exposure to the target thiol, provides a reagent that promotes selectivity by allowing precise control of reaction pH. Reaction selectivity plots of relative aminoethylation rates for cysteine, histidine, and N-terminus imine demonstrate increasing alkaline conditions favors thiol modification. When applied to protein modification, the conversion of bromoethylamine into ethylene imine and buffering at alkaline pH will allow optimal cysteine residue aminoethylation.
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Venkataraman P, Lamb RA, Pinto LH. Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus. J Biol Chem 2005; 280:21463-72. [PMID: 15784624 DOI: 10.1074/jbc.m412406200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The influenza virus M2 proton-selective ion channel activity facilitates virus uncoating, a process that occurs in the acidic environment of the endosome. The M2 channel causes acidification of the interior of the virus particle, which results in viral protein-protein dissociation. The M2 protein is a homotetramer that contains in its aqueous pore a histidine residue (His-37) that acts as a selectivity filter and a tryptophan residue (Trp-41) that acts as a channel gate. Substitution of His-37 modifies M2 ion channel properties drastically. However, the results of such experiments are difficult to interpret because substitution of His-37 could cause gross structural changes to the channel pore. We described here experiments in which partial or, in some cases, full rescue of specific M2 ion channel properties of His-37 substitution mutants was achieved by addition of imidazole to the bathing medium. Chemical rescue was demonstrated for three histidine substitution mutant ion channels (M2-H37G, M2-H37S, and M2-H37T) and for two double mutants in which the Trp-41 channel gate was also mutated (H37G/W41Y and H37G/W41A). Currents of the M2-H37G mutant ion channel were inhibited by Cu(II), which has been shown to coordinate with His-37 in the wild-type channel. Chemical rescue was very specific for imidazole. Buffer molecules that were neutral when protonated (4-morpholineethanesulfonic acid and 3-morpholino-2-hydroxypropanesulfonic acid) did not rescue ion channel activity of the M2-H37G mutant ion channel, but 1-methylimidazole did provide partial rescue of function. These results were consistent with a model for proton transport through the pore of the wild-type channel in which the imidazole side chain of His-37 acted as an intermediate proton acceptor/donor group.
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Affiliation(s)
- Padmavati Venkataraman
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois 60208-3500, USA
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25
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Golemi-Kotra D, Meroueh SO, Kim C, Vakulenko SB, Bulychev A, Stemmler AJ, Stemmler TL, Mobashery S. The importance of a critical protonation state and the fate of the catalytic steps in class A beta-lactamases and penicillin-binding proteins. J Biol Chem 2004; 279:34665-73. [PMID: 15152012 PMCID: PMC3371256 DOI: 10.1074/jbc.m313143200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Beta-lactamases and penicillin-binding proteins are bacterial enzymes involved in antibiotic resistance to beta-lactam antibiotics and biosynthetic assembly of cell wall, respectively. Members of these large families of enzymes all experience acylation by their respective substrates at an active site serine as the first step in their catalytic activities. A Ser-X-X-Lys sequence motif is seen in all these proteins, and crystal structures demonstrate that the side-chain functions of the serine and lysine are in contact with one another. Three independent methods were used in this report to address the question of the protonation state of this important lysine (Lys-73) in the TEM-1 beta-lactamase from Escherichia coli. These techniques included perturbation of the pK(a) of Lys-73 by the study of the gamma-thialysine-73 variant and the attendant kinetic analyses, investigation of the protonation state by titration of specifically labeled proteins by nuclear magnetic resonance, and by computational treatment using the thermodynamic integration method. All three methods indicated that the pK(a) of Lys-73 of this enzyme is attenuated to 8.0-8.5. It is argued herein that the unique ground-state ion pair of Glu-166 and Lys-73 of class A beta-lactamases has actually raised the pK(a) of the active site lysine to 8.0-8.5 from that of the parental penicillin-binding protein. Whereas we cannot rule out that Glu-166 might activate the active site water, which in turn promotes Ser-70 for the acylation event, such as proposed earlier, we would like to propose as a plausible alternative for the acylation step the possibility that the ion pair would reconfigure to the protonated Glu-166 and unprotonated Lys-73. As such, unprotonated Lys-73 could promote serine for acylation, a process that should be shared among all active-site serine beta-lactamases and penicillin-binding proteins.
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Affiliation(s)
- Dasantila Golemi-Kotra
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Samy O. Meroueh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Choonkeun Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Alexey Bulychev
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Ann J. Stemmler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Timothy L. Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University, Detroit, Michigan 48202
- To whom correspondence may be addressed: Dept. of Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48202. Tel.: 313-577-5712; Fax: 313-577-2765;
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
- To whom correspondence may be addressed: Dept. of Chemistry and Biochemistry, University of Notre Dame, 423 Nieuwland Science Hall, Notre Dame, IN 46556. Tel.: 574-631-2933; Fax: 574-631-6652;
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26
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Abstract
Although several powerful methods exist for the redesign of enzyme structure and function these are typically limited to the 20 most abundant proteinogenic amino acids. The use of chemical modification overcomes this limitation to allow virtually unlimited alteration of amino acid sidechain structures. If heterogeneous mixtures of enzyme products are to be avoided, however, the required chemistry should be efficient, selective and compatible with aqueous conditions. Recent advances have been made in the modification of proteinases, aminotransferases and redox enzymes.
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Affiliation(s)
- Benjamin G Davis
- Dyson Perrins Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QY, UK.
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27
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Sharp JS, Becker JM, Hettich RL. Protein surface mapping by chemical oxidation: structural analysis by mass spectrometry. Anal Biochem 2003; 313:216-25. [PMID: 12605858 DOI: 10.1016/s0003-2697(02)00612-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The solvent-accessible surface area of proteins is important in biological function for many reasons, including protein-protein interactions, protein folding, and catalytic sites. Here we present a chemical technique to oxidize amino acid side chains in a model protein, apomyoglobin, and subsequent elucidation of the effect of solvent accessibility on the sites of oxidation. Under conditions of low protein oxidation (zero to three oxygen atoms added per apomyoglobin molecule), we have positively identified five oxidation sites by liquid chromatography-tandem mass spectrometry and high-resolution Fourier transform mass spectrometry. Our results indicate that all oxidized amino acids, with the exception of methionine, have highly solvent-accessible side chains, but the rate of oxidation may not be dictated solely by solvent accessibility and amino acid identity.
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Affiliation(s)
- Joshua S Sharp
- Graduate School of Genome Science and Technology, The University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830-8026, USA
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