1
|
Goyon A, Nguyen D, Boulanouar S, Yehl P, Zhang K. Characterization of Impurities in Therapeutic RNAs at the Single Nucleotide Level. Anal Chem 2022; 94:16960-16966. [PMID: 36410036 DOI: 10.1021/acs.analchem.2c04681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The chemistry of guide RNA (gRNA) affects the performance of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome editing technique. However, the literature is very scarce about the study of gRNA degradation and in particular at the single nucleotide level. In this work, we developed a workflow to characterize the impurities of large RNAs at the single nucleotide level and identified the residues prone to degradation. Our strategy involves (i) the reduction of RNA length, (ii) a chromatographic mode able to capture subtle changes in impurity polarity, and (iii) a streamlined data treatment. To illustrate the approach, stressed gRNA samples were analyzed by coupling an immobilized ribonuclease T1 cartridge to a hydrophilic interaction liquid chromatography (HILIC) column hyphenated with tandem mass spectrometry (MS/MS). Critical findings were made possible by the presented technology. In particular, the desulfurization of phosphorothioate (PS) linkages was the major degradation observed at the single nucleotide level while no change in purity profile could be observed when using conventional ion-pairing reversed-phase (IPRP) liquid chromatography. To our knowledge, this is the first time that several impurity types are screened for a large RNA molecule using an automated online digestion analysis approach.
Collapse
Affiliation(s)
- Alexandre Goyon
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Nguyen
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Sara Boulanouar
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Yehl
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
2
|
Camperi J, Goyon A, Guillarme D, Zhang K, Stella C. Multi-dimensional LC-MS: the next generation characterization of antibody-based therapeutics by unified online bottom-up, middle-up and intact approaches. Analyst 2021; 146:747-769. [DOI: 10.1039/d0an01963a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review presents an overview of current analytical trends in antibody characterization by multidimensional LC-MS approaches.
Collapse
Affiliation(s)
- Julien Camperi
- Department of Protein Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Alexandre Goyon
- Department of Small Molecule Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Davy Guillarme
- School of Pharmaceutical Sciences
- University of Geneva
- 1206 Geneva
- Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO)
| | - Kelly Zhang
- Department of Small Molecule Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Cinzia Stella
- Department of Protein Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| |
Collapse
|
3
|
A triply modified human adult hemoglobin with low oxygen affinity, rapid autoxidation and high tetramer stability. Int J Biol Macromol 2020; 159:236-242. [DOI: 10.1016/j.ijbiomac.2020.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/24/2020] [Accepted: 05/01/2020] [Indexed: 12/12/2022]
|
4
|
From proof of concept to the routine use of an automated and robust multi-dimensional liquid chromatography mass spectrometry workflow applied for the charge variant characterization of therapeutic antibodies. J Chromatogr A 2020; 1615:460740. [DOI: 10.1016/j.chroma.2019.460740] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/26/2019] [Indexed: 11/24/2022]
|
5
|
Eom GE, Kim S. Identification of Nucleophilic Probes for Protease-Mediated Transpeptidation. Molecules 2018; 23:E2109. [PMID: 30131476 PMCID: PMC6225416 DOI: 10.3390/molecules23092109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022] Open
Abstract
Proteases have evolved to mediate the hydrolysis of peptide bonds but may perform transpeptidation in the presence of a proper nucleophilic molecule that can effectively compete with water to react with the acyl-enzyme intermediate. There have been several examples of protease-mediated transpeptidation, but they are generally inefficient, and little effort has been made to systematically control the transpeptidation activity of other proteases with good nucleophiles. Here, we developed an on-bead screening approach to find a probe that functions efficiently as a nucleophile in the protease-mediated transpeptidation reaction, and we identified good probes for a model protease DegP. These probes were covalently linked to the C-termini of the cleaved peptides in a mild condition and made the selective enrichment of ligated peptides possible. We suggest that good nucleophilic probes can be found for many other proteases that act via acyl-enzyme intermediates, and these probes will help characterize their substrates.
Collapse
Affiliation(s)
- Ga-Eul Eom
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| |
Collapse
|
6
|
Zhang L, Veith PD, Huq NL, Chen YY, Seers CA, Cross KJ, Gorasia DG, Reynolds EC. Porphyromonas gingivalis Gingipains Display Transpeptidation Activity. J Proteome Res 2018; 17:2803-2818. [PMID: 29984580 DOI: 10.1021/acs.jproteome.8b00286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Porphyromonas gingivalis is a keystone periodontal pathogen that has been associated with autoimmune disorders. The cell surface proteases Lys-gingipain (Kgp) and Arg-gingipains (RgpA and RgpB) are major virulence factors, and their proteolytic activity is enhanced by small peptides such as glycylglycine (GlyGly). The reaction kinetics suggested that GlyGly may function as an acceptor molecule for gingipain-catalyzed transpeptidation. Purified gingipains and P. gingivalis whole cells were used to digest selected substrates including human hemoglobin in the presence or absence of peptide acceptors. Mass spectrometric analysis of the substrates digested with gingipains in the presence of GlyGly showed that transpeptidation outcompeted hydrolysis, whereas the trypsin-digested controls exhibited predominantly hydrolysis activity. The transpeptidation levels increased with increasing concentration of GlyGly. Purified gingipains and whole cells exhibited extensive transpeptidation activities on human hemoglobin. All hemoglobin cleavage sites were found to be suitable for GlyGly transpeptidation, and this transpeptidation enhanced hemoglobin digestion. The transpeptidation products were often more abundant than the corresponding hydrolysis products. In the absence of GlyGly, hemoglobin peptides produced during digestion were utilized as acceptors leading to the detection of up to 116 different transpeptidation products in a single reaction. P. gingivalis cells were able to digest hemoglobin faster when acceptor peptides derived from human serum albumin were included in the reaction, suggesting that gingipain-catalyzed transpeptidation may be relevant for substrates encountered in vivo. The transpeptidation of host proteins in vivo may potentially lead to the breakdown of immunological tolerance, culminating in autoimmune reactions.
Collapse
Affiliation(s)
- Lianyi Zhang
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Paul D Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - N Laila Huq
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Yu-Yen Chen
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Christine A Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Keith J Cross
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Dhana G Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| |
Collapse
|
7
|
Propylbenzmethylation at Val-1(α) markedly increases the tetramer stability of the PEGylated hemoglobin: A comparison with propylation at Val-1(α). Biochim Biophys Acta Gen Subj 2012; 1820:2044-51. [DOI: 10.1016/j.bbagen.2012.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/15/2012] [Accepted: 09/20/2012] [Indexed: 11/19/2022]
|
8
|
Liu R, Li D, Wang J, Qiu R, Lin Q, Zhang G, Ma G, Su Z, Hu T. Preparation, characterization and in vitro bioactivity of N-terminally PEGylated staphylokinase dimers. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Wang J, Wang Y, Hu T, Li X, Huang Y, Liu Y, Ma G, Su Z. An oriented adsorption strategy for efficient solid phase PEGylation of recombinant staphylokinase by immobilized metal-ion affinity chromatography. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
Immobilized trypsin on epoxy organic monoliths with modulated hydrophilicity: Novel bioreactors useful for protein analysis by liquid chromatography coupled to tandem mass spectrometry. J Chromatogr A 2011; 1218:8937-45. [DOI: 10.1016/j.chroma.2011.05.059] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 05/16/2011] [Accepted: 05/17/2011] [Indexed: 10/18/2022]
|
11
|
Kinetic and stoichiometric analysis of the modification process for N-terminal PEGylation of staphylokinase. Anal Biochem 2011; 412:114-6. [DOI: 10.1016/j.ab.2010.12.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Revised: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 11/15/2022]
|
12
|
Richardson J, Shah B, Xiao G, Bondarenko PV, Zhang Z. Automated in-solution protein digestion using a commonly available high-performance liquid chromatography autosampler. Anal Biochem 2011; 411:284-91. [DOI: 10.1016/j.ab.2011.01.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Revised: 01/10/2011] [Accepted: 01/13/2011] [Indexed: 11/29/2022]
|
13
|
Nicoli R, Rudaz S, Stella C, Veuthey JL. Trypsin immobilization on an ethylenediamine-based monolithic minidisk for rapid on-line peptide mass fingerprinting studies. J Chromatogr A 2009; 1216:2695-9. [DOI: 10.1016/j.chroma.2008.10.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/09/2008] [Accepted: 10/13/2008] [Indexed: 10/21/2022]
|
14
|
Li D, Hu T, Manjula BN, Acharya SA. Non-conservative surface decoration of hemoglobin: Influence of neutralization of positive charges at PEGylation sites on molecular and functional properties of PEGylated hemoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1395-401. [DOI: 10.1016/j.bbapap.2008.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 03/26/2008] [Accepted: 03/31/2008] [Indexed: 11/13/2022]
|
15
|
Berkers CR, de Jong A, Ovaa H, Rodenko B. Transpeptidation and reverse proteolysis and their consequences for immunity. Int J Biochem Cell Biol 2008; 41:66-71. [PMID: 18817889 DOI: 10.1016/j.biocel.2008.08.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 08/29/2008] [Accepted: 08/29/2008] [Indexed: 11/27/2022]
Abstract
Reverse proteolysis and transpeptidation lead to the generation of polypeptide sequences that cannot be inferred directly from genome sequences as they are post-translational phenomena. These phenomena have so far received little attention although the physiological consequences may reach far. The protease-mediated synthesis of several immunodominant MHC class I antigens was recently reported, underscoring its importance to immunity. Reverse proteolytic and transpeptidation mechanisms as well as conditions that favor successful protease-catalyzed synthetic events are discussed here.
Collapse
Affiliation(s)
- Celia R Berkers
- Division of Cellular Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | | | | | | |
Collapse
|
16
|
Vukovic J, Loftheim H, Winther B, Reubsaet JLE. Improving off-line accelerated tryptic digestion. J Chromatogr A 2008; 1195:34-43. [DOI: 10.1016/j.chroma.2008.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 03/28/2008] [Accepted: 05/08/2008] [Indexed: 11/16/2022]
|
17
|
Nicoli R, Gaud N, Stella C, Rudaz S, Veuthey JL. Trypsin immobilization on three monolithic disks for on-line protein digestion. J Pharm Biomed Anal 2007; 48:398-407. [PMID: 18242915 DOI: 10.1016/j.jpba.2007.12.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 12/13/2007] [Accepted: 12/13/2007] [Indexed: 11/28/2022]
Abstract
The preparation and characterization of three trypsin-based monolithic immobilized enzyme reactors (IMERs) developed to perform rapid on-line protein digestion and peptide mass fingerprinting (PMF) are described. Trypsin (EC 3.4.21.4) was covalently immobilized on epoxy, carbonyldiimidazole (CDI) and ethylenediamine (EDA) Convective Interaction Media (CIM) monolithic disks. The amount of immobilized enzyme, determined by spectrophotometric measurements at 280nm, was comprised between 0.9 and 1.5mg per disk. Apparent kinetic parameters Km* and Vmax*, as well as apparent immobilized trypsin BAEE-units, were estimated in flow-through conditions using N-alpha-benzoyl-L-arginine ethyl ester (BAEE) as a low molecular mass substrate. The on-line digestion of five proteins (cytochrome c, myoglobin, alpha1-acid glycoprotein, ovalbumin and albumin) was evaluated by inserting the IMERs into a liquid chromatography system coupled to an electrospray ionization ion-trap mass spectrometer (LC-ESI-MS/MS) through a switching valve. Results were compared to the in-solution digestion in terms of obtained scores, number of matched queries and sequence coverages. The most efficient IMER was obtained by immobilizing trypsin on a CIM EDA disk previously derivatized with glutaraldehyde, as a spacer moiety. The proteins were recognized by the database with satisfactory sequence coverage using a digestion time of only 5min. The repeatability of the digestion (R.S.D. of 5.4% on consecutive injections of myoglobin 12microM) and the long-term stability of this IMER were satisfactory since no loss of activity was observed after 250 injections.
Collapse
Affiliation(s)
- R Nicoli
- Laboratory of Analytical Pharmaceutical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20 Bd d'Yvoy, 1211 Geneva 4, Switzerland
| | | | | | | | | |
Collapse
|
18
|
Hu T, Manjula B, Li D, Brenowitz M, Acharya S. Influence of intramolecular cross-links on the molecular, structural and functional properties of PEGylated haemoglobin. Biochem J 2007; 402:143-51. [PMID: 17049048 PMCID: PMC1783979 DOI: 10.1042/bj20061434] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 10/17/2006] [Accepted: 10/19/2006] [Indexed: 11/17/2022]
Abstract
The influence of intramolecular cross-links on the molecular, structural and functional properties of PEGylated {PEG [poly(ethylene glycol)]-conjugated} haemoglobin has been investigated. The sites and the extent of PEGylation of haemoglobin by reductive alkylation are not influenced by the presence of an alphaalpha-fumaryl cross-link at Lys-99(alpha). The propylated hexaPEGylated cross-linked haemoglobin, (propyl-PEG5K)(6)-alphaalpha-Hb, exhibits a larger molecular radius and lower colloidal osmotic pressure than propylated hexaPEGylated non-cross-linked haemoglobin, (propyl-PEG5K)(6)-Hb. Perturbation of the haem microenvironment and the alpha1beta2 interface by PEGylation of haemoglobin is reduced by intramolecular cross-linking. Sedimentation velocity analysis established that PEGylation destabilizes the tetrameric structure of haemoglobin. (Propyl-PEG5K)(6)-Hb and (propyl-PEG5K)(6)-alphaalpha-Hb sediment as stable dimeric and tetrameric molecules, respectively. The betabeta-succinimidophenyl PEG-2000 cross-link at Cys-93(beta) outside the central cavity also influences the molecular properties of haemoglobin, comparable to that by the alphaalpha-fumaryl cross-link within the central cavity. However, the influence of the two cross-links on the oxygen affinity of PEGylated haemoglobin are very distinct, indicating that the high oxygen affinity of PEGylated haemoglobin is not a direct consequence of the dissociation of the haemoglobin tetramers into dimers. alphaalpha-Fumaryl cross-linking is preferred to modulate both oxygen affinity and molecular properties of PEGylated haemoglobin, and cross-linking outside the central cavity could only modulate molecular properties of PEGylated haemoglobin. It is suggested that PEGylation induces a hydrodynamic drag on haemoglobin and this plays a role in the microcirculatory properties of PEGylated haemoglobin.
Collapse
Key Words
- cross-link
- haemoglobin
- pegylation
- reductive alkylation
- subunit dissociation
- cop, colloidal osmotic pressure
- αα-fumaryl hb, αα-intramolecular cross-linked haemoglobin at lys-99(α)
- ββ-hb, ββ-intramolecular succinimidophenyl-poly(ethylene glycol) 2000 cross-linked haemoglobin at cys-93(β)
- hba, human adult haemoglobin
- ief, isoelectric focusing
- peg, poly(ethylene glycol)
- peg2k, peg 2000
- peg20k, peg 20000
- peg5k, peg 5000
- peg5k aldehyde, ω-methoxy-peg5k propionaldehyde
- pegylation, conjugation with peg
- (propyl-peg5k)6-hb, propylated hexapegylated non-cross-linked haemoglobin
- (propyl-peg5k)6-αα-hb, propylated hexapegylated αα-intramolecular cross-linked haemoglobin
- (propyl-peg5k)6-ββ-hb, propylated hexapegylated ββ-intramolecular cross-linked haemoglobin
- rp, reverse-phase
- sec, size-exclusion chromatography
- (sp-peg5k)6-hb, succinimidophenylated hexapegylated haemoglobin
Collapse
Affiliation(s)
- Tao Hu
- *Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Belur N. Manjula
- *Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Dongxia Li
- *Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Brenowitz
- †Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Seetharama A. Acharya
- *Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
- ‡Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| |
Collapse
|
19
|
Jeng J, Lin MF, Cheng FY, Yeh CS, Shiea J. Using high-concentration trypsin-immobilized magnetic nanoparticles for rapid in situ protein digestion at elevated temperature. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3060-8. [PMID: 17705254 DOI: 10.1002/rcm.3191] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We describe an innovative approach - using a high concentration of trypsin-modified magnetic nanoparticles (TMNPs) - for the rapid and efficient digestion of proteins at elevated temperature. The required digestion time could be reduced to less than 10 s. After digestion, the TMNPs were collected magnetically from the sample solution for reuse and the digested peptides were characterized using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Protein digestion was optimized when using the TMNPs (5 microg/microL) at 57 degrees C; a significantly high peptide coverage was achieved for protein identification (e.g., 98% for lysozyme). Although a high concentration of TMNPs was used for digestion, the short digestion time led to much lower amounts of trypsin peptides being produced through self-digestion. As a result, interference in the mass spectrometric detection of the peptide ions was reduced significantly.
Collapse
Affiliation(s)
- Jingyueh Jeng
- Department of Biotechnology, Chia Nan University of Pharmacy & Science, 60, Erh-Jen RD., Sec.1, Jen-Te, Tainan 717, Taiwan
| | | | | | | | | |
Collapse
|
20
|
Fodor S, Zhang Z. Rearrangement of terminal amino acid residues in peptides by protease-catalyzed intramolecular transpeptidation. Anal Biochem 2006; 356:282-90. [PMID: 16859627 DOI: 10.1016/j.ab.2006.06.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2006] [Revised: 06/13/2006] [Accepted: 06/14/2006] [Indexed: 11/30/2022]
Abstract
Protease-catalyzed rearrangements of amino acid residues in peptides are observed during enzymatic digestion of proteins. When two enzyme-specific cleavage sites are within one or two residues of each other in the protein sequence, only one of the two sites usually is hydrolyzed by the protease, resulting in a peptide that contains an extra cleavage site near one of its termini. It is observed that in this type of peptide, the residues between the two cleavage sites often rearrange from one terminus of the peptide to the other terminus, catalyzed by the protease that created the peptide. It is proposed that the rearrangement is caused by protease-catalyzed intramolecular transpeptidation through a cyclic peptide intermediate. Several cases of this type of rearrangement were observed for different peptides generated by different proteases, indicating that this type of rearrangement is a general phenomenon occurring during enzymatic digestion of proteins.
Collapse
|
21
|
Freije JR, Mulder PPMFA, Werkman W, Rieux L, Niederlander HAG, Verpoorte E, Bischoff R. Chemically modified, immobilized trypsin reactor with improved digestion efficiency. J Proteome Res 2006; 4:1805-13. [PMID: 16212436 DOI: 10.1021/pr050142y] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tryptic digestion followed by identification using mass spectrometry is an important step in many proteomic studies. Here, we describe the preparation of immobilized, acetylated trypsin for enhanced digestion efficacy in integrated protein analysis platforms. Complete digestion of cytochrome c was obtained with two types of modified-trypsin beads with a contact time of only 4 s, while corresponding unmodified-trypsin beads gave only incomplete digestion. The digestion rate of myoglobin, a protein known to be rather resistant to proteolysis, was not altered by acetylating trypsin and required a buffer containing 35% acetonitrile to obtain complete digestion. The use of acetylated-trypsin beads led to fewer interfering tryptic autolysis products, indicating an increased stability of this modified enzyme. Importantly, the modification did not affect trypsin's substrate specificity, as the peptide map of myoglobin was not altered upon acetylation of immobilized trypsin. Kinetic digestion experiments in solution with low-molecular-weight substrates and cytochrome c confirmed the increased catalytic efficiency (lower K(M) and higher k(cat)) and increased resistance to autolysis of trypsin upon acetylation. Enhancement of catalytic efficiency was correlated with the number of acetylations per molecule. The favorable properties of the new chemically modified trypsin reactor should make it a valuable tool in automated protein analysis systems.
Collapse
Affiliation(s)
- J Robert Freije
- Center for Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
22
|
Hu T, Prabhakaran M, Acharya S, Manjula B. Influence of the chemistry of conjugation of poly(ethylene glycol) to Hb on the oxygen-binding and solution properties of the PEG-Hb conjugate. Biochem J 2005; 392:555-64. [PMID: 16111474 PMCID: PMC1316295 DOI: 10.1042/bj20050663] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 07/27/2005] [Accepted: 08/19/2005] [Indexed: 11/17/2022]
Abstract
Our recent studies on PEG-Hb [poly(ethylene glycol)-Hb] conjugates generated by thiolation-mediated maleimide-chemistry based PEGylation demonstrated that the vasoactivity of the PEG-Hb conjugates is a function of the configuration of the PEG chains on the surface of the protein and is independent of the PEG/protein-mass ratio [Manjula, A. G. Tsai, Intaglietta, H.-C. Tsai, Ho, Smith, Perumalsamy, Kanika, Friedman and Acharya (2005) Protein J. 24, 133-146]. A Hb conjugated with six PEG5k chains (SP-PEG5k)6-Hb, was vasoinactive. In an attempt to understand whether the chemistry of conjugation of PEG to Hb has any influence on the modulation of its functional and solution properties, we have now generated a new hexaPEGylated-Hb, (propyl-PEG5k)6-Hb, by reductive alkylation chemistry. CD (circular dichroism) spectral measurements indicated that the overall secondary structure of Hb is not adversely influenced upon PEGylation. (Propyl-PEG5k)6-Hb exhibited an increased O2 affinity with decreased co-operativity and decreased modulation by allosteric effectors comparable with that of (SP-PEG5k)6-Hb, although its Cys-93(b) is not derivatized as in the latter. On a molecular mass basis, PEG linked to Hb by reductive alkylation increased its COP (colloidal osmotic pressure) more efficiently than when linked by thiolation-mediated maleimide-chemistry. These results demonstrate that the functional properties of PEG-Hb conjugates may be a direct consequence of surface decoration of Hb with PEG, but are independent of the site (pattern) and/or the chemistry of PEGylation. However the solution properties of PEGylated Hb are influenced by the site (pattern) and/or the chemistry of PEGylation and the presence or absence of an 'extension arm' between the conjugating site of Hb and the PEG chain.
Collapse
Key Words
- colloidal osmotic pressure (cop)
- pegylation
- pegylated hb
- reductive alkylation
- thiolation-mediated male-imide-chemistry
- viscosity
- cd, circular dichroism
- cop, colloidal osmotic pressure
- 2,3-dpg, 2,3-diphosphoglycerate
- ihp, inositol hexaphosphate
- maldi, matrix-assisted laser-desorption ionization
- p50, partial oxygen pressure at 50% oxygen saturation
- 4-pds, 4,4′-dithiopyridine
- peg, poly(ethylene glycol)
- ri, refractive index
- rphplc, reverse phase hplc
- sec, size exclusion chromatography
- sp, succinimidophenyl
- tfa, trifluoro acetic acid
- 2,4,6-tnbs, 2,4,6-trinitrobenzenesulphonic acid
Collapse
Affiliation(s)
- Tao Hu
- *Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | | | - Seetharama A. Acharya
- *Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
- ‡Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Belur N. Manjula
- *Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| |
Collapse
|
23
|
Tang WH, Halpern BR, Shilov IV, Seymour SL, Keating SP, Loboda A, Patel AA, Schaeffer DA, Nuwaysir LM. Discovering Known and Unanticipated Protein Modifications Using MS/MS Database Searching. Anal Chem 2005; 77:3931-46. [PMID: 15987094 DOI: 10.1021/ac0481046] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an MS/MS database search algorithm with the following novel features: (1) a novel protein database structure containing extensive preindexing and (2) zone modification searching, which enables the rapid discovery of protein modifications of known (i.e., user-specified) and unanticipated delta masses. All of these features are implemented in Interrogator, the search engine that runs behind the Pro ID, Pro ICAT, and Pro QUANT software products. Speed benchmarks demonstrate that our modification-tolerant database search algorithm is 100-fold faster than traditional database search algorithms when used for comprehensive searches for a broad variety of modification species. The ability to rapidly search for a large variety of known as well as unanticipated modifications allows a significantly greater percentage of MS/MS scans to be identified. We demonstrate this with an example in which, out of a total of 473 identified MS/MS scans, 315 of these scans correspond to unmodified peptides, while 158 scans correspond to a wide variety of modified peptides. In addition, we provide specific examples where the ability to search for unanticipated modifications allows the scientist to discover: unexpected modifications that have biological significance; amino acid mutations; salt-adducted peptides in a sample that has nominally been desalted; peptides arising from nontryptic cleavage in a sample that has nominally been digested using trypsin; other unintended consequences of sample handling procedures.
Collapse
Affiliation(s)
- Wilfred H Tang
- Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA. tangwh@ appliedbiosystems.com
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Emmer Å, Roeraade J. Enzymatic protein digest in chip-based nanovials with immobilized proteolytic enzymes. Anal Chim Acta 2005. [DOI: 10.1016/j.aca.2005.03.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
25
|
|
26
|
Samskog J, Bylund D, Jacobsson SP, Markides KE. Miniaturized on-line proteolysis-capillary liquid chromatography-mass spectrometry for peptide mapping of lactate dehydrogenase. J Chromatogr A 2003; 998:83-91. [PMID: 12862374 DOI: 10.1016/s0021-9673(03)00647-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this study, methodology was developed for on-line and miniaturized enzymatic digestion with liquid chromatographic (LC) separation and mass spectrometric (MS) detection. A packed capillary LC-MS system was combined with on-line trypsin cleavage of a model protein, lactate dehydrogenase, to provide an efficient system for peptide mapping. The protein was injected onto an enzymatic capillary reactor and the resulting peptides were efficiently trapped on a capillary trapping column. Different trapping columns were evaluated to achieve a high binding capacity for the peptides generated in the enzyme reactor. The peptides were further eluted from the pre-column and separated on an analytical capillary column by a buffer more suitable for the following an electrospray ionisation (ESI) MS process. An important aspect of the on-line approach was the desalting of peptides performed in the trapping column to avoid detrimental signal suppression in the ESI process. The developed on-line system was finally compared to a classical digestion in solution, with reference to peptide sequence coverage and sensitivity. It was shown that the on-line system gave more than 100% higher peptide sequence coverage than traditional digestion methods.
Collapse
Affiliation(s)
- Jenny Samskog
- Department of Analytical Chemistry, Uppsala University, P.O. Box 599, SE-751 24 Uppsala, Sweden
| | | | | | | |
Collapse
|
27
|
Slysz GW, Schriemer DC. On-column digestion of proteins in aqueous-organic solvents. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1044-1050. [PMID: 12720284 DOI: 10.1002/rcm.1022] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Proteolytic digestion is an important step in protein identification by peptide mass mapping and tandem mass spectrometry (MS/MS)-based peptide sequencing. Traditional methods of protein digestion require extended incubation times and have difficulty with proteolytically resistant proteins. Here, we describe a method in which a protein solution was combined with a mixed aqueous-organic solution (methanol, isopropanol, or acetonitrile) and passed through a microcolumn containing immobilized trypsin. Myoglobin sequence coverage was high (>85%) in all three solvents, and differences in spectra were seen among the different solution conditions. Notably, methanol-based digestions produced fewer missed cleavages while acetonitrile-based digestions produced the most peptides and the most intense mass spectra. Flow rates through the column were varied from 0.5 to 15 micro L/min, corresponding to column residence times of 78 and 2.6 s, respectively. All flow rates produced high sequence coverage of myoglobin, although, at higher flow rates, more missed cleavages were observed. No significant increase in undigested myoglobin was observed with flow rates up to 15 micro L/min. The described method was applied to the digestion of human transferrin (hTf), a proteolytically resistant protein. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOFMS) analysis detected 42 peptides covering 46% of the hTf sequence. The traditional aqueous method resulted in 12 peptides (8% sequence coverage) only when high concentrations of trypsin were used. Lastly, digestion of low nanomolar myoglobin was shown to produce detectable peptides and resulted in a correct database hit. Thus, we demonstrate a method that is capable of rapid on-line digestion, thereby lending itself to high-throughput identification of proteins.
Collapse
Affiliation(s)
- Gordon W Slysz
- Department of Molecular Biology and Biochemistry, 3330 Hospital Dr. NW, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | | |
Collapse
|
28
|
Abstract
This review highlights the many roles mass spectrometry plays in the discovery and development of new therapeutics by both the pharmaceutical and the biotechnology industries. Innovations in mass spectrometer source design, improvements to mass accuracy, and implementation of computer-controlled automation have accelerated the purification and characterization of compounds derived from combinatorial libraries, as well as the throughput of pharmacokinetics studies. The use of accelerator mass spectrometry, chemical reaction interface-mass spectrometry and continuous flow-isotope ratio mass spectrometry are promising alternatives for conducting mass balance studies in man. To meet the technical challenges of proteomics, discovery groups in biotechnology companies have led the way to development of instruments with greater sensitivity and mass accuracy (e.g., MALDI-TOF, ESI-Q-TOF, Ion Trap), the miniaturization of separation techniques and ion sources (e.g., capillary HPLC and nanospray), and the utilization of bioinformatics. Affinity-based methods coupled to mass spectrometry are allowing rapid and selective identification of both synthetic and biological molecules. With decreasing instrument cost and size and increasing reliability, mass spectrometers are penetrating both the manufacturing and the quality control arenas. The next generation of technologies to simplify the investigation of the complex fate of novel pharmaceutical entities in vitro and in vivo will be chip-based approaches coupled with mass spectrometry.
Collapse
Affiliation(s)
- D I Papac
- Department of Development Research, NPS Pharmaceuticals, Inc., Salt Lake City, Utah 84108, USA
| | | |
Collapse
|
29
|
Lippincott J, Fattor TJ, Lemon DD, Apostol I. Application of native-state electrospray mass spectrometry to identify zinc-binding sites on engineered hemoglobin. Anal Biochem 2000; 284:247-55. [PMID: 10964407 DOI: 10.1006/abio.2000.4679] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the utility of native-state mass spectrometry to detect zinc ion binding to the engineered hemoglobin rHb52. Various preparations of this recombinant hemoglobin had significantly different oxygen affinities. Detailed characterization of denatured globins did not show any difference between analyzed hemoglobin molecules. However, when solutions of intact hemoglobin pseudotetramers were analyzed by native-state electrospray mass spectrometry, a significant shift in the mass spectrum was observed, indicating labile modification of hemoglobin. Using collision-induced dissociation (CID), we found a mass gain of 63 Da located on the beta-globin. EDTA treatment of modified hemoglobin prior to the infusion removed the modification and restored the predicted oxygen affinity. Ion-trap fragmentation of the +8 charged ion of modified beta-globin showed a neutral loss of 96+/-1 Da, consistent with neutral loss of zinc sulfide. These findings indicated zinc binding to the beta-globin through a cysteine residue. Involvement of Cys93 was confirmed by kinetics of cysteine residue reactivity with dithiodipyridine and peptide mapping. Presence of zinc was confirmed by ICP-MS metal analysis.
Collapse
Affiliation(s)
- J Lippincott
- Baxter Hemoglobin Therapeutics, 2545 Central Avenue, Boulder, Colorado 80301, USA
| | | | | | | |
Collapse
|
30
|
Gatlin CL, Eng JK, Cross ST, Detter JC, Yates JR. Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. Anal Chem 2000; 72:757-63. [PMID: 10701260 DOI: 10.1021/ac991025n] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid sequence variations resulting from single-nucleotide polymorphisms (SNPs) were identified using a novel mass spectrometric method. This method obtains 99+% protein sequence coverage for human hemoglobin in a single LC-microspray tandem mass spectrometry (microLC-MS/MS) experiment. Tandem mass spectrometry data was analyzed using a modified version of the computer program SEQUEST to identify the sequence variations. Conditions of sample preparation, chromatographic separation, and data collection were optimized to correctly identify amino acid changes in six variants of human hemoglobin (Hb C, Hb E, Hb D-Los Angeles, Hb G-Philadelphia, Hb Hope, and Hb S). Hemoglobin proteins were isolated and purified, dehemed, (S)-carboxyami-domethylated, and then subjected to a combination proteolytic digestion to obtain a complex peptide mixture with multiple overlaps in sequence. Reversed-phase chromatographic separation of peptides was achieved on-line with MS utilizing a robust fritless microelectrospray interface. Tandem mass spectrometry was performed on an ion trap mass spectrometer using automated data-dependent MS/MS procedures. Tandem mass spectra were collected from the five most abundant ions in each scan using dynamic and isotopic exclusion to minimize redundancy. The spectra were analyzed by a version of the SEQUEST algorithm modified to identify amino acid substations resulting from SNPs.
Collapse
Affiliation(s)
- C L Gatlin
- Department of Molecular Biotechnology, University of Washington, Seattle 98195-7730, USA
| | | | | | | | | |
Collapse
|
31
|
Lippincott J, Apostol I. Carbamylation of cysteine: a potential artifact in peptide mapping of hemoglobins in the presence of urea. Anal Biochem 1999; 267:57-64. [PMID: 9918655 DOI: 10.1006/abio.1998.2970] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peptide mapping is a useful technique for identifying posttranslational modifications. However, sometimes artifacts can be introduced during the mapping procedure which can be misleading in identifying the origin and nature of the modifications. During peptide mapping of unalkylated hemoglobins with Staphylococcus aureus V8 proteinase, we found a significant level of carbamylated cysteines. Carbamylation was not detected if recombinant human hemoglobin (rHb1.1) was alkylated prior to digestion. Our experiments indicated that this modification was an artifact of the digestion procedure in which the slightly acidic conditions promoted the reaction of cysteine sulfhydryls with residual cyanate derived from urea. Carbamylmercaptans were found to be stable under acidic conditions but were unstable in base. The extent of cysteine carbamylation can be moderated by the use of scavengers.
Collapse
Affiliation(s)
- J Lippincott
- Baxter Hemoglobin Therapeutics, Inc., Boulder, Colorado, 80301, USA
| | | |
Collapse
|
32
|
Doyle MP, Apostol I, Kerwin BA. Glutaraldehyde modification of recombinant human hemoglobin alters its hemodynamic properties. J Biol Chem 1999; 274:2583-91. [PMID: 9891031 DOI: 10.1074/jbc.274.4.2583] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many cell-free hemoglobin solutions designed as oxygen-carrying therapeutics produce a hypertensive effect in animals. The response is likely due to oxidation of nitric oxide by hemoglobin. Since the site of oxidation may lie outside the vascular compartment, we tested the hypothesis that polymerization of hemoglobin, rHb1.1, by glutaraldehyde would attenuate the hypertensive response. Two products of the cross-linking reaction were isolated, a glutaraldehyde-derivatized monomer (mono-glxrHb) and a glutaraldehyde cross-linked polymer (poly-glxrHb), and evaluated for their effects on systemic hemodynamics in conscious rats. Administration of rHb1.1 caused a mean arterial pressure elevation of approximately 20 mm Hg and an increase in total peripheral resistance of approximately 30%. Administration of mono-glxrHb induced changes in mean arterial pressure and vascular resistance that were significantly diminished relative to those observed with rHb1.1. Poly-glxrHb elicited a mean arterial pressure response that was further reduced compared with that obtained with mono-glxrHb and a change in vascular resistance that was the same as the response to mono-glxrHb. These results suggest that rHb peripheral vasoconstriction elicited by rHb1.1 is significantly attenuated by glutaraldehyde modification of the hemoglobin monomer and that the effect of glutaraldehyde polymerization is likely due to surface modification and/or intramolecular cross-linking, rather than an increase in molecular size.
Collapse
Affiliation(s)
- M P Doyle
- Baxter Healthcare Corporation, Boulder, Colorado 80301, USA
| | | | | |
Collapse
|
33
|
Kerwin BA, Akers MJ, Apostol I, Moore-Einsel C, Etter JE, Hess E, Lippincott J, Levine J, Mathews AJ, Revilla-Sharp P, Schubert R, Looker DL. Acute and long-term stability studies of deoxy hemoglobin and characterization of ascorbate-induced modifications. J Pharm Sci 1999; 88:79-88. [PMID: 9874706 DOI: 10.1021/js980221r] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of ascorbate with recombinant hemoglobin (rHb1.1) in the presence of differing partial pressures of oxygen was studied. In the presence of 15 000 ppm (1.5%) residual oxygen, ascorbate/oxygen-mediated reactions resulted in an increased rate of autoxidation, modification of the beta-globin, increased oxygen affinity and decreased maximum Hill coefficient. One of the observed modifications to the beta-globin was a 72 Da addition to its N-terminus. Detailed characterization indicates the modification was an imidazolidinone type structure. Thorough deoxygenation of the hemoglobin solution to <150 ppm of oxygen prior to addition of ascorbate was required to prevent these modifications. Addition of ascorbate to the deoxy hemoglobin (deoxyHb) at pH 8 induced aggregation, eventually leading to precipitation. No such precipitation was observed at pH 7. Long-term storage of the hemoglobin was carried out by addition of ascorbate to deoxyHb at pH 7. The level of methemoglobin remained at <2% for up to 1 year at 4 degreesC, with no detectable precipitation of the protein. Modifications similar to those observed by the acute studies were observed over the 1-year period and correlated with disappearance of the added ascorbate.
Collapse
Affiliation(s)
- B A Kerwin
- Amgen, One Amgen Center Drive, Mail Drop 8-1-C, Thousand Oaks, California 91320-1799, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Levine J, Weickert M, Pagratis M, Etter J, Mathews A, Fattor T, Lippincott J, Apostol I. Identification of a nickel(II) binding site on hemoglobin which confers susceptibility to oxidative deamination and intramolecular cross-linking. J Biol Chem 1998; 273:13037-46. [PMID: 9582340 DOI: 10.1074/jbc.273.21.13037] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complexation of Ni(II) with native state recombinant hemoglobin is shown to produce NH2-terminal deamination and globin cross-linking in the presence of the oxidant potassium peroxymonosulfate (OxoneTM). Both the oxidative deamination and cross-linking are exclusive to the beta chains. Recombinant hemoglobin mutants have been created to identify protein sequence requirements for these reactions. It was found that His-2 of the beta globin is required for redox active Ni(II) complexation, oxidative deamination, and cross-linking. The oxidative deamination results in the formation of a free carbonyl in place of the NH2-terminal amine of the beta chain. Most cross-linking of the beta globin occurs intramolecularly, forming beta globin dimers. Structural characterization of the beta globin dimers indicates the presence of heterogeneous cross-links within the central hemoglobin cavity between the NH2 terminus of one beta chain and the COOH-terminal region of the other.
Collapse
Affiliation(s)
- J Levine
- Somatogen Inc., Boulder, Colorado 80301, USA
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Weickert MJ, Apostol I. High-fidelity translation of recombinant human hemoglobin in Escherichia coli. Appl Environ Microbiol 1998; 64:1589-93. [PMID: 9572921 PMCID: PMC106200 DOI: 10.1128/aem.64.5.1589-1593.1998] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coexpression of di-alpha-globin and beta-globin in Escherichia coli in the presence of exogenous heme yielded high levels of soluble, functional recombinant human hemoglobin (rHb1.1). High-level expression of rHb1.1 provides a good model for measuring mistranslation in heterologous proteins. rHb1.1 does not contain isoleucine; therefore, any isoleucine present could be attributed to mistranslation, most likely mistranslation of one or more of the 200 codons that differ from an isoleucine codon by 1 bp. Sensitive amino acid analysis of highly purified rHb1.1 typically revealed < or = 0.2 mol of isoleucine per mol of hemoglobin. This corresponds to a translation error rate of < or = 0.001, which is not different from typical translation error rates found for E. coli proteins. Two different expression systems that resulted in accumulation of globin proteins to levels equivalent to approximately 20% of the level of E. coli soluble proteins also resulted in equivalent translational fidelity.
Collapse
|
36
|
Apostol I, Levine J, Lippincott J, Leach J, Hess E, Glascock CB, Weickert MJ, Blackmore R. Incorporation of norvaline at leucine positions in recombinant human hemoglobin expressed in Escherichia coli. J Biol Chem 1997; 272:28980-8. [PMID: 9360970 DOI: 10.1074/jbc.272.46.28980] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report here a novel finding that norvaline can be incorporated in place of leucine in recombinant human hemoglobin expressed in Escherichia coli. The presence of the norvaline was confirmed by several analytical methods such as amino acid analysis, peptide mapping, electrospray mass spectrometry, and Edman protein sequencing. It appears that substitution is distributed across both the beta- and di-alpha-globins in purified recombinant hemoglobin. The level of misincorporation correlated with the ratio of the free norvaline/leucine pool available in the cell culture. This suggests that the incorporation of norvaline for leucine occurs through misaminoacylation of tRNALeu, similar to the misincorporation of norleucine for methionine found in many recombinant proteins expressed in E. coli.
Collapse
Affiliation(s)
- I Apostol
- Somatogen, Inc., Boulder, Colorado 80301, USA
| | | | | | | | | | | | | | | |
Collapse
|