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Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021; 49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.
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Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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2
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Thermal dissociation of the singly protonated Arginine: Competition between side-chain and backbone fragmentation. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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3
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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4
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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5
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Frost DC, Buchberger AR, Li L. Mass Defect-Based Dimethyl Pyrimidinyl Ornithine (DiPyrO) Tags for Multiplex Quantitative Proteomics. Anal Chem 2017; 89:10798-10805. [PMID: 28795795 PMCID: PMC7491675 DOI: 10.1021/acs.analchem.7b02098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have developed a novel amine-reactive mass defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), that is compact in size, is suitable for various biological samples, and enables highly multiplexed quantification of peptides at the MS1 level without increasing mass spectral complexity. The DiPyrO tag structure incorporates heavy isotopes in a variety of configurations to impart as much as 45.3 mDa or as little as 5.8 mDa per tag between labeled peptides. Notably, peptides containing lysine are labeled with two tags, doubling the imparted mass defect to up to 90.6 mDa for the duplex tags and effectively reducing the resolving power requirement compared to previously reported mass defect-based quantification approaches. This permits current and previous generation LTQ-Orbitrap platforms to perform confident quantitative analyses of two DiPyrO-labeled samples at 100K resolving power, whereas 3-plex and 6-plex quantifications are possible at 240K and 480K resolving powers, respectively. In this work, we discuss the design and synthesis of the DiPyrO tag, characterize its effect on labeled proteome analysis by nanoLC-MS2, and demonstrate proof-of-principle applications of the duplex and triplex tags for quantitative proteomics using high-resolution MS acquisition on the Orbitrap Elite and Orbitrap Fusion Lumos.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Amanda R Buchberger
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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6
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Hsu CC, Xue L, Arrington JV, Wang P, Paez Paez JS, Zhou Y, Zhu JK, Tao WA. Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1127-1135. [PMID: 28283928 PMCID: PMC5438756 DOI: 10.1007/s13361-017-1603-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/08/2017] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events. To evaluate current mass spectrometric performance, we present here a novel method to estimate the efficiency of phosphopeptide identification by tandem mass spectrometry. Phosphopeptides were directly isolated from whole plant cell extracts, dephosphorylated, and then incubated with one of three purified kinases-casein kinase II, mitogen-activated protein kinase 6, and SNF-related protein kinase 2.6-along with 16O4- and 18O4-ATP separately for in vitro kinase reactions. Phosphopeptides were enriched and analyzed by LC-MS. The phosphopeptide identification rate was estimated by comparing phosphopeptides identified by tandem mass spectrometry with phosphopeptide pairs generated by stable isotope labeled kinase reactions. Overall, we found that current high speed and high accuracy mass spectrometers can only identify 20%-40% of total phosphopeptides primarily due to relatively poor fragmentation, additional modifications, and low abundance, highlighting the urgent need for continuous efforts to improve phosphopeptide identification efficiency. Graphical Abstract ᅟ.
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Affiliation(s)
- Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Liang Xue
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Celgene Corporation, Cambridge, MA, USA
| | - Justine V Arrington
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Pengcheng Wang
- Department of Horticulture and Landscape, Purdue University, West Lafayette, IN, 47907, USA
| | | | - Yuan Zhou
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape, Purdue University, West Lafayette, IN, 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.
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7
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Cotham VC, McGee WM, Brodbelt JS. Modulation of Phosphopeptide Fragmentation via Dual Spray Ion/Ion Reactions Using a Sulfonate-Incorporating Reagent. Anal Chem 2016; 88:8158-65. [PMID: 27467576 DOI: 10.1021/acs.analchem.6b01901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The labile nature of phosphoryl groups has presented a long-standing challenge for the characterization of protein phosphorylation via conventional mass spectrometry-based bottom-up proteomics methods. Collision-induced dissociation (CID) causes preferential cleavage of the phospho-ester bond of peptides, particularly under conditions of low proton mobility, and results in the suppression of sequence-informative fragmentation that often prohibits phosphosite determination. In the present study, the fragmentation patterns of phosphopeptides are improved through ion/ion-mediated peptide derivatization with 4-formyl-1,3-benezenedisulfonic acid (FBDSA) anions using a dual spray reactor. This approach exploits the strong electrostatic interactions between the sulfonate moieties of FBDSA and basic sites to facilitate gas-phase bioconjugation and to reduce charge sequestration and increase the yield of phosphate-retaining sequence ions upon CID. Moreover, comparative CID fragmentation analysis between unmodified phosphopeptides and those modified online with FBDSA or in solution via carbamylation and 4-sulfophenyl isothiocyanate (SPITC) provided evidence for sulfonate interference with charge-directed mechanisms that result in preferential phosphate elimination. Our results indicate the prominence of charge-directed neighboring group participation reactions involved in phosphate neutral loss, and the implementation of ion/ion reactions in a dual spray reactor setup provides a means to disrupt the interactions by competing hydrogen-bonding interactions between sulfonate groups and the side chains of basic residues.
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Affiliation(s)
- Victoria C Cotham
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - William M McGee
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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8
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Pascal BD, West GM, Scharager-Tapia C, Flefil R, Moroni T, Martinez-Acedo P, Griffin PR, Carvalloza AC. Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2133-2140. [PMID: 26265041 DOI: 10.1007/s13361-015-1229-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 06/04/2023]
Abstract
The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS(1) data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS(1) data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS(2) analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com . Graphical Abstract ᅟ.
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Affiliation(s)
- Bruce D Pascal
- Informatics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA.
| | - Graham M West
- Proteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | | | - Ricardo Flefil
- Proteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Tina Moroni
- Proteomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | | | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA
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9
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Automatisierte Detektion von Proteinphosphorylierung durch Nanoliter-Enzymreaktionen auf Mikroarrays. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Screening for protein phosphorylation using nanoscale reactions on microdroplet arrays. Angew Chem Int Ed Engl 2014; 54:1671-5. [PMID: 25504774 DOI: 10.1002/anie.201409440] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/25/2022]
Abstract
We present a novel and straightforward screening method to detect protein phosphorylations in complex protein mixtures. A proteolytic digest is separated by a conventional nanoscale liquid chromatography (nano-LC) separation and the eluate is immediately compartmentalized into microdroplets, which are spotted on a microarray MALDI plate. Subsequently, the enzyme alkaline phosphatase is applied to every second microarray spot to remove the phosphate groups from phosphorylated peptides, which results in a mass shift of n×-80 Da. The MALDI-MS scan of the microarray is then evaluated by a software algorithm to automatically identify the phosphorylated peptides by exploiting the characteristic chromatographic peak profile induced by the phosphatase treatment. This screening method does not require extensive MS/MS experiments or peak list evaluation and can be easily extended to other enzymatic or chemical reactions.
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Affiliation(s)
- Simon K Küster
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich (Switzerland)
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11
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A sensitive quantification of the peptide apidaecin 1 isoforms in single bee tissues using a weak cation exchange pre-separation and nanocapillary liquid chromatography coupled with mass spectrometry. J Chromatogr A 2014; 1374:134-144. [DOI: 10.1016/j.chroma.2014.11.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 11/20/2022]
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12
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Taniguchi K, Kuyama H, Kajihara S, Tanaka K. MALDI mass spectrometry-based sequence analysis of arginine-containing glycopeptides: improved fragmentation of glycan and peptide chains by modifying arginine residue. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:951-960. [PMID: 23893643 DOI: 10.1002/jms.3241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/20/2013] [Accepted: 05/27/2013] [Indexed: 06/02/2023]
Abstract
This paper describes an improved method for the sequence analysis of Arg-containing glycopeptide by MALDI mass spectrometry (MS). The method uses amino group derivatization (4-aza-6-(2,6-dimethyl-1-piperidinyl)-5-oxohexanoic acid N-succinimidyl ester) and removal (carboxypeptidase B) or modification (peptidylarginine deiminase 4) of the arginine residue of the peptide. The derivatization attaches a basic tertiary amine moiety onto the peptides, and the enzymatic treatment removes or modifies the arginine residue. Fragmentation of the resulting glycopeptide under low-energy collision-induced dissociation yielded a simplified ion series of both the glycan and the peptide that can facilitate their sequencing. The feasibility of the method was studied using α1 -acid glycoprotein-derived N-linked glycopeptides, and glycan and peptide in each glycopeptide were successfully sequenced by MALDI tandem MS (MS/MS).
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Affiliation(s)
- Kenichi Taniguchi
- Koichi Tanaka Laboratory of Advanced Science and Technology (KTLAST), Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
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13
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Encephalomyocarditis virus Leader protein hinge domain is responsible for interactions with Ran GTPase. Virology 2013; 443:177-85. [PMID: 23711384 DOI: 10.1016/j.virol.2013.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/28/2013] [Accepted: 05/02/2013] [Indexed: 11/21/2022]
Abstract
Encephalomyocarditis virus (EMCV), a Cardiovirus, initiates its polyprotein with a short 67 amino acid Leader (L) sequence. The protein acts as a unique pathogenicity factor, with anti-host activities which include the triggering of nuclear pore complex hyperphosphorylation and direct binding inhibition of the active cellular transport protein, Ran GTPase. Chemical modifications and protein mutagenesis now map the Ran binding domain to the L hinge-linker region, and in particular, to amino acids 35-40. Large deletions affecting this region were shown previously to diminish Ran binding. New point mutations, especially K35Q, D37A and W40A, preserve the intact L structure, abolish Ran binding and are deficient for nucleoporin (Nup) hyperphosphorylation. Ran itself morphs through multiple configurations, but reacts most effectively with L when in the GDP format, preferably with an empty nucleotide binding pocket. Therefore, L:Ran binding, mediated by the linker-hinge, is a required step in L-induced nuclear transport inhibition.
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14
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Nihashi Y, Miyashita M, Awane H, Miyagawa H. Differential 14N/15N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing. Mass Spectrom (Tokyo) 2013; 2:A0024. [DOI: 10.5702/massspectrometry.a0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 10/29/2013] [Indexed: 11/23/2022] Open
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Wang M, Zhang P, Zong W, Xu Q, Liu R. The charge ratio between O and N on amide bonds: a new approach to the mobile proton model. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 79:1915-1919. [PMID: 21689971 DOI: 10.1016/j.saa.2011.05.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/24/2011] [Accepted: 05/25/2011] [Indexed: 05/30/2023]
Abstract
The influence of charge distribution on the cleavage of the peptides was investigated by fragmentation efficiency curves and quantum chemical calculations in order to clarify the fragmentation mechanism in this paper. The peptide Arg-Gly-Asp-Cys (RGDC) was oxidized to change the charge distribution, but its main sequence was retained. Under this study, it was illustrated that the fragmentation of the peptide RGDC became easier with each addition of an O atom to the Cys hydrosulfide group and the relative charge ratios between O and N (QO/QN) in the amide bonds had much to do with the cleavage of the peptide RGDC. For each amide bond, the situations coincided with overall conclusion: the increase of the QO/QN values results in a higher fragmentation efficiency and vice versa. The methods which combined fragmentation efficiency curves with the charge distribution of peptides provided a way to refine the mobile proton model for peptide fragmentation and to probe the discrepant fragmentation of peptides in peptide/protein identification.
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Affiliation(s)
- Meijie Wang
- Shandong Key Laboratory of Water Pollution Control and Resource 4 Reuse, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 27# Shanda South Road, Jinan 250100, PR China
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16
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Leitner A, Sturm M, Lindner W. Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: a review. Anal Chim Acta 2011; 703:19-30. [PMID: 21843671 DOI: 10.1016/j.aca.2011.07.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/07/2011] [Accepted: 07/10/2011] [Indexed: 11/28/2022]
Abstract
Enrichment, separation and mass spectrometric analysis of biomolecules carrying a phosphate group plays an important role in current analytical chemistry. Application areas range from the preparative enrichment of phospholipids for biotechnological purposes and the separation and purification of plasmid DNA or mRNA to the specific preconcentration of phosphoproteins and -peptides to facilitate their later identification and characterization by mass spectrometry. Most of the recent improvements in this field were triggered by the need for phosphopeptide enrichment technology for the analysis of cellular protein phosphorylation events with the help of liquid chromatography-mass spectrometry. The high sensitivity of mass spectrometry and the possibility to combine this technique with different separation modes in liquid chromatography have made it the method of choice for proteome analysis. However, in the case of phosphoprotein analysis, the low abundance of the resulting phosphopeptides and their low quality fragment spectra interfere with the identification of phosphorylation events. Recent developments in phosphopeptide enrichment and fragmentation technologies successfully helped to overcome these limitations. In this review, we will focus on sample preparation techniques in the field of phosphoproteomics, but also highlight recent advancements for the analysis of other phosphorylated biomolecules.
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Palumbo AM, Smith SA, Kalcic CL, Dantus M, Stemmer PM, Reid GE. Tandem mass spectrometry strategies for phosphoproteome analysis. MASS SPECTROMETRY REVIEWS 2011; 30:600-25. [PMID: 21294150 DOI: 10.1002/mas.20310] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.
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Affiliation(s)
- Amanda M Palumbo
- Department of Chemistry, Michigan State University, East Lansing, USA
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18
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Taouatas N, Mohammed S, Heck AJR. Exploring new proteome space: combining Lys-N proteolytic digestion and strong cation exchange (SCX) separation in peptide-centric MS-driven proteomics. Methods Mol Biol 2011; 753:157-167. [PMID: 21604122 DOI: 10.1007/978-1-61779-148-2_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The current advances in mass spectrometry technology have led to the possibility of analyzing more complex biological samples such as entire proteomes. Here, we describe a new and powerful methodology that combines the use of the metalloendopeptidase Lys-N and strong cation exchange with mass spectrometric analysis. The approach described here allows one to separate peptides with different functional groups. The peptides we are able to isolate are N-terminal peptides, phosphorylated peptides with a single lysine, peptides with a single basic residue (lysine), and peptides with multiply basic residues. When this separation strategy is combined with tandem mass spectrometry that involves both collision-induced dissociation and electron transfer dissociation, one can achieve an optimal targeted strategy for proteome analysis.
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Affiliation(s)
- Nadia Taouatas
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands
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19
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Trost M, Bridon G, Desjardins M, Thibault P. Subcellular phosphoproteomics. MASS SPECTROMETRY REVIEWS 2010; 29:962-90. [PMID: 20931658 DOI: 10.1002/mas.20297] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Protein phosphorylation represents one of the most extensively studied post-translational modifications, primarily due to the emergence of sensitive methods enabling the detection of this modification both in vitro and in vivo. The availability of enrichment methods combined with sensitive mass spectrometry instrumentation has played a crucial role in uncovering the dynamic changes and the large expanding repertoire of this reversible modification. The structural changes imparted by the phosphorylation of specific residues afford exquisite mechanisms for the regulation of protein functions by modulating new binding sites on scaffold proteins or by abrogating protein-protein interactions. However, the dynamic interplay of protein phosphorylation is not occurring randomly within the cell but is rather finely orchestrated by specific kinases and phosphatases that are unevenly distributed across subcellular compartments. This spatial separation not only regulates protein phosphorylation but can also control the activity of other enzymes and the transfer of other post-translational modifications. While numerous large-scale phosphoproteomics studies highlighted the extent and diversity of phosphoproteins present in total cell lysates, the further understanding of their regulation and biological activities require a spatio-temporal resolution only achievable through subcellular fractionation. This review presents a first account of the emerging field of subcellular phosphoproteomics where cell fractionation approaches are combined with sensitive mass spectrometry methods to facilitate the identification of low abundance proteins and to unravel the intricate regulation of protein phosphorylation.
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Affiliation(s)
- Matthias Trost
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
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Sun F, Zong W, Liu R, Wang M, Zhang P, Xu Q. The relative charge ratio between C and N atoms in amide bond acts as a key factor to determine peptide fragment efficiency in different charge states. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1857-1862. [PMID: 20688527 DOI: 10.1016/j.jasms.2010.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 06/24/2010] [Accepted: 06/30/2010] [Indexed: 05/29/2023]
Abstract
The influence of charge state on the peptide dissociation behavior in tandem mass spectrometry (MS/MS) is worthy of discussion. Comparative studies of singly- and doubly-protonated peptide molecules are performed to explore the effect and mechanism of charge state on peptide fragmentation. In view of the charge-directed cleavage of protonated peptides described in the mobile proton model, radiolytic oxidation was applied to change the charge distribution of peptides but retain the sequence. Experimental studies of collision energy-dependent fragmentation efficiencies coupled with quantum chemical calculations indicated that the cleavage of ARRA and its side-chain oxidation products with oxygen atoms added followed a trend that doubly-protonated peptides fragment more easily than singly-protonated forms, while the oxidation product with the guanidine group deleted showed the opposite trend. By analyzing the charge distribution around the amide bonds, we found that the relative charge ratios between C and N atoms (Q(C)/Q(N)) in the amide bonds provided a reasonable explanation for peptide fragmentation efficiencies. An increase of the Q(C)/Q(N) value of the amide bond means that a peptide fragments more easily, and vice versa. The results described in this paper provide an experimental and calculation strategy for predicting peptide fragmentation efficiency.
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Affiliation(s)
- Feng Sun
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment and Health, Jinan, PR China
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21
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Moritz A, Li Y, Guo A, Villén J, Wang Y, MacNeill J, Kornhauser J, Sprott K, Zhou J, Possemato A, Ren JM, Hornbeck P, Cantley LC, Gygi SP, Rush J, Comb MJ. Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Sci Signal 2010; 3:ra64. [PMID: 20736484 DOI: 10.1126/scisignal.2000998] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Receptor tyrosine kinases (RTKs) activate pathways mediated by serine-threonine kinases, such as the PI3K (phosphatidylinositol 3-kinase)-Akt pathway, the Ras-MAPK (mitogen-activated protein kinase)-RSK (ribosomal S6 kinase) pathway, and the mTOR (mammalian target of rapamycin)-p70 S6 pathway, that control important aspects of cell growth, proliferation, and survival. The Akt, RSK, and p70 S6 family of protein kinases transmits signals by phosphorylating substrates on an RxRxxS/T motif (R, arginine; S, serine; T, threonine; and x, any amino acid). We developed a large-scale proteomic approach to identify more than 300 substrates of this kinase family in cancer cell lines driven by the c-Met, epidermal growth factor receptor (EGFR), or platelet-derived growth factor receptor alpha (PDGFRalpha) RTKs. We identified a subset of proteins with RxRxxS/T sites for which phosphorylation was decreased by RTK inhibitors (RTKIs), as well as by inhibitors of the PI3K, mTOR, and MAPK pathways, and we determined the effects of small interfering RNA directed against these substrates on cell viability. Phosphorylation of the protein chaperone SGTA (small glutamine-rich tetratricopeptide repeat-containing protein alpha) at serine-305 was essential for PDGFRalpha stabilization and cell survival in PDGFRalpha-dependent cancer cells. Our approach provides a new view of RTK and Akt-RSK-S6 kinase signaling, revealing previously unidentified Akt-RSK-S6 kinase substrates that merit further consideration as targets for combination therapy with RTKIs.
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22
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Ahrné E, Müller M, Lisacek F. Unrestricted identification of modified proteins using MS/MS. Proteomics 2010; 10:671-86. [PMID: 20029840 DOI: 10.1002/pmic.200900502] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins undergo PTM, which modulates their structure and regulates their function. Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap between what is currently known and what remains to be discovered. The highest throughput and most comprehensive efforts to catalogue protein mixtures have so far been using MS-based shotgun proteomics. The standard approach to analyse MS/MS data is to use Peptide Fragment Fingerprinting tools such as Sequest, MASCOT or Phenyx. These tools commonly identify 5-30% of the spectra in an MS/MS data set while only a limited list of predefined protein modifications can be screened. An important part of the unidentified spectra is likely to be spectra of peptides carrying modifications not considered in the search. Bioinformatics for PTM discovery is an active area of research. In this review we focus on software solutions developed for unrestricted identification of modifications in MS/MS data, here referred to as open modification search tools. We give an overview of the conceptually different algorithmic solutions to evaluate the large number of candidate peptides per spectrum when accounting for modifications of unrestricted size and demonstrate the value of results of large-scale open modification search studies. Efficient and easy-to-use tools for protein modification discovery should prove valuable in the quest for mapping the dynamics of proteomes.
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Affiliation(s)
- Erik Ahrné
- Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland.
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23
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Taouatas N, Heck AJR, Mohammed S. Evaluation of Metalloendopeptidase Lys-N Protease Performance under Different Sample Handling Conditions. J Proteome Res 2010; 9:4282-8. [DOI: 10.1021/pr100341e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nadia Taouatas
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and The Netherlands Proteomics Center
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and The Netherlands Proteomics Center
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and The Netherlands Proteomics Center
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Optimizing the performance of tin dioxide microspheres for phosphopeptide enrichment. Anal Chim Acta 2009; 638:51-7. [DOI: 10.1016/j.aca.2009.01.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/29/2009] [Accepted: 01/30/2009] [Indexed: 01/10/2023]
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25
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Liu J, Erassov A, Halina P, Canete M, Nguyen DV, Chung C, Cagney G, Ignatchenko A, Fong V, Emili A. Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications. Anal Chem 2008; 80:7846-54. [PMID: 18788753 DOI: 10.1021/ac8009017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tandem mass spectrometry is the prevailing approach for large-scale peptide sequencing in high-throughput proteomic profiling studies. Effective database search engines have been developed to identify peptide sequences from MS/MS fragmentation spectra. Since proteins are polymorphic and subject to post-translational modifications (PTM), however, computational methods for detecting unanticipated variants are also needed to achieve true proteome-wide coverage. Different from existing "unrestrictive" search tools, we present a novel algorithm, termed SIMS (for Sequential Motif Interval Search), that interprets pairs of product ion peaks, representing potential amino acid residues or "intervals", as a means of mapping PTMs or substitutions in a blind database search mode. An effective heuristic software program was likewise developed to evaluate, rank, and filter optimal combinations of relevant intervals to identify candidate sequences, and any associated PTM or polymorphism, from large collections of MS/MS spectra. The prediction performance of SIMS was benchmarked extensively against annotated reference spectral data sets and compared favorably with, and was complementary to, current state-of-the-art methods. An exhaustive discovery screen using SIMS also revealed thousands of previously overlooked putative PTMs in a compendium of yeast protein complexes and in a proteome-wide map of adult mouse cardiomyocytes. We demonstrate that SIMS, freely accessible for academic research use, addresses gaps in current proteomic data interpretation pipelines, improving overall detection coverage, and facilitating comprehensive investigations of the fundamental multiplicity of the expressed proteome.
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Affiliation(s)
- Jian Liu
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
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Onofrejova L, Leitner A, Lindner W. Malondialdehyde tagging improves the analysis of arginine oligomers and arginine-containing dendrimers by HPLC-MS. J Sep Sci 2008; 31:499-506. [PMID: 18210380 DOI: 10.1002/jssc.200700485] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The selective modification of arginine residues by malondialdehyde (MDA) was used to improve the mass spectrometric analysis of arginine oligomers (Arg(x), x = 4, 6, 7, 8, 9) and an arginine-containing dendrimeric peptide. MDA tagging significantly increased the hydrophobicity of the arginine side-chain and resulted in improved retention in RP HPLC of the oligoarginines using formic acid as mobile phase additive. This avoided the use of TFA to generate sufficient retention, as TFA was shown to lead to a dramatically reduced sensitivity (up to ten-fold for Arg(8) and Arg(9)) as a result of the strong signal suppression by ion pairing with multiple basic residues. MDA modification of Arg oligomers not only resulted in improved detection sensitivity for most of the peptides studied (e. g., more than six-fold for Arg(7)), but also greatly enhanced the quality of MS/MS spectra, in line with previous results for other peptides. Furthermore, MDA modification helped to identify major side products in a sample of a dendrimeric peptide, a class of peptides that is typically difficult to analyze by MS.
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Affiliation(s)
- Lucia Onofrejova
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, Vienna, Austria
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Zhang Q, Wang Y. Homeodomain-interacting protein kinase-2 (HIPK2) phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77 and modulates its DNA binding affinity. J Proteome Res 2007; 6:4711-9. [PMID: 17960875 DOI: 10.1021/pr700571d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The chromosomal high-mobility group A (HMGA) proteins, composed of HMGA1a, HMGA1b and HMGA2, play important roles in the regulation of numerous processes in eukaryotic cells, such as transcriptional regulation, DNA repair, RNA processing, and chromatin remodeling. The biological activities of HMGA1 proteins are highly regulated by their post-translational modifications (PTMs), including acetylation, methylation, and phosphorylation. Recently, it was found that the homeodomain-interacting protein kinase-2 (HIPK2), a newly identified serine/threonine kinase, co-immunoprecipitated with, and phosphorylated, HMGA1 proteins. However, the sites and the biological significance of the phosphorylation have not been elucidated. Here, we found that HIPK2 phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77, and HMGA1b at Thr-41 and Thr-66. In addition, we demonstrated that cdc2, which is known to phosphorylate HMGA1 proteins, could induce the phosphorylation of HMGA1 proteins at the same Ser/Thr sites. The two kinases, however, exhibited different site preferences for the phosphorylation: The preference for HIPK2 phosphorylation followed the order of Thr-77 > Thr-52 > Ser-35, whereas the order for cdc2 phosphorylation was Thr-52 > Thr-77 > Ser-35. Moreover, we found that the HIPK2-phosphorylated HMGA1a reduced the binding affinity of HMGA1a to human germ line promoter, and the drop in binding affinity induced by HIPK2 phosphorylation was lower than that introduced by cdc2 phosphorylation, which is consistent with the notion that the second AT-hook in HMGA1a is more important for DNA binding than the third AT-hook.
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