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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [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: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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2
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Bilbrough T, Piemontese E, Seitz O. Dissecting the role of protein phosphorylation: a chemical biology toolbox. Chem Soc Rev 2022; 51:5691-5730. [PMID: 35726784 DOI: 10.1039/d1cs00991e] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.
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Affiliation(s)
- Tim Bilbrough
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Emanuele Piemontese
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
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3
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Kim C, Roh B, Lee HG. Restoration of catalytic activity by the preservation of ligand structure: Cu-catalysed asymmetric conjugate addition with 1,1-diborylmethane. Chem Sci 2021; 12:3668-3673. [PMID: 34163641 PMCID: PMC8179450 DOI: 10.1039/d0sc06543a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/21/2021] [Indexed: 11/21/2022] Open
Abstract
Reported herein is a novel reaction engineering protocol to enhance the efficiency of a transition metal-catalysed process by strategically preventing ligand degradation. Based on spectroscopic investigations, a decomposition pathway of a chiral phosphoramidite ligand during a Cu-catalysed reaction was identified. The involvement of the destructive process could be minimized under the modified reaction conditions that control the amount of nucleophilic alkoxide base, which is the origin of ligand decomposition. Overall, the strategy has been successfully applied to a new class of asymmetric conjugate addition reactions with bis[(pinacolato)boryl]methane, in which α,β-unsaturated enones are utilised as substrates.
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Affiliation(s)
- Changhee Kim
- Department of Chemistry, Seoul National University Seoul 08826 Republic of Korea
| | - Byeongdo Roh
- Department of Chemistry, Seoul National University Seoul 08826 Republic of Korea
| | - Hong Geun Lee
- Department of Chemistry, Seoul National University Seoul 08826 Republic of Korea
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4
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Makukhin N, Ciulli A. Recent advances in synthetic and medicinal chemistry of phosphotyrosine and phosphonate-based phosphotyrosine analogues. RSC Med Chem 2020; 12:8-23. [PMID: 34041480 PMCID: PMC8130623 DOI: 10.1039/d0md00272k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/30/2020] [Indexed: 11/21/2022] Open
Abstract
Phosphotyrosine-containing compounds attract significant attention due to their potential to modulate signalling pathways by binding to phospho-writers, erasers and readers such as SH2 and PTB domain containing proteins. Phosphotyrosine derivatives provide useful chemical tools to study protein phosphorylation/dephosphorylation, and as such represent attractive starting points for the development of binding ligands and chemical probes to study biology, and for inhibitor and degrader drug design. To overcome enzymatic lability of the phosphate group, physiologically stable phosphonate-based phosphotyrosine analogues find utility in a wide range of applications. This review covers advances over the last decade in the design of phosphotyrosine and its phosphonate-based derivatives, highlights the improved and expanded synthetic toolbox, and illustrates applications in medicinal chemistry.
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Affiliation(s)
- Nikolai Makukhin
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
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5
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Fallek A, Weiss-Shtofman M, Kramer M, Dobrovetsky R, Portnoy M. Phosphorylation Organocatalysts Highly Active by Design. Org Lett 2020; 22:3722-3727. [PMID: 32319783 DOI: 10.1021/acs.orglett.0c01226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The activity of nucleophilic organocatalysts for alcohol/phenol phosphorylation was enhanced through attaching oligoether appendages to a benzyl substituent on imidazole- or aminopyridine-based active units, presumably because of stabilizing n-cation interactions of the ethereal oxygens with the positively charged aza-heterocycle in the catalytic intermediates, and was substantially higher than that of known benchmark catalysts for a range of substrates. Density functional theory calculations and the study of analogues having a lower potential for such stabilizing interactions support our hypothesis.
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Affiliation(s)
- Amit Fallek
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Mor Weiss-Shtofman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Maria Kramer
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roman Dobrovetsky
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moshe Portnoy
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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6
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Harris LD, Harijan RK, Ducati RG, Evans GB, Hirsch BM, Schramm VL. Synthesis of bis-Phosphate Iminoaltritol Enantiomers and Structural Characterization with Adenine Phosphoribosyltransferase. ACS Chem Biol 2018; 13:152-160. [PMID: 29178779 DOI: 10.1021/acschembio.7b00601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphoribosyl transferases (PRTs) are essential in nucleotide synthesis and salvage, amino acid, and vitamin synthesis. Transition state analysis of several PRTs has demonstrated ribocation-like transition states with a partial positive charge residing on the pentose ring. Core chemistry for synthesis of transition state analogues related to the 5-phospho-α-d-ribosyl 1-pyrophosphate (PRPP) reactant of these enzymes could be developed by stereospecific placement of bis-phosphate groups on an iminoaltritol ring. Cationic character is provided by the imino group and the bis-phosphates anchor both the 1- and 5-phosphate binding sites. We provide a facile synthetic path to these molecules. Cyclic-nitrone redox methodology was applied to the stereocontrolled synthesis of three stereoisomers of a selectively monoprotected diol relevant to the synthesis of transition-state analogue inhibitors. These polyhydroxylated pyrrolidine natural product analogues were bis-phosphorylated to generate analogues of the ribocationic form of 5-phosphoribosyl 1-phosphate. A safe, high yielding synthesis of the key intermediate represents a new route to these transition state mimics. An enantiomeric pair of iminoaltritol bis-phosphates (L-DIAB and D-DIAB) was prepared and shown to display inhibition of Plasmodium falciparum orotate phosphoribosyltransferase and Saccharomyces cerevisiae adenine phosphoribosyltransferase (ScAPRT). Crystallographic inhibitor binding analysis of L- and D-DIAB bound to the catalytic sites of ScAPRT demonstrates accommodation of both enantiomers by altered ring geometry and bis-phosphate catalytic site contacts.
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Affiliation(s)
- Lawrence D. Harris
- The
Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield
Rd, Lower Hutt, 5010, New Zealand
| | - Rajesh K. Harijan
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rodrigo G. Ducati
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Gary B. Evans
- The
Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield
Rd, Lower Hutt, 5010, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Brett M. Hirsch
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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7
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Engelmann BW. High-Throughput Quantification of SH2 Domain-Phosphopeptide Interactions with Cellulose-Peptide Conjugate Microarrays. Methods Mol Biol 2017; 1555:375-394. [PMID: 28092044 DOI: 10.1007/978-1-4939-6762-9_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Src Homology 2 (SH2) domain family primarily recognizes phosphorylated tyrosine (pY) containing peptide motifs. The relative affinity preferences among competing SH2 domains for phosphopeptide ligands define "specificity space," and underpins many functional pY mediated interactions within signaling networks. The degree of promiscuity exhibited and the dynamic range of affinities supported by individual domains or phosphopeptides is best resolved by a carefully executed and controlled quantitative high-throughput experiment. Here, I describe the fabrication and application of a cellulose-peptide conjugate microarray (CPCMA) platform to the quantitative analysis of SH2 domain specificity space. Included herein are instructions for optimal experimental design with special attention paid to common sources of systematic error, phosphopeptide SPOT synthesis, microarray fabrication, analyte titrations, data capture, and analysis.
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Affiliation(s)
- Brett W Engelmann
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
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8
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Murray JI, Woscholski R, Spivey AC. Highly efficient and selective phosphorylation of amino acid derivatives and polyols catalysed by 2-aryl-4-(dimethylamino)pyridine-N-oxides--towards kinase-like reactivity. Chem Commun (Camb) 2015; 50:13608-11. [PMID: 25248055 DOI: 10.1039/c4cc05388e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The chemoselective phosphorylation of hydroxyl containing amino acid derivatives and polyols by phosphoryl chlorides catalyzed by 2-aryl-4-(dimethylamino)pyridine-N-oxides is described.
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Affiliation(s)
- James I Murray
- Department of Chemistry, South Kensington Campus, Imperial College London, SW7 2AZ, UK.
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9
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Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
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10
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Qvit N. Microwave-assisted synthesis of cyclic phosphopeptide on solid support. Chem Biol Drug Des 2014; 85:300-5. [PMID: 25042903 DOI: 10.1111/cbdd.12388] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/03/2014] [Accepted: 06/26/2014] [Indexed: 12/30/2022]
Abstract
Phosphopeptides are important tools for studying intracellular signal transduction events in vitro and in vivo and are also potential drugs due to their direct competition with phosphoprotein recognition elements. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, cyclic phosphopeptide synthesis may not be straightforward due to the sterically hindered phosphorylated side-chain amino acid derivatives. One option to overcome this hurdle is to use microwave-assisted synthesis, which has been shown to increase efficiency and reduce synthesis time. Herein, a detailed protocol is provided for synthesizing cyclic phosphopeptides using automated microwave. The overall synthesis duration was reduced and yields increased compared with a manual conventional method. This method provides a general, fast and facile way to synthesize cyclic peptides, demonstrating the synthesis of cyclic phosphorylated peptides which are known to be among the most challenging to produce.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA, 94305-5174, USA
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11
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Qian WJ, Lai CC, Kelley JA, Burke TR. Design and synthesis of Fmoc-Thr[PO(OH)(OPOM)] for the preparation of peptide prodrugs containing phosphothreonine in fully protected form. Chem Biodivers 2014; 11:784-91. [PMID: 24827688 PMCID: PMC6362454 DOI: 10.1002/cbdv.201300202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Indexed: 01/11/2023]
Abstract
The design and efficient synthesis of N-Fmoc-phosphothreonine protected by a mono-(pivaloyloxy)methyl (POM) moiety at its phosphoryl group (Fmoc-Thr[PO(OH)(OPOM)]-OH, 1, is reported. This reagent is suitable for solid-phase syntheses employing acid-labile resins and Fmoc-based protocols. It allows the preparation of phosphothreonine (pThr)-containing peptides bearing bis-POM-phosphoryl protection. The methodology allows the first reported synthesis of pThr-containing polypeptides having bioreversible prodrug protection, and as such it should be useful in a variety of biological applications.
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Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Frederick, MD 21702, USA, (phone: +1-301-8465906; fax: +1-301-8466033)
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12
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Jessen HJ, Ahmed N, Hofer A. Phosphate esters and anhydrides--recent strategies targeting nature's favoured modifications. Org Biomol Chem 2014; 12:3526-30. [PMID: 24781815 DOI: 10.1039/c4ob00478g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Esters and anhydrides of phosphoric acid are essential in biology. It is very difficult to identify processes in life that do not involve these modifications and their transformation at some point. Consequently, phosphorylation chemistry is an essential methodology with significant impact on the biological sciences. This perspective gives an overview of some very recent achievements in synthetic phosphorylation chemistry and aims at identifying challenges that lie ahead.
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Affiliation(s)
- Henning J Jessen
- University of Zürich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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13
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Marmelstein AM, Yates LM, Conway JH, Fiedler D. Chemical pyrophosphorylation of functionally diverse peptides. J Am Chem Soc 2013; 136:108-11. [PMID: 24350643 DOI: 10.1021/ja411737c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A highly selective and convenient method for the synthesis of pyrophosphopeptides in solution is reported. The remarkable compatibility with functional groups (alcohol, thiol, amine, carboxylic acid) in the peptide substrates suggests that the intrinsic nucleophilicity of the phosphoserine residue is much higher than previously appreciated. Because the methodology operates in polar solvents, including water, a broad range of pyrophosphopeptides can be accessed. We envision these peptides will find widespread applications in the development of mass spectrometry and antibody-based detection methods for pyrophosphoproteins.
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Affiliation(s)
- Alan M Marmelstein
- Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
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14
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Murray JI, Spivey AC, Woscholski R. Alternative synthetic tools to phospho-specific antibodies for phosphoproteome analysis: progress and prospects. J Chem Biol 2013; 6:175-84. [PMID: 24432133 DOI: 10.1007/s12154-013-0100-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 06/18/2013] [Indexed: 12/17/2022] Open
Abstract
Signal transduction cascades in living systems are often controlled via post-translational phosphorylation and dephosphorylation of proteins. These processes are catalyzed in vivo by kinase and phosphatase enzymes, which consequently play an important role in many disease states, including cancer and immune system disorders. Current techniques for studying the phosphoproteome (isotopic labeling, chromatographic techniques, and phosphospecific antibodies), although undoubtedly very powerful, have yet to provide a generic tool for phosphoproteomic analysis despite the widespread utility such a technique would have. The use of small molecule organic catalysts that can promote selective phosphate esterification could provide a useful alternative to current state-of-the-art techniques for use in, e.g., the labeling and pull-down of phosphorylated proteins. This report reviews current techniques used for phosphoproteomic analysis and the recent use of small molecule peptide-based catalysts in phosphorylation reactions, indicating possible future applications for this type of catalyst as synthetic alternatives to phosphospecific antibodies for phosphoproteome analysis.
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Affiliation(s)
- James I Murray
- Department of Chemistry, Imperial College London, London, SW7 2AZ UK
| | - Alan C Spivey
- Department of Chemistry, Imperial College London, London, SW7 2AZ UK
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15
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Abstract
Phosphopeptides are generally prepared by incorporation of suitable, protected phosphoamino acid derivatives during peptide synthesis using routine coupling protocols. The feasibility of chemical synthesis of phosphorylated peptides by Fmoc-SPPS was greatly enhanced by the introduction of the monobenzyl protecting group for the phosphate group. This minimized β-elimination of the phosphate group and made Fmoc-based synthesis of phosphopeptides the preferred synthesis strategy. Described here is our strategy for the synthesis of phosphopeptides attached to the solid support PEGA via a backbone amide linker type. This linker allows removal of side-chain protection groups without releasing the phosphopeptide from the solid support, thus enabling solid-phase-based pull-down reactions and peptide-protein interaction studies.
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16
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Chen S, Zhang J, Lumley L, Cashman JR. Immunodetection of serum albumin adducts as biomarkers for organophosphorus exposure. J Pharmacol Exp Ther 2012. [PMID: 23192655 DOI: 10.1124/jpet.112.201368] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A major challenge in organophosphate (OP) research has been the identification and utilization of reliable biomarkers for the rapid, sensitive, and efficient detection of OP exposure. Although Tyr 411 OP adducts to human serum albumin (HSA) have been suggested to be one of the most robust biomarkers in the detection of OP exposure, the analysis of HSA-OP adduct detection has been limited to techniques using mass spectrometry. Herein, we describe the procurement of two monoclonal antibodies (mAb-HSA-GD and mAb-HSA-VX) that recognized the HSA Tyr 411 adduct of soman (GD) or S-[2-(diisopropylamino)ethyl]-O-ethyl methylphosphonothioate (VX), respectively, but did not recognize nonphosphonylated HSA. We showed that mAb-HSA-GD was able to detect the HSA Tyr 411 OP adduct at a low level (i.e., human blood plasma treated with 180 nM GD) that could not be detected by mass spectrometry. mAb-HSA-GD and mAb-HSA-VX showed an extremely low-level detection of GD adducted to HSA (on the order of picograms). mAb-HSA-GD could also detect serum albumin OP adducts in blood plasma samples from different animals administered GD, including rats, guinea pigs, and monkeys. The ability of the two antibodies to selectively recognize nerve agents adducted to serum albumin suggests that these antibodies could be used to identify biomarkers of OP exposure and provide a new biologic approach to detect OP exposure in animals.
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Affiliation(s)
- Sigeng Chen
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, USA
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17
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Analysis of CaM-kinase signaling in cells. Cell Calcium 2011; 50:1-8. [PMID: 21529938 DOI: 10.1016/j.ceca.2011.02.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/15/2011] [Accepted: 02/17/2011] [Indexed: 12/18/2022]
Abstract
A change in intracellular free calcium is a common signaling mechanism that modulates a wide array of physiological processes in most cells. Responses to increased intracellular Ca(2+) are often mediated by the ubiquitous protein calmodulin (CaM) that upon binding Ca(2+) can interact with and alter the functionality of numerous proteins including a family of protein kinases referred to as CaM-kinases (CaMKs). Of particular interest are multifunctional CaMKs, such as CaMKI, CaMKII, CaMKIV and CaMKK, that can phosphorylate multiple downstream targets. This review will outline several protocols we have used to identify which members and/or isoforms of this CaMK family mediate specific cellular responses with a focus on studies in neurons. Many previous studies have relied on a single approach such as pharmacological inhibitors or transfected dominant-negative kinase constructs. Since each of these protocols has its limitations, that will be discussed, we emphasize the necessity to use multiple, independent approaches in mapping out cellular signaling pathways.
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18
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Jaradat DMM, Hamouda H, Hackenberger CPR. Solid-Phase Synthesis of Phosphoramidate-Linked Glycopeptides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000627] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Böhrsch V, Serwa R, Majkut P, Krause E, Hackenberger CPR. Site-specific functionalisation of proteins by a Staudinger-type reaction using unsymmetrical phosphites. Chem Commun (Camb) 2010; 46:3176-8. [DOI: 10.1039/b926818a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Dabkowski W, Kazimierczak Ł. O-Methyl-bis-O-(4-nitrophenyl)phosphite: a novel chemoselective O-phosphitylating reagent. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.06.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Mandal PK, Limbrick D, Coleman DR, Dyer GA, Ren Z, Birtwistle JS, Xiong C, Chen X, Briggs JM, McMurray JS. Conformationally constrained peptidomimetic inhibitors of signal transducer and activator of transcription. 3: Evaluation and molecular modeling. J Med Chem 2009; 52:2429-42. [PMID: 19334714 DOI: 10.1021/jm801491w] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Signal transducer and activator of transcription 3 (Stat3) is involved in aberrant growth and survival signals in malignant tumor cells and is a validated target for anticancer drug design. We are targeting its SH2 domain to prevent docking to cytokine and growth factor receptors and subsequent signaling. The amino acids of our lead phosphopeptide, Ac-pTyr-Leu-Pro-Gln-Thr-Val-NH(2), were replaced with conformationally constrained mimics. Structure-affinity studies led to the peptidomimetic, pCinn-Haic-Gln-NHBn (21), which had an IC(50) of 162 nM (fluorescence polarization), compared to 290 nM for the lead phosphopeptide (pCinn = 4-phosphoryloxycinnamate, Haic = (2S,5S)-5-amino-1,2,4,5,6,7-hexahydro-4-oxo-azepino[3,2,1-hi]indole-2-carboxylic acid). pCinn-Haic-Gln-OH was docked to the SH2 domain (AUTODOCK), and the two highest populated clusters were subjected to molecular dynamics simulations. Both converged to a common peptide conformation. The complex exhibits unique hydrogen bonding between Haic and Gln and Stat3 as well as hydrophobic interactions between the protein and pCinn and Haic.
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Affiliation(s)
- Pijus K Mandal
- Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
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22
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Qvit N, Hatzubai A, Shalev DE, Friedler A, Ben-Neriah Y, Gilon C. Design and synthesis of backbone cyclic phosphorylated peptides: The IkappaB model. Biopolymers 2009; 91:157-68. [PMID: 19025995 DOI: 10.1002/bip.21098] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Phosphopeptides have been used to study phosphorylation and dephosphorylation, which are key events in protein expression. Backbone cyclization has been shown to increase the stability and selectivity of peptides. Backbone cyclic peptides with conformational diversity have produced bioactive peptides with improved pharmaceutical properties, metabolic stability, and enhanced intestinal permeability. We demonstrate a successful methodology for incorporating phospho-amino acids into backbone cyclic peptides. The nuclear factor-kappa B (NF-kappaB) is a latent mammalian protein prototype of dimeric transcription factors that exists in all cell types and plays a pivotal role in a huge number of genes, such as those responsible for chronic and acute inflammatory diseases. To inhibit NF-kappaB, backbone cyclic phosphopeptides were designed and synthesized based on the conserved sequence of the Inhibitor kappa B (IkappaB). The peptides were screened for inhibiting IkappaB ubiquitylation. The best compound showed 90% inhibition at a concentration of 3 microM, and its solution structure showed similarity to a related beta-catenin protein. This general methodology can be use for synthesizing cyclic phosphorylated, as well as backbone cyclic phosphorylated peptides for various biological targets.
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Affiliation(s)
- Nir Qvit
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Israel
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Richter S, Bergmann R, Pietzsch J, Ramenda T, Steinbach J, Wuest F. Fluorine-18 labeling of phosphopeptides: A potential approach for the evaluation of phosphopeptide metabolism in vivo. Biopolymers 2009; 92:479-88. [DOI: 10.1002/bip.21263] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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van der Heden van Noort GJ, Verhagen CP, van der Horst MG, Overkleeft HS, van der Marel GA, Filippov DV. A Versatile One-Pot Procedure to Phosphate Monoesters and Pyrophosphates Using Di(p-methoxybenzyl)-N,N-diisopropylphosphoramidite. Org Lett 2008; 10:4461-4. [DOI: 10.1021/ol801608j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Carlo P. Verhagen
- Leiden Institute of Chemistry, Leiden Unversity, PO Box 9502, 2300 RA Leiden, The Netherlands
| | | | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden Unversity, PO Box 9502, 2300 RA Leiden, The Netherlands
| | | | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden Unversity, PO Box 9502, 2300 RA Leiden, The Netherlands
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25
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Eberhard H, Seitz O. N→O-Acyl shift in Fmoc-based synthesis of phosphopeptides. Org Biomol Chem 2008; 6:1349-55. [DOI: 10.1039/b718568e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Abstract
Most mammalian proteins are transiently phosphorylated on seryl, threonyl, or tyrosyl positions by kinases and dephosphorylated by phosphatases in response to specific intra- or extracellular signals. Many diseases, such as cancer, are caused by altered kinase and phosphatase activities or changed expression levels of either of these enzymes. Thus phosphopeptides are important and universal tools to study disease-specific changes, such as protein-protein/DNA interactions or hyperactive kinases, using phosphopeptides or the corresponding mimics. Here we describe two generally applicable techniques to synthesize multiply phosphorylated peptides as basic tools for drug development. The phosphopeptides were purified to homogeneity and characterized by mass spectrometry.
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Affiliation(s)
- David Singer
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany
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O’Brien-Simpson NM, Attard TJ, Loganathan A, Huq NL, Cross KJ, Riley PF, Reynolds EC. Synthesis and Characterisation of a Multiphosphorylated Phosphophoryn Repeat Motif; H-[Asp-(Ser(P))2]3-Asp-OH. Int J Pept Res Ther 2007. [DOI: 10.1007/s10989-007-9106-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Teichmann K, Winkler R, Hampel K, Trümpler A, Böhmer FD, Imhof D. Monitoring phosphatase reactions of multiple phosphorylated substrates by reversed-phase HPLC. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 853:204-13. [PMID: 17416557 DOI: 10.1016/j.jchromb.2007.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 01/26/2007] [Accepted: 03/12/2007] [Indexed: 10/23/2022]
Abstract
In an approach to gain insight into the sequence-dependent dephosphorylation of multiple phosphotyrosyl-containing peptides by the phosphatases SHP-1 and PTP1B, we applied a chromatographic technique for the analysis of the dephosphorylation products. Mono-, bi- and triphosphorylated reference peptides corresponding to positions 1999-2014 in the activation loop of the receptor tyrosine kinase Ros were first analyzed by reversed-phase HPLC and MALDI-TOF/TOF mass spectrometry. Then, the respective products from enzymatic treatment were investigated by HPLC and compared to the standard peptides. The results obtained in this study emphasize the advantage of monitoring phosphatase reactions for mono- and biphosphorylated peptides using the described procedure rather than spectrophotometric and fluorimetric methods that do not allow for a clear identification of the products formed.
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Affiliation(s)
- Kathleen Teichmann
- Institute of Biochemistry and Biophysics, Biological-Pharmaceutical Faculty, Friedrich-Schiller-University, Philosophenweg 12, D-07743 Jena, Germany
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Attard TJ, Reynolds EC, Perich JW. The synthesis of phosphopeptides via the Bpoc-based approach. Org Biomol Chem 2007; 5:664-70. [PMID: 17285175 DOI: 10.1039/b617699m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 2-(p-biphenylyl)-2-propyloxycarbonyl (Bpoc) group was examined as an N(alpha)-protecting group in the stepwise assembly of the MAP Kinase ERK2 [178-188; Thr(P)(183), Tyr(P)(185)] peptide. The mild acid deprotection of the Bpoc group permitted (i) incorporation of a fully protected phosphothreonyl derivative and (ii) a TFA-based final cleavage step. The first five C-terminal residues (184-188) were incorporated in the Fmoc mode of peptide synthesis, with all subsequent amino acids coupled as their Bpoc-Xxx-OH derivatives. The target product was obtained in high purity and yield, indicating that a Bpoc-based approach to phosphopeptide synthesis was compatible with both the acid-labile side chain protecting groups employed and Hmp-Wang resin.
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Affiliation(s)
- Troy J Attard
- Department of Chemistry, University of Melbourne, Victoria, Australia.
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Oka N, Shimizu M, Saigo K, Wada T. 1,3-Dimethyl-2-(3-nitro-1,2,4-triazol-1-yl)-2-pyrrolidin-1-yl-1,3,2-diazaphospholidinium hexafluorophosphate (MNTP): a powerful condensing reagent for phosphate and phosphonate esters. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.01.084] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Brandt M, Madsen JC, Bunkenborg J, Jensen ON, Gammeltoft S, Jensen KJ. On-Bead Chemical Synthesis and Display of Phosphopeptides for Affinity Pull-Down Proteomics. Chembiochem 2006; 7:623-30. [PMID: 16502475 DOI: 10.1002/cbic.200500378] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We describe a new method for phosphopeptide proteomics based on the solid-phase synthesis of phosphopeptides on beads suitable for affinity pull-down experiments. Peptide sequences containing the Bad Ser112 and Ser136 phosphorylation motifs were used as bait in affinity pull-down experiments to determine their ability to bind 14-3-3 proteins. Support-bound peptides were assembled directly on the solid support (PEGA) by standard solid-phase synthesis through a BAL-type handle. The peptides were varied in length and sequence. This synthetic strategy also allowed introduction of a soft electrophile (aldehyde) at the C terminus for potential activity-based proteomics. The synthetic support-bound Bad phosphopeptides were able to pull down 14-3-3zeta. Furthermore, Bad phosphopeptides bound endogenous 14-3-3 proteins, and all seven members of the 14-3-3 family were identified by mass spectrometry. In control experiments, none of the unphosphorylated Bad peptides bound transfected 14-3-3zeta or endogenous 14-3-3. We conclude that the combined synthesis and display of phosphopeptides on-bead is a fast and efficient method for affinity pull-down proteomics.
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Affiliation(s)
- Malene Brandt
- Department of Natural Sciences, Section for Bioorganic Chemistry, The Royal Veterinary and Agricultural University, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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Du JT, Li YM, Ma QF, Qiang W, Zhao YF, Abe H, Kanazawa K, Qin XR, Aoyagi R, Ishizuka Y, Nemoto T, Nakanishi H. Synthesis and conformational properties of phosphopeptides related to the human tau protein. ACTA ACUST UNITED AC 2005; 130:48-56. [PMID: 15869817 DOI: 10.1016/j.regpep.2005.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 02/20/2005] [Accepted: 03/02/2005] [Indexed: 11/16/2022]
Abstract
In the brains of Alzheimer's disease patients, the tau protein dissociates from the axonal microtubule and abnormally aggregates to form a paired helical filament (PHF). One of the priorities in Alzheimer research is to determine the effects of abnormal phosphorylation on the local structure. A series of peptides corresponding to isolated regions of tau protein have been successfully synthesized using Fmoc-based chemistry and their conformations were determined by 1H NMR spectroscopy and circular dichroism (CD) spectroscopy. Immunodominant peptides corresponding to tau-(256-273), tau-(350-367) and two phosphorylated derivatives in which a single Ser was phosphorylated at positions 262 and 356, respectively, were the main focus of the study. A direct alteration of the local structure after phosphorylation constitutes a new strategy through which control of biological activity can be enforced. In our study on Ser262 in R1 peptide and Ser356 in R4 peptide, phosphorylation modifies both the negative charge and the local conformation nearby the phosphorylation sites. Together, these structural changes indicate that phosphorylation may act as a conformational switch in the binding domain of tau protein to alter specificity and affinity of binding to microtubule, particularly in response to the abnormal phosphorylation events associated with Alzheimer's disease.
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Affiliation(s)
- Jin-Tang Du
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, PR China
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Imhof D, Nothmann D, Zoda MS, Hampel K, Wegert J, Böhmer FD, Reissmann S. Synthesis of linear and cyclic phosphopeptides as ligands for theN-terminal SH2-domain of protein tyrosine phosphatase SHP-1. J Pept Sci 2005; 11:390-400. [PMID: 15635669 DOI: 10.1002/psc.631] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Linear and cyclic phosphopeptides related to the pY2267 binding site of the epithelial receptor tyrosine kinase Ros have been synthesized as ligands for the amino-terminal SH2 (src homology) domain of protein tyrosine phosphatase SHP-1. The synthesis was accomplished by Fmoc-based solid-phase methodology using side-chain unprotected phosphotyrosine for the linear and mono-benzyl protected phosphotyrosine for the cyclic peptides. According to molecular modelling, the incorporation of a glycine residue between Lys (position pY-1 relative to phosphotyrosine) and Asp or Glu (position pY+2) was recommended for the cyclic candidates. The preparation of these peptides was successfully performed by the incorporation of a Fmoc-Xxx(Gly-OAll)-OH (Xxx = Asp, Glu) dipeptide building block that was prepared in solution prior to SPPS. The cyclization was achieved with PyBOP following Alloc/OAll-deprotection. This study demonstrates the usefulness of allyl-type protecting groups for the generation of side-chain cyclized phosphopeptides. Alloc/OAll-deprotection and cyclization are compatible with phosphorylated tyrosine.
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Affiliation(s)
- Diana Imhof
- Institute of Biochemistry and Biophysics, Biological-Pharmaceutical Faculty, Friedrich-Schiller-University, Philosophenweg 12, D-07743 Jena, Germany.
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