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Recent Advances in Protein Caging Tools for Protein Photoactivation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In biosciences and biotechnologies, it is recently critical to promote research regarding the regulation of the dynamic functions of proteins of interest. Light-induced control of protein activity is a strong tool for a wide variety of applications because light can be spatiotemporally irradiated in high resolutions. Therefore, synthetic, semi-synthetic, and genetic engineering techniques for photoactivation of proteins have been actively developed. In this review, the conventional approaches will be outlined. As a solution for overcoming barriers in conventional ones, our recent approaches in which proteins were chemically modified with biotinylated caging reagents are introduced to photo-activate a variety of proteins without genetic engineering and elaborate optimization. This review mainly focuses on protein caging and describes the concepts underlying the development of reported approaches that can contribute to the emergence of both novel protein photo-regulating methods and their killer applications.
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2
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Gimenez D, Phelan A, Murphy CD, Cobb SL. 19F NMR as a tool in chemical biology. Beilstein J Org Chem 2021; 17:293-318. [PMID: 33564338 PMCID: PMC7849273 DOI: 10.3762/bjoc.17.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.
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Affiliation(s)
- Diana Gimenez
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| | - Aoife Phelan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
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3
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Ma Y, Yates JR. Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications? Expert Rev Proteomics 2018; 15:545-554. [PMID: 30005169 PMCID: PMC6329588 DOI: 10.1080/14789450.2018.1500902] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs). AHA-NSPs can be coupled to biotin via CuAAC-mediated click-chemistry and enriched using avidin-based affinity purification. Thus, AHA-containing proteins or peptides can be enriched and efficiently separated from the whole proteome. In this review, we describe the development of mass spectrometry (MS) based AHA strategies and discuss their potential to measure proteins involved in immune response, secretome, gut microbiome, and proteostasis as well as their potential for clinical uses. Expert commentary: AHA strategies have been used to identify synthesis activity and to compare two biological conditions in various biological model organisms. In combination with instrument development, improved sample preparation and fractionation strategies, MS-based AHA strategies have the potential for broad application, and the methods should translate into clinical use.
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Affiliation(s)
- Yuanhui Ma
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
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4
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Freidel C, Kaloyanova S, Peneva K. Chemical tags for site-specific fluorescent labeling of biomolecules. Amino Acids 2016; 48:1357-72. [DOI: 10.1007/s00726-016-2204-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/18/2016] [Indexed: 01/24/2023]
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Marsh ENG, Suzuki Y. Using (19)F NMR to probe biological interactions of proteins and peptides. ACS Chem Biol 2014; 9:1242-50. [PMID: 24762032 DOI: 10.1021/cb500111u] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorine is a valuable probe for investigating the interactions of biological molecules because of its favorable NMR characteristics, its small size, and its near total absence from biology. Advances in biosynthetic methods allow fluorine to be introduced into peptides and proteins with high precision, and the increasing sensitivity of NMR spectrometers has facilitated the use of (19)F NMR to obtain molecular-level insights into a wide range of often-complex biological interactions. Here, we summarize the advantages of solution-state (19)F NMR for studying the interactions of peptides and proteins with other biological molecules, review methods for the production of fluorine-labeled materials, and describe some representative recent examples in which (19)F NMR has been used to study conformational changes in peptides and proteins and their interactions with other biological molecules.
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Affiliation(s)
- E. Neil G. Marsh
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yuta Suzuki
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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De Rosa L, Russomanno A, Romanelli A, D’Andrea LD. Semi-synthesis of labeled proteins for spectroscopic applications. Molecules 2013; 18:440-65. [PMID: 23282535 PMCID: PMC6269674 DOI: 10.3390/molecules18010440] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 12/21/2012] [Accepted: 12/24/2012] [Indexed: 12/24/2022] Open
Abstract
Since the introduction of SPPS by Merrifield in the 60s, peptide chemists have considered the possibility of preparing large proteins. The introduction of native chemical ligation in the 90s and then of expressed protein ligation have opened the way to the preparation of synthetic proteins without size limitations. This review focuses on semi-synthetic strategies useful to prepare proteins decorated with spectroscopic probes, like fluorescent labels and stable isotopes, and their biophysical applications. We show that expressed protein ligation, combining the advantages of organic chemistry with the easy and size limitless recombinant protein expression, is an excellent strategy for the chemical synthesis of labeled proteins, enabling a single protein to be functionalized at one or even more distinct positions with different probes.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, Napoli 80134, Italy; E-Mails: (L.D.R.); (A.R.)
| | - Anna Russomanno
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, Napoli 80134, Italy; E-Mails: (L.D.R.); (A.R.)
| | - Alessandra Romanelli
- Dipartimento delle Scienze Biologiche, Università di Napoli “Federico II”, Via Mezzocannone 16, Napoli 80134, Italy; E-Mail:
| | - Luca Domenico D’Andrea
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, Napoli 80134, Italy; E-Mails: (L.D.R.); (A.R.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-081-253-6679; Fax: +39-081-253-4574
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7
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Wang C, Guo Q, Fu Y. Theoretical Analysis of the Detailed Mechanism of Native Chemical Ligation Reactions. Chem Asian J 2011; 6:1241-51. [DOI: 10.1002/asia.201000760] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Indexed: 12/22/2022]
Affiliation(s)
- Chen Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
| | - Qing‐Xiang Guo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
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8
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Li X, Lam HY, Zhang Y, Chan CK. Salicylaldehyde Ester-Induced Chemoselective Peptide Ligations: Enabling Generation of Natural Peptidic Linkages at the Serine/Threonine Sites. Org Lett 2010; 12:1724-7. [DOI: 10.1021/ol1003109] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xuechen Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hiu Yung Lam
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yinfeng Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chun Kei Chan
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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9
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Tsukiji S, Nagamune T. Sortase-mediated ligation: a gift from Gram-positive bacteria to protein engineering. Chembiochem 2009; 10:787-98. [PMID: 19199328 DOI: 10.1002/cbic.200800724] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Shinya Tsukiji
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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10
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Barry AN, Blackburn NJ. A selenocysteine variant of the human copper chaperone for superoxide dismutase. A Se-XAS probe of cluster composition at the domain 3-domain 3 dimer interface. Biochemistry 2008; 47:4916-28. [PMID: 18393442 DOI: 10.1021/bi8001049] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the semisynthesis of a selenocysteine (Sec) derivative of the human copper chaperone for superoxide dismutase, substituted with Sec at the C-terminal C246 residue. Measurements of hCCS-induced SOD1 activation were used to show that the C-terminal CXC sequence is both necessary and sufficient for EZn-SOD maturation. Therefore, an active CAU variant carrying Sec as the terminal amino acid was prepared by expressed protein ligation of a single selenocysteine amino acid to a 243-CA truncation. This reaction proceeded in high yield and generated the desired 243-CAX (X = C or U) protein with the expected mass. Se-edge XAS of the apoprotein indicated that both Se-S and Se-Se interactions were present in a 0.3:0.7 ratio, indicating an equilibrium between species with either a selenosulfide or a diselenide cross-link. After reduction on immobilized TCEP, the ligated Cys and Sec apoproteins bound up to 2.5 Cu(I) ions per hCCS monomer with both Cu and Se as constituent atoms of the cluster which forms at the domain 3 interface of a hCCS dimer. Merging of XAS data at the Cu and Se K-absorption edges provided additional details of the cluster composition, specifically the fact that both Se atoms occupied bridging positions between two Cu(I) atoms. Further, the requirement for identical Cu-Se bond lengths and Debye-Waller factors at each absorption edge allowed us to rule out simple models for the cluster composition such as a bis-Cys(Sec)-bridged dinuclear cluster and was indicative of a more complex cluster with a nuclearity of >or=3.
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Affiliation(s)
- Amanda N Barry
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Sciences University, Beaverton, Oregon 97006-8921, USA
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11
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Romanini DW, Francis MB. Attachment of Peptide Building Blocks to Proteins Through Tyrosine Bioconjugation. Bioconjug Chem 2007; 19:153-7. [DOI: 10.1021/bc700231v] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dante W. Romanini
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and Materials Sciences Division, Lawrence Berkeley National Labs, Berkeley, California 94720-1460
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and Materials Sciences Division, Lawrence Berkeley National Labs, Berkeley, California 94720-1460
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12
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Wu B, Chen J, Warren JD, Chen G, Hua Z, Danishefsky SJ. Building complex glycopeptides: Development of a cysteine-free native chemical ligation protocol. Angew Chem Int Ed Engl 2007; 45:4116-25. [PMID: 16710874 DOI: 10.1002/anie.200600538] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bin Wu
- The Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY 10021, USA
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13
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Silvaggi NR, Martin LJ, Schwalbe H, Imperiali B, Allen KN. Double-Lanthanide-Binding Tags for Macromolecular Crystallographic Structure Determination. J Am Chem Soc 2007; 129:7114-20. [PMID: 17497863 DOI: 10.1021/ja070481n] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A double-lanthanide-binding tag (dLBT), a small peptide sequence engineered to bind two lanthanide ions (e.g., Tb3+) with high affinity, was used to solve the phase problem for the structure determination of ubiquitin by the single-wavelength anomalous diffraction (SAD) method. Since the dLBT is comprised exclusively of encoded amino acids, the necessity for the incorporation of unnatural amino acids or chemical modification of the protein as a prerequisite for X-ray structure determination is eliminated. A construct encoding the dLBT as an N-terminal fusion with ubiquitin provides for facile expression and purification using standard methods. Phasing of the single-wavelength X-ray data (at 2.6 A resolution) using only the anomalous signal from the two tightly bound Tb3+ ions in the dLBT led to clear electron-density maps. Nearly 75% of the ubiquitin structure was built using automated model-building software without user intervention. It is anticipated that this technique will be broadly applicable, complementing existing macromolecular phasing methodologies. The dLBT should be particularly useful in cases where protein derivatization with heavy atoms proves to be problematic or synchrotron facilities are unavailable.
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Affiliation(s)
- Nicholas R Silvaggi
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, Massachusetts 02118, USA
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14
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Nakata E, Tsukiji S, Hamachi I. Development of New Methods to Introduce Unnatural Functional Molecules into Native Proteins for Protein Engineering. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1268] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Wu B, Chen J, Warren JD, Chen G, Hua Z, Danishefsky SJ. Building Complex Glycopeptides: Development of a Cysteine-Free Native Chemical Ligation Protocol. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600538] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Agafonov DE, Rabe KS, Grote M, Voertler CS, Sprinzl M. C-terminal modifications of a protein by UAG-encoded incorporation of puromycin during in vitro protein synthesis in the absence of release factor 1. Chembiochem 2006; 7:330-6. [PMID: 16444758 DOI: 10.1002/cbic.200500358] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Deactivation of release factor 1 by polyclonal antibodies in an in vitro translation system, which was used to express the esterase gene, led to the reversible elimination of naturally occurring termination. This technique allowed the antibiotic puromycin to be used as an acceptor substrate for the peptidyl residue in the peptidyl-transferase reaction. This resulted in more than 80 % yield of protein with C-terminally incorporated puromycin. pCpPuromycin that was either conjugated with the Cy3 fluorophor or biotin by N4 alkylation of cytosine, also acted as an acceptor substrate for the peptidyl-transferase reaction and was incorporated into the protein C terminus. The resulting conjugates possessed Cy3-specific fluorescence and affinity to streptavidin-coated surfaces, respectively. This left the enzymatic activity of the reporter protein unaffected. It was also shown that extension of puromycin on its 5'-hydroxyl end by up to ten deoxyoligonucleotides also allowed conjugation with the C terminus of in vitro translated protein when RF1-dependent termination was suppressed. However, the conjugation yield decreased upon addition of more than six nucleotides.
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Affiliation(s)
- Dmitry E Agafonov
- Fellow of the Alexander von Humboldt Foundation on leave from the Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
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18
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Vila-Perelló M, Gutiérrez Gallego R, Andreu D. A Simple Approach to Well-Defined Sugar-Coated Surfaces for Interaction Studies. Chembiochem 2005; 6:1831-8. [PMID: 16142819 DOI: 10.1002/cbic.200500125] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein-carbohydrate interactions play a crucial role in many relevant biological processes, and the development of simple and reliable tools for their study is a well-recognized need. Surface-based methods are particularly attractive because they i) can effectively mimic cell-surface recognition events, ii) allow the identification of low-affinity binders, iii) are easily adaptable to high-throughput screening, and iv) require minimal sample amounts. We describe here the design and synthesis of a peptide module that efficiently captures glycans through its reducing end, by oxime ligation. Immobilization to carboxyl-functionalized supports was thereby made possible. Chemically well-defined surfaces coated with selected glycan targets were generated by this approach for surface plasmon resonance (SPR) studies. The usefulness of the method was demonstrated in the analysis of interactions that covered a five-orders-of-magnitude affinity range; namely, the strong binding (KA approximately 10(9) M(-1)) of a well-known lectin (wheat germ agglutinin) to chitopentose (GlcNAc5), and that of the same sugar with a weak binder (KA approximately 10(4) M(-1)), HEV32--the smallest hevein domain described.
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Affiliation(s)
- Miquel Vila-Perelló
- Department of Experimental and Health Sciences, Pompeu Fabra University, Dr. Aiguader 80, 08003 Barcelona, Spain
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19
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Abstract
Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.
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Affiliation(s)
- Bradley L. Nilsson
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Matthew B. Soellner
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
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Galeazzi R, Martelli G, Natali D, Orena M, Rinaldi S. Chiral 3-hydroxypyrrolidin-2-ones. Part 2: Stereodivergent synthesis of conformationally restricted analogues of β-homoserine. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2005.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Takeda S, Tsukiji S, Nagamune T. Site-specific conjugation of oligonucleotides to the C-terminus of recombinant protein by expressed protein ligation. Bioorg Med Chem Lett 2004; 14:2407-10. [PMID: 15109622 DOI: 10.1016/j.bmcl.2004.03.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Revised: 03/08/2004] [Accepted: 03/09/2004] [Indexed: 10/26/2022]
Abstract
We developed a convenient method for synthesizing homogeneous DNA-protein conjugates. The method is based on expressed protein ligation of intein-fusion proteins and oligonucleotides derivatized with a cysteine. A range of cysteinyl oligonucleotides were synthesized by using a new reagent 1 and were successfully applied to expressed protein ligation to attach the oligonucleotides specifically at the C-terminus of a recombinant protein.
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Affiliation(s)
- Shuji Takeda
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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22
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Montanari V, Kumar K. Just Add Water: A New Fluorous Capping Reagent for Facile Purification of Peptides Synthesized on the Solid Phase. J Am Chem Soc 2004; 126:9528-9. [PMID: 15291542 DOI: 10.1021/ja0479033] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel fluorous capping reagent is introduced to facilitate purification during solid-phase peptide synthesis (SPPS). Reagent 1 is a trivalent iodonium salt that reacts vigorously with free amines to deliver a long-chain fluoroalkyl group. It has been used to tag all unreacted amines following the peptide coupling step in SPPS. The resulting fluoroalkylated amine is no longer able to couple in further peptide coupling steps and is also stable to standard peptide synthesis conditions. Deletion products are removed using flash fluorous chromatography to yield the pure, full-length peptide.
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Affiliation(s)
- Vittorio Montanari
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
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23
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Ralle M, Berry SM, Nilges MJ, Gieselman MD, van der Donk WA, Lu Y, Blackburn NJ. The Selenocysteine-Substituted Blue Copper Center: Spectroscopic Investigations of Cys112SeCys Pseudomonas aeruginosa Azurin. J Am Chem Soc 2004; 126:7244-56. [PMID: 15186162 DOI: 10.1021/ja031821h] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azurin is a small electron-transfer protein belonging to the cupredoxin family. The Cu atom is located within a trigonal plane coordinated by two histidines (His46 and His117) and a cysteine (Cys112) with two more distant ligands (Gly45 and Met121) providing axial interactions. A Cys112SeCys derivative has been prepared by expressed protein ligation, and detailed UV/vis, EPR and EXAFS studies at the Cu and Se K-edges have been carried out. Marked changes are observed between the EPR parameters of the Cys112SeCys and WT azurin derivatives, which include a 2-fold increase in A(||), a decrease in g-values, and a large increase in rhombicity of the g-tensor. The Cu-Se and Se-Cu bond lengths obtained from analysis of the Cu and Se K-EXAFS of the oxidized protein were found to be 2.30 and 2.31 A, respectively, 0.14 A longer than the Cu-S distance of the WT protein. Unexpectedly, the Cu-Se bond lengths were found to undergo only minor changes during reduction, suggesting a very similar structure in both redox states and extending the "rack" hypothesis to the Se-substituted protein.
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Affiliation(s)
- Martina Ralle
- Department of Environmental & Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006, USA
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Abstract
The proximity of the alpha-amine and beta-thiol of alpha-amino terminal-cysteine (NT-Cys) residues in peptides imparts unique chemical properties that have been exploited for inter- and intra-molecular ligation of unprotected peptides obtained through both synthetic and biological means. A reversible protecting group orthogonal to other protection strategies and reversible under mild conditions would be useful in simplifying the synthesis, cleavage, purification and handling of such NT-Cys peptides. It could also be useful for the sequential ligation of peptides. To this end, we explored tri-one chemistry and found that ninhydrin (indane-1,2,3 trione) reacted readily with cysteine or an NT-Cys-containing peptide on- or off-resin at pH 2-5 to form Ninhydrin-protected Cys (Nin-Cys) as a thiazolidine (Thz). The Thz ring, protecting both the amino and thiol groups in Nin-Cys, completely avoids the formylation and Thz side reactions found during hydrofluoric acid (HF) cleavage when N-pi-benzyloxymethyl histidine groups are present. Nin-Cys is stable during coupling reactions and various cleavage conditions with trifluoroacetic acid or HF, but is deprotected under thiolytic or reducing conditions. These properties enable a facile one-step deprotection and end-to-end-cyclization reaction of Nin-Cys peptides containing C-terminal thioesters.
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Affiliation(s)
- C T Pool
- Department of Microbiology/Immunology, Vanderbilt University, Nashville, TN, USA
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25
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Abstract
Expressed protein ligation (EPL) is a protein engineering approach that allows recombinant and synthetic polypeptides to be chemoselectively and regioselectively joined together. The approach makes the primary structure of most proteins accessible to the tools of synthetic organic chemistry, enabling the covalent structure of proteins to be modified in an unprecedented fashion. The ability to incorporate noncoded amino acids, biophysical probes, and stable isotopes into specific locations within proteins provides research tools to peer into the inner workings of these molecules. In this review I discuss the development of this technology, its broad application to biological systems, and its possible role in the area of proteomics.
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Affiliation(s)
- Tom W Muir
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
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Craik DJ, Barry DG, Clark RJ, Daly NL, Sando L. Structure‐Function Studies of the Plant Cyclotides: The Role of a Circular Protein Backbone. ACTA ACUST UNITED AC 2003. [DOI: 10.1081/txr-120026914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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27
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Michalet X, Kapanidis AN, Laurence T, Pinaud F, Doose S, Pflughoefft M, Weiss S. The power and prospects of fluorescence microscopies and spectroscopies. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2003; 32:161-82. [PMID: 12598370 DOI: 10.1146/annurev.biophys.32.110601.142525] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.
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Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, UCLA, Young Hall, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA.
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28
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Pál G, Santamaria F, Kossiakoff AA, Lu W. The first semi-synthetic serine protease made by native chemical ligation. Protein Expr Purif 2003; 29:185-92. [PMID: 12767808 DOI: 10.1016/s1046-5928(03)00022-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Selective incorporation of non-natural amino acid residues into proteins is a powerful approach to delineate structure-function relationships. Although many methodologies are available for chemistry-based protein engineering, more facile methods are needed to make this approach suitable for routine laboratory practice. Here, we describe a new strategy and provide a proof of concept for engineering semi-synthetic proteins. We chose a serine protease Streptomyces griseus trypsin (SGT) for this study to show that it is possible to efficiently couple a synthetic peptide containing a catalytically critical residue to a recombinant fragment containing the other active site residues. The 223-residue hybrid SGT molecule was prepared by fusing a chemically synthesized N-terminal peptide to a large C-terminal fragment of recombinant origin using native chemical ligation. This C-terminal polypeptide was produced from full-length SGT by cyanogen bromide cleavage at a genetically engineered Met57 position. This semi-synthetic hybrid trypsin is fully active, showing kinetics identical to the wild-type enzyme. Thus, we believe that it is an ideal model enzyme for studying the catalytic mechanisms of serine proteases by providing a straightforward approach to incorporate non-natural amino acids in the N-terminal region of the protein. In particular, this strategy will allow for replacement of the catalytic His57 residue and the buried N-terminus, which is thought to help align the active site, with synthetic analogs. Our approach relies on readily available recombinant proteins and small synthetic peptides, thus having general applications in chemical engineering of large proteins where the N-terminal region is the focal interest.
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Affiliation(s)
- Gábor Pál
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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29
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Pascal R. Catalysis through Induced Intramolecularity: What Can Be Learned by Mimicking Enzymes with Carbonyl Compounds that Covalently Bind Substrates? European J Org Chem 2003. [DOI: 10.1002/ejoc.200200530] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Robert Pascal
- Centre National de la Recherche Scientifique, UPR 9023, CCIPE, 141, Rue de la Cardonille, 34094 Montpellier Cedex 5, France
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30
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Abstract
Comprehensive proteomic analyses require new methodologies to accelerate the correlation of gene sequence with protein function. Key tools for such efforts include biophysical probes that integrate into the covalent architecture of proteins. Lanthanide-binding tags (LBTs) are expressible, multitasking fusion partners that are optimized to bind lanthanide ions and have several desirable attributes, which include long-lived luminescence, excellent X-ray scattering power for phase determination, and magnetic properties to facilitate NMR spectroscopic structure elucidation. Herein, we present peptide sequences with a 40-fold higher affinity for Tb(3+) ions and significantly brighter luminescence intensity compared with existing peptides. Incorporation of an LBT onto ubiquitin as a prototype fusion protein allows the use of powerful protein-visualization techniques, which include rapid luminescence detection of LBT-tagged proteins in SDS-PAGE gels, as well as determination of protein concentrations in complex mixtures. The LBT strategy is a new alternative for expressing fluorescent fusion proteins by routine molecular biological techniques.
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Affiliation(s)
- Katherine J Franz
- Department of Chemistry Massachusetts Institute of Technology Cambridge, MA 02139, USA
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31
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Kapanidis AN, Weiss S. Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules. J Chem Phys 2002. [DOI: 10.1063/1.1521158] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H, Soma A, Kobayashi T, Kitabatake M, Takio K, Saito K, Shirouzu M, Hirao I, Yokoyama S. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res 2002; 30:4692-9. [PMID: 12409460 PMCID: PMC135798 DOI: 10.1093/nar/gkf589] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Revised: 08/23/2002] [Accepted: 08/23/2002] [Indexed: 11/13/2022] Open
Abstract
A suppressor tRNA(Tyr) and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-L-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNA(Tyr) gene was mutated, at three positions in the D arm, to generate the internal promoter for expression. However, this tRNA, together with the cognate TyrRS, failed to exhibit suppressor activity in mammalian cells. Then, we found that amber suppression can occur with the heterologous pair of E.coli TyrRS and Bacillus stearothermophilus suppressor tRNA(Tyr), which naturally contains the promoter sequence. Furthermore, the efficiency of this suppression was significantly improved when the suppressor tRNA was expressed from a gene cluster, in which the tRNA gene was tandemly repeated nine times in the same direction. For incorporation of 3-iodo-L-tyrosine, its specific E.coli TyrRS variant, TyrRS(V37C195), which we recently created, was expressed in mammalian cells, together with the B.stearothermophilus suppressor tRNA(Tyr), while 3-iodo-L-tyrosine was supplied in the growth medium. 3-Iodo-L-tyrosine was thus incorporated into the proteins at amber positions, with an occupancy of >95%. Finally, we demonstrated conditional 3-iodo-L-tyrosine incorporation, regulated by inducible expression of the TyrRS(V37C195) gene from a tetracycline-regulated promoter.
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Affiliation(s)
- Kensaku Sakamoto
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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33
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Borodovsky A, Ovaa H, Kolli N, Gan-Erdene T, Wilkinson KD, Ploegh HL, Kessler BM. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. CHEMISTRY & BIOLOGY 2002; 9:1149-59. [PMID: 12401499 DOI: 10.1016/s1074-5521(02)00248-x] [Citation(s) in RCA: 452] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ubiquitin (Ub)-proteasome system includes a large family of deubiquitinating enzymes (DUBs). Many members are assigned to this enzyme class by sequence similarity but without evidence for biological activity. A panel of novel DUB-specific probes was generated by a chemical ligation method. These probes allowed identification of DUBs and associated components by tandem mass spectrometry, as well as rapid demonstration of enzymatic activity for gene products whose functions were inferred from primary structure. We identified 23 active DUBs in EL4 cells, including the tumor suppressor CYLD1. At least two DUBs tightly interact with the proteasome 19S regulatory complex. An OTU domain-containing protein, with no sequence homology to any known DUBs, was isolated. We show that this polypeptide reacts with the C terminus of Ub, thus demonstrating DUB-like enzymatic activity for this novel superfamily of proteases.
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Affiliation(s)
- Anna Borodovsky
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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34
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Valiyaveetil FI, MacKinnon R, Muir TW. Semisynthesis and folding of the potassium channel KcsA. J Am Chem Soc 2002; 124:9113-20. [PMID: 12149015 DOI: 10.1021/ja0266722] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this contribution we describe the semisynthesis of the potassium channel, KcsA. A truncated form of KcsA, comprising the first 125 amino acids of the 160-amino acid protein, was synthesized using expressed protein ligation. This truncated form corresponds to the entire membrane-spanning region of the protein and is similar to the construct previously used in crystallographic studies on the KcsA protein. The ligation reaction was carried out using an N-terminal recombinant peptide alpha-thioester, corresponding to residues 1-73 of KcsA, and a synthetic C-terminal peptide corresponding to residues 74-125. Chemical synthesis of the C-peptide was accomplished by optimized Boc-SPPS techniques. A dual fusion strategy, involving glutathione-S-transferase (GST) and the GyrA intein, was developed for recombinant expression of the N-peptide alpha-thioester. The fusion protein, expressed in the insoluble form as inclusion bodies, was refolded and then cleaved successively to remove the GST tag and the intein, thereby releasing the N-peptide alpha-thioester. Following chemical ligation, the KcsA polypeptide was folded into the tetrameric state by incorporation into lipid vesicles. The correctness of the folded state was verified by the ability of the KcsA tetramer to bind to agitoxin-2. To our knowledge, this work represents the first reported semisynthesis of a polytopic membrane protein and highlights the potential application of native chemical ligation and expressed protein ligation for the (semi)synthesis of integral membrane proteins.
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Affiliation(s)
- Francis I Valiyaveetil
- Howard Hughes Medical Institute, The Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, New York 10021, USA
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35
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Cobos ES, Filimonov VV, Gálvez A, Valdivia E, Maqueda M, Martínez JC, Mateo PL. The denaturation of circular enterocin AS-48 by urea and guanidinium hydrochloride. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1598:98-107. [PMID: 12147349 DOI: 10.1016/s0167-4838(02)00341-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The unfolding thermodynamics of the circular enterocin protein AS-48, produced by Enterococcus faecalis, has been studied. The native structure of the 70-amino-acid-long protein turned out to be extremely stable against heat and denaturant-induced unfolding. At pH 2.5 and low ionic strength, it denatures at 102 degrees C, while at 25 degrees C, the structure only unfolds in 6.3 M guanidinium hydrochloride (GuHCl) and does not unfold even in 8 M urea. A comparison of its thermal unfolding in water and in the presence of urea shows a good correspondence between the two deltaGw(298) values, which are about 30 kJ mol(-1) at pH 2.5 and low ionic strength. The stability of the structure is highly dependent upon ionic strength and so GuHCl acts both as a denaturant and a stabilising agent. This seems to be why the deltaGw(298) value calculated from the unfolding data in GuHCl is twice as high as in the absence of this salt. At least part of the high stability of native AS-48 can almost certainly be put down to its circular organization since other structural features are quite normal for a protein of this size.
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Affiliation(s)
- Eva S Cobos
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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36
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Markidis T, Kokotos G. Synthesis of enantiopure omega-functionalized C15 alpha-amino carboxylates. J Org Chem 2002; 67:1685-8. [PMID: 11871904 DOI: 10.1021/jo015768w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient route for the synthesis of enantiopure omega-hydroxy, omega-carboxy, omega-oxo, and omega-amino alpha-amino acids and bis-alpha-amino acids was developed. The synthesis of omega-trityloxy delta,epsilon-unsaturated alpha-amino acids was based on the Wittig reaction of methyl (2S)-2-[bis(tert-butoxycarbonyl)amino]-5-oxopentanoate with omega-trityloxy alkylidene triphenylphosphoranes. After hydrogenation, the omega-hydroxy alpha-amino acid was used as starting material for the synthesis of other omega-functionalized alpha-amino acids. The length of the side chain of alpha-amino acids or bis-alpha-amino acids depends on the starting alkanediol or dibromide used to prepare the phosphoranes.
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Affiliation(s)
- Theodoros Markidis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
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37
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Affiliation(s)
- I Giriat
- Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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38
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Shogren-Knaak MA, Alaimo PJ, Shokat KM. Recent advances in chemical approaches to the study of biological systems. Annu Rev Cell Dev Biol 2002; 17:405-33. [PMID: 11687495 DOI: 10.1146/annurev.cellbio.17.1.405] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A number of novel chemical methods for studying biological systems have recently been developed that provide a means of addressing biological questions not easily studied with other techniques. In this review, examples that highlight the development and use of such chemical approaches are discussed. Specifically, strategies for modulating protein activity or protein-protein interactions using small molecules are presented. In addition, methods for generating and utilizing novel biomolecules (proteins, oligonucleotides, oligosaccharides, and second messengers) are examined.
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Affiliation(s)
- M A Shogren-Knaak
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143-0450, USA
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39
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Kiick KL, Saxon E, Tirrell DA, Bertozzi CR. Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation. Proc Natl Acad Sci U S A 2002; 99:19-24. [PMID: 11752401 PMCID: PMC117506 DOI: 10.1073/pnas.012583299] [Citation(s) in RCA: 710] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2001] [Accepted: 10/31/2001] [Indexed: 11/18/2022] Open
Abstract
The introduction of chemically unique groups into proteins by means of non-natural amino acids has numerous applications in protein engineering and functional studies. One method to achieve this involves the utilization of a non-natural amino acid by the cell's native translational apparatus. Here we demonstrate that a methionine surrogate, azidohomoalanine, is activated by the methionyl-tRNA synthetase of Escherichia coli and replaces methionine in proteins expressed in methionine-depleted bacterial cultures. We further show that proteins containing azidohomoalanine can be selectively modified in the presence of other cellular proteins by means of Staudinger ligation with triarylphosphine reagents. Incorporation of azide-functionalized amino acids into proteins in vivo provides opportunities for protein modification under native conditions and selective labeling of proteins in the intracellular environment.
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Affiliation(s)
- Kristi L Kiick
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
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40
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Wu JW, Hu M, Chai J, Seoane J, Huse M, Li C, Rigotti DJ, Kyin S, Muir TW, Fairman R, Massagué J, Shi Y. Crystal structure of a phosphorylated Smad2. Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling. Mol Cell 2001; 8:1277-89. [PMID: 11779503 DOI: 10.1016/s1097-2765(01)00421-x] [Citation(s) in RCA: 211] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Ligand-induced phosphorylation of the receptor-regulated Smads (R-Smads) is essential in the receptor Ser/Thr kinase-mediated TGF-beta signaling. The crystal structure of a phosphorylated Smad2, at 1.8 A resolution, reveals the formation of a homotrimer mediated by the C-terminal phosphoserine (pSer) residues. The pSer binding surface on the MH2 domain, frequently targeted for inactivation in cancers, is highly conserved among the Co- and R-Smads. This finding, together with mutagenesis data, pinpoints a functional interface between Smad2 and Smad4. In addition, the pSer binding surface on the MH2 domain coincides with the surface on R-Smads that is required for docking interactions with the serine-phosphorylated receptor kinases. These observations define a bifunctional role for the MH2 domain as a pSer-X-pSer binding module in receptor Ser/Thr kinase signaling pathways.
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Affiliation(s)
- J W Wu
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA
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41
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Hamachi I, Watanabe JI, Eboshi R, Hiraoka T, Shinkai S. Incorporation of artificial receptors into a protein/peptide surface: a strategy for on/off type of switching of semisynthetic enzymes. Biopolymers 2001; 55:459-68. [PMID: 11304673 DOI: 10.1002/1097-0282(2000)55:6<459::aid-bip1021>3.0.co;2-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent developments in new bioorganic methodologies have greatly facilitated the site-specific incorporation of non-natural amino acids into the protein framework. It is now desirable for chemists to explore promising concepts based on chemistry for regulation and extension of functions of naturally occurring enzymes using non-natural molecules, in order to promote the new trends in protein/enzyme engineering. This article demonstrates that the concepts of host-guest (or supramolecular) chemistry, which have been developed over the last few decades, provide powerful tools for the artificial control of the functions of native proteins and enzymes.
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Affiliation(s)
- I Hamachi
- Department of Chemistry & Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, 812-8581, Japan.
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42
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Affiliation(s)
- T M Penning
- Department of Pharmacology, University of Pennsylvania School of Medicine, 135 John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104-6084, USA.
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43
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Affiliation(s)
- J Venkatraman
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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44
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Wang ZG, Zhang X, Visser M, Live D, Zatorski A, Iserloh U, Lloyd KO, Danishefsky SJ. Toward Fully Synthetic Homogeneous Glycoproteins: A High Mannose Core Containing Glycopeptide Carrying Full H-Type 2 Human Blood Group Specificity. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3773(20010504)40:9<1728::aid-anie17280>3.0.co;2-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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45
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Wang ZG, Zhang X, Visser M, Live D, Zatorski A, Iserloh U, Lloyd KO, Danishefsky SJ. Toward Fully Synthetic Homogeneous Glycoproteins: A High Mannose Core Containing Glycopeptide Carrying Full H-Type 2 Human Blood Group Specificity. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010504)113:9<1778::aid-ange17780>3.0.co;2-k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Camarero JA, Fushman D, Sato S, Giriat I, Cowburn D, Raleigh DP, Muir TW. Rescuing a destabilized protein fold through backbone cyclization. J Mol Biol 2001; 308:1045-62. [PMID: 11352590 DOI: 10.1006/jmbi.2001.4631] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe the physicochemical characterization of various circular and linear forms of the approximately 60 residue N-terminal Src homology 3 (SH3) domain from the murine c-Crk adapter protein. Structural, dynamic, thermodynamic, kinetic and biochemical studies reveal that backbone circularization does not prevent the adoption of the natural folded structure in any of the circular proteins. Both the folding and unfolding rate of the protein increased slightly upon circularization. Circularization did not lead to a significant thermodynamic stabilization of the full-length protein, suggesting that destabilizing enthalpic effects (e.g. strain) negate the expected favorable entropic contribution to overall stability. In contrast, we find circularization results in a dramatic stabilization of a truncated version of the SH3 domain lacking a key glutamate residue. The ability to rescue the destabilized mutant indicates that circularization may be a useful tool in protein engineering programs geared towards generating minimized proteins.
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Affiliation(s)
- J A Camarero
- The Laboratory of Synthetic Protein Chemistry, New York, NY 10021, USA
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47
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Gieselman MD, Xie L, van Der Donk WA. Synthesis of a Selenocysteine-Containing Peptide by Native Chemical Ligation. Org Lett 2001; 3:1331-4. [PMID: 11348227 DOI: 10.1021/ol015712o] [Citation(s) in RCA: 177] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction in text] A new method for the synthesis of selenocysteine derivatives and selenocysteine-containing peptides is described. Fmoc-Se-p-methoxybenzylselenocysteine (1) was prepared and used for solid-phase synthesis of peptides with an N-terminal unprotected selenocysteine. Subsequent native chemical ligation with a peptide thioester provided a 17-mer that corresponds to the C-terminus of ribonucleotide reductase with selenocysteine in place of cysteine.
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Affiliation(s)
- M D Gieselman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, USA
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48
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Zhu Y, van der Donk WA. Convergent Synthesis of Peptide Conjugates Using Dehydroalanines for Chemoselective Ligations. Org Lett 2001; 3:1189-92. [PMID: 11348191 DOI: 10.1021/ol015648a] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text]. Protein and peptide conjugates such as glycopeptides, prenylated peptides, and lipopeptides play essential roles in biology. A rapid and convergent entry into a variety of these compounds is described. The methodology involves the introduction of a dehydroalanine into peptides and subsequent chemoselective conjugate addition of an appropriate thiolate nucleophile, including farnesylthiolate or thioglycosides.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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49
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Alexandrov K, Scheidig AJ, Goody RS. Fluorescence methods for monitoring interactions of Rab proteins with nucleotides, Rab escort protein, and geranylgeranyltransferase. Methods Enzymol 2001; 329:14-31. [PMID: 11210530 DOI: 10.1016/s0076-6879(01)29062-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- K Alexandrov
- Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Dortmund 44202, Germany
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50
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Abstract
Chemical tools have proven indispensable for studies in glycobiology. Synthetic oligosaccharides and glycoconjugates provide materials for correlating structure with function. Synthetic mimics of the complex assemblies found on cell surfaces can modulate cellular interactions and are under development as therapeutic agents. Small molecule inhibitors of carbohydrate biosynthetic and processing enzymes can block the assembly of specific oligosaccharide structures. Inhibitors of carbohydrate recognition and biosynthesis can reveal the biological functions of the carbohydrate epitope and its cognate receptors. Carbohydrate biosynthetic pathways are often amenable to interception with synthetic unnatural substrates. Such metabolic interference can block the expression of oligosaccharides or alter the structures of the sugars presented on cells. Collectively, these chemical approaches are contributing great insight into the myriad biological functions of oligosaccharides.
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Affiliation(s)
- C R Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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