51
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Schultz C. Molecular tools for cell and systems biology. HFSP JOURNAL 2007; 1:230-48. [PMID: 19404424 DOI: 10.2976/1.2812442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 10/24/2007] [Indexed: 01/25/2023]
Abstract
The sequencing of the genomes of key organisms and the subsequent identification of genes merely leads us to the next real challenge in modern biology-revealing the precise functions of these genes. Further, detailed knowledge of how the products of these genes behave in space and time is required, including their interactions with other molecules. In order to tackle these considerable tasks, a large and continuously expanding toolbox is required to probe the functions of proteins on a cellular level. Here, the currently available tools are described and future developments are projected. There is no doubt that only the close interplay between the life science disciplines in addition to advances in engineering will be able to meet the challenge.
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Affiliation(s)
- Carsten Schultz
- Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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52
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Young DD, Edwards WF, Lusic H, Lively MO, Deiters A. Light-triggered polymerase chain reaction. Chem Commun (Camb) 2007:462-4. [PMID: 18188468 DOI: 10.1039/b715152g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemical control of the polymerase chain reaction has been achieved through the incorporation of light-triggered nucleotides into DNA.
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, USA
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53
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Lemke EA, Summerer D, Geierstanger BH, Brittain SM, Schultz PG. Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol 2007; 3:769-72. [PMID: 17965709 DOI: 10.1038/nchembio.2007.44] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 09/20/2007] [Indexed: 01/15/2023]
Abstract
We genetically encoded the photocaged amino acid 4,5-dimethoxy-2-nitrobenzylserine (DMNB-Ser) in Saccharomyces cerevisiae in response to the amber nonsense codon TAG. This amino acid was converted to serine in living cells by irradiation with relatively low-energy blue light and was used to noninvasively photoactivate phosphorylation of the transcription factor Pho4, which controls the cellular response to inorganic phosphate. When substituted at phosphoserine sites that control nuclear export of Pho4, blocks phosphorylation and subsequent export by the receptor Msn5 (ref. 2). We triggered phosphorylation of individual serine residues with a visible laser pulse and monitored nuclear export of Pho4-GFP fusion constructs in real time. We observed distinct export kinetics for differentially phosphorylated Pho4 mutants, which demonstrates dynamic regulation of Pho4 function. This methodology should also facilitate the analysis of other cellular processes involving free serine residues, including catalysis, biomolecular recognition and ion transport.
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Affiliation(s)
- Edward A Lemke
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road SR202, La Jolla, California 92037, USA
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54
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Chattopadhaya S, Tan LP, Yao SQ. Strategies for site-specific protein biotinylation using in vitro, in vivo and cell-free systems: toward functional protein arrays. Nat Protoc 2007; 1:2386-98. [PMID: 17406482 DOI: 10.1038/nprot.2006.338] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol details methodologies for the site-specific biotinylation of proteins using in vitro, in vivo and cell-free systems for the purpose of fabricating functional protein arrays. Biotinylation of recombinant proteins, in vitro as well as in vivo, relies on the chemoselective reaction between cysteine-biotin and a reactive thioester group at the C-terminus of a protein generated via intein-mediated cleavage. The cell-free system utilizes low concentrations of biotin-conjugated puromycin. Unlike other approaches that require tedious and costly downstream steps of protein purification, C-terminal biotinylated proteins can be captured directly onto avidin-functionalized slides from a mixture of other cellular proteins to generate the corresponding protein array. These methods were designed to maintain the integrity and activity of proteins in a microarray format, which potentially allows simultaneous functional assays of thousands of proteins. Assuming that the target proteins have been cloned into the expression vector, transformation of bacterial strain and growth of starter culture would take approximately 2 days. Expression and in vitro protein purification and biotinylation will take approximately 3 days whereas the in vivo method would take approximately 2 days. The cell-free protein biotinylation strategy requires only 6-8 h.
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Affiliation(s)
- Souvik Chattopadhaya
- Department of Biological Science, National University of Singapore, 3 Science Drive 3, Singapore 117543, Republic of Singapore
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55
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Ellis-Davies GCR. Caged compounds: photorelease technology for control of cellular chemistry and physiology. Nat Methods 2007; 4:619-28. [PMID: 17664946 PMCID: PMC4207253 DOI: 10.1038/nmeth1072] [Citation(s) in RCA: 710] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Caged compounds are light-sensitive probes that functionally encapsulate biomolecules in an inactive form. Irradiation liberates the trapped molecule, permitting targeted perturbation of a biological process. Uncaging technology and fluorescence microscopy are 'optically orthogonal': the former allows control, and the latter, observation of cellular function. Used in conjunction with other technologies (for example, patch clamp and/or genetics), the light beam becomes a uniquely powerful tool to stimulate a selected biological target in space or time. Here I describe important examples of widely used caged compounds, their design features and synthesis, as well as practical details of how to use them with living cells.
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Affiliation(s)
- Graham C R Ellis-Davies
- Department of Pharmacology & Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.
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56
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Aemissegger A, Carrigan CN, Imperiali B. Caged O-phosphorothioyl amino acids as building blocks for Fmoc-based solid phase peptide synthesis. Tetrahedron 2007; 63:6185-6190. [PMID: 19543448 DOI: 10.1016/j.tet.2007.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The synthesis of 1-(2-nitrophenylethyl) caged O-phosphorothioylserine, -threonine and -tyrosine derivatives is reported. These amino acid building blocks can be directly incorporated into peptides by Fmoc-based solid phase synthesis as their pentafluorophenyl esters or as symmetric anhydrides. Upon irradiation with UV light, the thiophosphate group, representing a hydrolysis resistant phosphate analog, is revealed.
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Affiliation(s)
- Andreas Aemissegger
- Massachusetts Institute of Technology, Department of Chemistry, 18-590, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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57
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Sohma Y, Kiso Y. "Click peptides"--chemical biology-oriented synthesis of Alzheimer's disease-related amyloid beta peptide (abeta) analogues based on the "O-acyl isopeptide method". Chembiochem 2007; 7:1549-57. [PMID: 16915597 DOI: 10.1002/cbic.200600112] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A clear understanding of the pathological mechanism of amyloid beta peptide (Abeta) 1-42, a currently unexplained process, would be of great significance for the discovery of novel drug targets for Alzheimer's disease (AD) therapy. To date, though, the elucidation of these Abeta1-42 dynamic events has been a difficult issue because of uncontrolled polymerization, which also poses a significant obstacle in establishing experimental systems with which to clarify the pathological function of Abeta1-42. We have recently developed chemical biology-oriented pH- or phototriggered "click peptide" isoform precursors of Abeta1-42, based on the "O-acyl isopeptide method", in which a native amide bond at a hydroxyamino acid residue, such as Ser, is isomerized to an ester bond, the target peptide subsequently being generated by an O-N intramolecular acyl migration reaction. These click peptide precursors did not exhibit any self-assembling character under physiological conditions, thanks to the presence of the one single ester bond, and were able to undergo migration to give the target Abeta1-42 in a quick and easy, one-way (so-called "click")conversion reaction. The use of click peptides could be a useful strategy to investigate the biological functions of Abeta1-42 in AD through inducible activation of Abeta1-42 self-assembly.
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Affiliation(s)
- Youhei Sohma
- Department of Medicinal Chemistry Center for Frontier Research in Medicinal Science 21st Century COE Program, Kyoto Pharmaceutical University Yamashina-ku, Kyoto 607-8412, Japan
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58
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Vila-Perelló M, Pratt MR, Tulin F, Muir TW. Covalent capture of phospho-dependent protein oligomerization by site-specific incorporation of a diazirine photo-cross-linker. J Am Chem Soc 2007; 129:8068-9. [PMID: 17567014 PMCID: PMC3242410 DOI: 10.1021/ja072013j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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59
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Abstract
Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.
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Affiliation(s)
- Günter Mayer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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60
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Sohma Y, Yoshiya T, Taniguchi A, Kimura T, Hayashi Y, Kiso Y. Development of O-acyl isopeptide method. Biopolymers 2007; 88:253-62. [PMID: 17236207 DOI: 10.1002/bip.20683] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
During over a decade of study on aspartic protease inhibitors and water-soluble prodrugs, in 2003, we discovered that the presence of an O-acyl instead of N-acyl residue within the peptide backbone significantly changed the secondary structure of the native peptide. In addition, the target peptide was subsequently generated by an O-N intramolecular acyl migration reaction. These findings led to the development of a novel method, called "O-acyl isopeptide method," for the synthesis of peptides containing difficult sequence. Further application of the method to Alzheimer's Abeta1-42 revealed that the O-acyl isopeptide of Abeta1-42 could be effectively synthesized and stored without spontaneous self-assembly. Intact monomer Abeta1-42 could then be obtained from the isopeptide under physiological experimental conditions. We named the O-acyl isopeptide as "Click Peptide," because of its "quick and easy one-way conversion" to the parent Abeta1- 42. Application of the click peptide has provided a new basis for the investigation of the biological functions of Abeta1-42 by inducible activation of its self-assembly. The O-acyl isopeptide method has further evolved as a general method for peptides synthesis with our recent developments of "O-acyl isodipeptide units" and "racemization-free segment condensation methodology." Isodipeptide units have enabled routine use of the O-acyl isopeptide method by avoiding the often difficult esterification reaction on resin. "Racemizationfree segment condensation methodology" has been achieved by employing N-segments possessing a C-terminal urethaneprotected O-acyl Ser/Thr residues. The synthesis of long peptides/proteins by racemization-free segment condensation has thus become possible at Ser/Thr residues instead of Cterminal Gly/Pro residues. As the O-acyl isopeptide method becomes more widely utilized, we have composed this review to facilitate its application for the production of peptides and proteins.
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Affiliation(s)
- Youhei Sohma
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Kyoto, Japan
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61
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Vogel EM, Imperiali B. Semisynthesis of unnatural amino acid mutants of paxillin: protein probes for cell migration studies. Protein Sci 2007; 16:550-6. [PMID: 17242376 PMCID: PMC2203312 DOI: 10.1110/ps.062549407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Caged phosphopeptides and phosphoproteins are valuable tools for dissecting the dynamic role of phosphorylation in complex signaling networks with temporal and spatial control. Demonstrating the broad scope of phosphoamino acid caging for studying signaling events, we report here the semisynthesis of a photolabile precursor to the cellular migration protein paxillin, which is a complex, multidomain phosphoprotein. This semisynthetic construct provides a powerful probe for investigating the influence that phosphorylation of paxillin at a single site has on cellular migration. The 61-kDa paxillin construct was assembled using native chemical ligation to install a caged phosphotyrosine residue at position 31 of the 557-residue protein, and the probe includes all other binding and localization determinants in the paxillin macromolecule, which are essential for creating a native environment to investigate phosphorylation. Following semisynthesis, paxillin variants were characterized through detailed biochemical analyses and by quantitative uncaging studies.
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Affiliation(s)
- Elizabeth M Vogel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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62
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Abstract
Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Campus Box 8204, Raleigh, NC 27695, USA
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63
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64
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Affiliation(s)
- Rasmus P Clausen
- Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, 2100 Copenhagen, Denmark.
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65
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Muir TW. 2005 Irving Sigal Young Investigator Award. Protein Sci 2005; 14:3140-4. [PMID: 16322585 PMCID: PMC2253235 DOI: 10.1110/ps.051848105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Tom W Muir
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
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66
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Lawrence DS. The preparation and in vivo applications of caged peptides and proteins. Curr Opin Chem Biol 2005; 9:570-5. [PMID: 16182597 DOI: 10.1016/j.cbpa.2005.09.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 09/08/2005] [Indexed: 11/21/2022]
Abstract
Cellular behavior, such as mitosis and motility, are controlled by both when and where specific intracellular signaling pathways are activated in response to environmental cues. Analogous temporally and spatially controlled events occur throughout the lifetime of an organism (e.g. embryogenesis). Consequently, reagents that can be switched on (or off) at any time or at any place in a cell, a tissue, or a living animal, represent the means by which the biochemical basis of spatially and temporally sensitive biological behavior can be evaluated. This review summarizes recent advances in the design and synthesis of light-activated ('caged') peptides and proteins as well as the application of these caged reagents to unanswered questions in biology.
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Affiliation(s)
- David S Lawrence
- Department of Biochemistry, The Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA.
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67
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Durek T, Becker CFW. Protein semi-synthesis: New proteins for functional and structural studies. ACTA ACUST UNITED AC 2005; 22:153-72. [PMID: 16188500 DOI: 10.1016/j.bioeng.2005.07.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 07/26/2005] [Accepted: 07/27/2005] [Indexed: 12/19/2022]
Abstract
Our ability to alter and control the structure and function of biomolecules, and of proteins in particular, will be of utmost importance in order to understand their respective biological roles in complex systems such as living organisms. This challenge has prompted the development of powerful modern techniques in the fields of molecular biology, physical biochemistry and chemical biology. These fields complement each other and their successful combination has provided unique insights into protein structure and function at the level of isolated molecules, cells and organisms. Chemistry is without doubt most suited for introducing subtle changes into biomolecules down to the atomic level, but often struggles when it comes to large targets, such as proteins. In this review, we attempt to give an overview of modern and broadly applicable techniques that permit chemical synthesis to be applied to complex protein targets in order to gain control over their structure and function. As will be demonstrated, these approaches offer unique possibilities in our efforts to understand the molecular basis of protein functioning in vitro and in vivo. We will discuss modern synthetic reactions that can be applied to proteins and give examples of recent highlights. Another focus of this review will be the application of inteins as versatile protein engineering tools.
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Affiliation(s)
- Thomas Durek
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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68
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Schwarzer D, Cole PA. Protein semisynthesis and expressed protein ligation: chasing a protein's tail. Curr Opin Chem Biol 2005; 9:561-9. [PMID: 16226484 DOI: 10.1016/j.cbpa.2005.09.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Accepted: 09/30/2005] [Indexed: 11/25/2022]
Abstract
The adaptation of native chemical ligation to protein semisynthesis has become a powerful way to address problems in the analysis of protein structure and function. In particular, the exploitation of nature's inteins in expressed protein ligation is now a standard approach in the study of proteins. Site-specific incorporation of unnatural amino acids, biophysical probes and post-translational modifications in proteins have led to new insights into enzyme mechanisms, protein folding, ion channel function, translation and signaling.
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Affiliation(s)
- Dirk Schwarzer
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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69
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Pellois JP, Muir TW. A Ligation and Photorelease Strategy for the Temporal and Spatial Control of Protein Function in Living Cells. Angew Chem Int Ed Engl 2005; 44:5713-7. [PMID: 16059958 DOI: 10.1002/anie.200501244] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jean-Philippe Pellois
- The Laboratory of Synthetic Protein Chemistry, The Rockefeller University, Box 223, 1230 York Avenue, New York, NY 10021, USA
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70
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Pellois JP, Muir TW. A Ligation and Photorelease Strategy for the Temporal and Spatial Control of Protein Function in Living Cells. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501244] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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71
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Abstract
Genome sequencing projects have provided researchers with an unprecedented boon of molecular information that promises to revolutionize our understanding of life and lead to new treatments of its disorders. However, genome sequences alone offer only limited insights into the biochemical pathways that determine cell and tissue function. These complex metabolic and signaling networks are largely mediated by proteins. The vast number of uncharacterized proteins found in prokaryotic and eukaryotic systems suggests that our knowledge of cellular biochemistry is far from complete. Here, we highlight a new breed of 'postgenomic' methods that aim to assign functions to proteins through the integrated application of chemical and biological techniques.
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Affiliation(s)
- Alan Saghatelian
- The Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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