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Turner AH, Lebhar MS, Proctor A, Wang Q, Lawrence DS, Allbritton NL. Rational Design of a Dephosphorylation-Resistant Reporter Enables Single-Cell Measurement of Tyrosine Kinase Activity. ACS Chem Biol 2016; 11:355-62. [PMID: 26587880 DOI: 10.1021/acschembio.5b00667] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Although peptide-based reporters of protein tyrosine kinase (PTK) activity have been used to study PTK enzymology in vitro, the application of these reporters to intracellular conditions is compromised by their dephosphorylation, preventing PTK activity measurements. Nonproteinogenic amino acids may be utilized to rationally design selective peptidic ligands by accessing greater chemical and structural diversity than is available using the native amino acids. We describe a peptidic reporter that, upon phosphorylation by the epidermal growth factor receptor (EGFR), is resistant to dephosphorylation both in vitro and in cellulo. The reporter contains a conformationally constrained phosphorylatable moiety (7-(S)-hydroxy-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) in the place of L-tyrosine and is efficiently phosphorylated in A431 epidermoid carcinoma cells. Dephosphorylation of the reporter occurs 3 orders of magnitude more slowly compared with that of the conventional tyrosine-containing reporter.
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Affiliation(s)
| | - Michael S. Lebhar
- Joint
Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and North Carolina State University,
Raleigh, North Carolina 27695, United States
| | | | | | | | - Nancy L. Allbritton
- Joint
Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and North Carolina State University,
Raleigh, North Carolina 27695, United States
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Bhardwaj N, Gerstein M. Relating protein conformational changes to packing efficiency and disorder. Protein Sci 2009; 18:1230-40. [PMID: 19472340 DOI: 10.1002/pro.132] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Changes in protein conformation play key roles in facilitating various biochemical processes, ranging from signaling and phosphorylation to transport and catalysis. While various factors that drive these motions such as environmental changes and binding of small molecules are well understood, specific causative effects on the structural features of the protein due to these conformational changes have not been studied on a large scale. Here, we study protein conformational changes in relation to two key structural metrics: packing efficiency and disorder. Packing has been shown to be crucial for protein stability and function by many protein design and engineering studies. We study changes in packing efficiency during conformational changes, thus extending the analysis from a static context to a dynamic perspective and report some interesting observations. First, we study various proteins that adopt alternate conformations and find that tendencies to show motion and change in packing efficiency are correlated: residues that change their packing efficiency show larger motions. Second, our results suggest that residues that show higher changes in packing during motion are located on the changing interfaces which are formed during these conformational changes. These changing interfaces are slightly different from shear or static interfaces that have been analyzed in previous studies. Third, analysis of packing efficiency changes in the context of secondary structure shows that, as expected, residues buried in helices show the least change in packing efficiency, whereas those embedded in bends are most likely to change packing. Finally, by relating protein disorder to motions, we show that marginally disordered residues which are ordered enough to be crystallized but have sequence patterns indicative of disorder show higher dislocation and a higher change in packing than ordered ones and are located mostly on the changing interfaces. Overall, our results demonstrate that between the two conformations, the cores of the proteins remain mostly intact, whereas the interfaces display the most elasticity, both in terms of disorder and change in packing efficiency. By doing a variety of tests, we also show that our observations are robust to the solvation state of the proteins.
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Affiliation(s)
- Nitin Bhardwaj
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK. DisProt: the Database of Disordered Proteins. Nucleic Acids Res 2006; 35:D786-93. [PMID: 17145717 PMCID: PMC1751543 DOI: 10.1093/nar/gkl893] [Citation(s) in RCA: 623] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Database of Protein Disorder (DisProt) links structure and function information for intrinsically disordered proteins (IDPs). Intrinsically disordered proteins do not form a fixed three-dimensional structure under physiological conditions, either in their entireties or in segments or regions. We define IDP as a protein that contains at least one experimentally determined disordered region. Although lacking fixed structure, IDPs and regions carry out important biological functions, being typically involved in regulation, signaling and control. Such functions can involve high-specificity low-affinity interactions, the multiple binding of one protein to many partners and the multiple binding of many proteins to one partner. These three features are all enabled and enhanced by protein intrinsic disorder. One of the major hindrances in the study of IDPs has been the lack of organized information. DisProt was developed to enable IDP research by collecting and organizing knowledge regarding the experimental characterization and the functional associations of IDPs. In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at .
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Affiliation(s)
- Megan Sickmeier
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of MedicineIndianapolis, IN 46202, USA
| | - Justin A. Hamilton
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of MedicineIndianapolis, IN 46202, USA
| | - Tanguy LeGall
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of MedicineIndianapolis, IN 46202, USA
| | - Vladimir Vacic
- Computer Science and Engineering, University of California RiversideRiverside, CA 92521, USA
| | - Marc S. Cortese
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of MedicineIndianapolis, IN 46202, USA
| | - Agnes Tantos
- Institute of Enzymology, Biological Research CenterHungarian Academy of Sciences, Budapest, Hungary
| | - Beata Szabo
- Institute of Enzymology, Biological Research CenterHungarian Academy of Sciences, Budapest, Hungary
| | - Peter Tompa
- Institute of Enzymology, Biological Research CenterHungarian Academy of Sciences, Budapest, Hungary
| | - Jake Chen
- School of Informatics, Indiana UniversityIndianapolis, IN 46202, USA
| | - Vladimir N. Uversky
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of MedicineIndianapolis, IN 46202, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences142292 Pushchino, Moscow Region, Russia
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple UniversityPhiladelphia, PA 19122, USA
| | - A. Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of MedicineIndianapolis, IN 46202, USA
- School of Informatics, Indiana UniversityIndianapolis, IN 46202, USA
- To whom correspondence should be addressed. Tel: +1 317 278 9650; Fax: +1 317 278 9217;
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Ruzza P, Cesaro L, Tourwé D, Calderan A, Biondi B, Maes V, Menegazzo I, Osler A, Rubini C, Guiotto A, Pinna LA, Borin G, Donella-Deana A. Spatial Conformation and Topography of the Tyrosine Aromatic Ring in Substrate Recognition by Protein Tyrosine Kinases. J Med Chem 2006; 49:1916-24. [PMID: 16539378 DOI: 10.1021/jm051080q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The side chain orientation of the tyrosine residue included in a peptide, which is an excellent substrate of Syk tyrosine kinase, was fixed in different conformations by either incorporating the tyrosine in cyclic structures (6-OH-Tic, 5-OH-Aic, and Hat derivatives) or adding a sterically bulky substituent in the tyrosine side chain moiety (beta-MeTyr). Synthetic peptides containing tyrosine analogues displaying different side chain orientations were analyzed by NMR techniques and tested as potential substrates of the nonreceptor tyrosine kinases Syk, Csk, Lyn, and Fyn. The "rotamer scan" of the phosphorylatable residue generated optimal substrates in terms of both phosphorylation efficiency and selectivity for Syk tyrosine kinase, while the peptidomimetics were not recognized by the other tyrosine kinases. In particular, l-beta-MeTyr and d-Hat containing peptides resulted to be both suitable substrates for the specific monitoring of Syk and consensus sequence scaffolds for the design of potential inhibitors highly selective for this tyrosine kinase.
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Affiliation(s)
- Paolo Ruzza
- Institute of Biomolecular Chemistry of CNR, Padova Unit, via F. Marzolo 1, 35131 Padova, Italy.
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Ruzza P, Calderan A, Donella-Deana A, Biondi B, Cesaro L, Osler A, Elardo S, Guiotto A, Pinna LA, Borin G. Conformational constraints of tyrosine in protein tyrosine kinase substrates: Information about preferred bioactive side-chain orientation. Biopolymers 2003; 71:478-88. [PMID: 14517899 DOI: 10.1002/bip.10469] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The side-chain orientation of a tyrosine residue located in a peptide, which is an excellent substrate of Syk tyrosine kinase (A. M. Brunati, A. Donella-Deana, M. Ruzzene, O. Marin, L. A. Pinna, FEBS Letters, 1995, Vol. 367, pp. 149-152), was fixed in the gauche (+) or gauche (-) conformation by using the 7-hydroxy-1,2,3,4-tetrahydro isoquinoline-3-carboxylic (Htc) structure. The tyrosine trans conformation was blocked by using an aminobenzazepine-type (Hba) structure. The proposed side-chain orientations were confirmed by the analysis of the (1)H-NMR parameters: chemical shifts, coupling constants, and nuclear Overhauser effects to the tyrosine constraints in the different analogs. This "rotamer scan" of the phosphorylatable residue allowed us to generate optimal substrates in terms of both phosphorylation efficiency and selectivity for Syk tyrosine kinase. In contrast, these conformationally restricted tyrosine analogs were not tolerated by the Src-related tyrosine kinases Lyn and c-Fgr.
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Affiliation(s)
- Paolo Ruzza
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131 Padua, Italy.
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Donella-Deana A, Ruzza P, Cesaro L, Brunati AM, Calderan A, Borin G, Pinna LA. Specific monitoring of Syk protein kinase activity by peptide substrates including constrained analogs of tyrosine. FEBS Lett 2002; 523:48-52. [PMID: 12123802 DOI: 10.1016/s0014-5793(02)02932-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The ability of Syk protein tyrosine kinase (PTK) to phosphorylate peptides, where tyrosine had been replaced by conformationally constrained analogs, has been exploited to develop highly selective substrates suitable for the specific monitoring of Syk activity. In particular we have synthesized a peptidomimetic, RRRAAEDDE(L-Htc)EEV (syktide), with the 3(S)-7-hydroxy-1,2,3,4-tetrahydroisoquinoline-3-carboxyl acid residue (L-Htc) replaced for tyrosine, which is phosphorylated by Syk with remarkable efficiency (K(cat)=73 min(-1), K(m)=11 microM), while it is not affected to any appreciable extent by a number of PTKs tested so far. These properties make syktide the first choice substrate for the specific monitoring of Syk.
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Affiliation(s)
- Arianna Donella-Deana
- Dipartimento di Chimica Biologica and Centro di Studio delle Biomembrane del CNR, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy
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Difficulties in coupling to conformationally constrained aromatic amino acids. Int J Pept Res Ther 2000. [DOI: 10.1007/bf02443583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Solid-phase synthesis of an Htc-containing dimer analog of the autophosphorylation site of pp60 src PTK: Effective acylation conditions for Htc residues. ACTA ACUST UNITED AC 2000. [DOI: 10.1007/bf02443565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ruzza P, Donella-Deana A, Calderan A, Biondi B, Pinna LA, Borin G. Synthesis and biological activities of cyclic lactam peptides as substrates for non-receptors PTKs. Int J Pept Res Ther 1999. [DOI: 10.1007/bf02443625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Separation of acidic protein tyrosine kinase substrates by strong anion-exchange chromatography. J Chromatogr A 1998. [DOI: 10.1016/s0021-9673(98)00352-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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