1
|
Freimark D, Jèrôme V, Freitag R. A GFP-based method facilitates clonal selection of transfected CHO cells. Biotechnol J 2010; 5:24-31. [DOI: 10.1002/biot.200800264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
2
|
Warbrick E. A functional analysis of PCNA-binding peptides derived from protein sequence, interaction screening and rational design. Oncogene 2006; 25:2850-9. [PMID: 16407840 PMCID: PMC2699888 DOI: 10.1038/sj.onc.1209320] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) has no intrinsic enzymatic function, but functions as a sliding platform to mediate protein interactions with the DNA strand. Many proteins interact with PCNA through a small conserved motif with consensus QxxLxxFF. This work uses Schizosaccharomyces pombe and human cells to analyse the function of PCNA-binding peptides. Interacting peptides were identified using two-hybrid screening; one (pep102) binds directly to a physiologically relevant site on PCNA. The EGFP-pep102 overexpression phenotype is consistent with competitive blocking of PCNA-protein interactions. Various PCNA-binding peptides were all shown to inhibit PCNA function by competitive binding in both human and S. pombe cells as EGFP fusion proteins. The action of a p21(WAF1/Cip1)-derived peptide was complicated by the presence of additional functional domains and possible post-translational modification. The activity of pep102 was hampered by low expression in both model systems. The peptide derived from rational design (con1) was stable, highly active in inhibiting PCNA function both S. pombe and human cells and showed a high affinity for PCNA both in vitro and in vivo. These results validate the use of functional screening in yeast to identify peptide aptamers that are functional in mammalian cells; such aptamers provide excellent leads for small molecule antiproliferative therapies.
Collapse
Affiliation(s)
- E Warbrick
- Department of Surgery and Molecular Oncology, University of Dundee, Ninewells Hospital and Medical School, UK.
| |
Collapse
|
3
|
Naumann TA, Savinov SN, Benkovic SJ. Engineering an affinity tag for genetically encoded cyclic peptides. Biotechnol Bioeng 2006; 92:820-30. [PMID: 16155946 DOI: 10.1002/bit.20644] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Peptide expression libraries are valuable probes of cellular function. SICLOPPS technology merges the principal advantages of both genetic methods and small-molecule approaches in yielding superior library sizes of operationally stable, structurally well-defined entities with an established biological and medicinal record. Here, we describe development, application, and the first-generation library implementation of an expressed affinity tag for a library of cyclic peptides. A tripeptide streptavidin-binding motif (HPQ) proved to be compatible with presentation from a backbone cyclized template. A resulting peptide was employed as a sensitive indicator of peptide splicing, expression, and recovery as well as an affinity tag for one-step purification. Specific recognition of the tag by streptavidin was also critical for an analysis of intein mutants. Finally, the initially identified probe was used as a template for design of a streptavidin-responsive cyclic peptide library.
Collapse
Affiliation(s)
- Todd A Naumann
- Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, PA 16802, USA
| | | | | |
Collapse
|
4
|
Amstutz P, Binz HK, Parizek P, Stumpp MT, Kohl A, Grütter MG, Forrer P, Plückthun A. Intracellular Kinase Inhibitors Selected from Combinatorial Libraries of Designed Ankyrin Repeat Proteins. J Biol Chem 2005; 280:24715-22. [PMID: 15851475 DOI: 10.1074/jbc.m501746200] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The specific intracellular inhibition of protein activity at the protein level allows the determination of protein function in the cellular context. We demonstrate here the use of designed ankyrin repeat proteins as tailor-made intracellular kinase inhibitors. The target was aminoglycoside phosphotransferase (3')-IIIa (APH), which mediates resistance to aminoglycoside antibiotics in pathogenic bacteria and shares structural homology with eukaryotic protein kinases. Combining a selection and screening approach, we isolated 198 potential APH inhibitors from highly diverse combinatorial libraries of designed ankyrin repeat proteins. A detailed analysis of several inhibitors revealed that they bind APH with high specificity and with affinities down to the subnanomolar range. In vitro, the most potent inhibitors showed complete enzyme inhibition, and in vivo, a phenotype comparable with the gene knockout was observed, fully restoring antibiotic sensitivity in resistant bacteria. These results underline the great potential of designed ankyrin repeat proteins for modulation of intracellular protein function.
Collapse
Affiliation(s)
- Patrick Amstutz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Intrabodies: Development and Application in Functional Genomics and Therapy. Antibodies (Basel) 2004. [DOI: 10.1007/978-1-4419-8877-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
|
6
|
Poritz MA, Malmstrom S, Schmitt A, Kim MKH, Zharkikh L, Kamb A, Teng DHF. Isolation of a peptide inhibitor of human rhinovirus. Virology 2003; 313:170-83. [PMID: 12951031 DOI: 10.1016/s0042-6822(03)00301-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cell culture-based transdominant genetic techniques provide new methods for discovering peptide/RNA modulators of cellular pathways. We applied this technology to isolate a peptide inhibitor of human rhinovirus. A green fluorescent protein (GFP)-scaffolded library of cDNA fragments was expressed in HeLa cells from a retroviral vector and screened for inhibitors of rhinovirus-mediated cell killing. A DNA clone, I421, increased cell survival in an HRV14 challenge assay from less than 0.5% to greater than 60%. It encodes a 53-amino-acid C-terminal extension of the GFP scaffold. Particular subclones of Hela cells expressing I421 (exemplified by I421dp3) show a delay in virus production and a 50-fold decrease in viral RNA levels at 6-8 h postinfection. HRV2, HRV14, and HRV16 show a dramatic decrease in plaque-forming ability on I421dp3 while Coxsackievirus B3 showed a small reduction. Levels of ICAM-1, the receptor for the main rhinovirus serotype, are not altered in I421dp3.
Collapse
Affiliation(s)
- Mark A Poritz
- Deltagen Proteomics, Inc., 615 Arapeen Drive, Suite 300, Salt Lake City, UT 84108, USA.
| | | | | | | | | | | | | |
Collapse
|
7
|
Rudolph C, Schreier PH, Uhrig JF. Peptide-mediated broad-spectrum plant resistance to tospoviruses. Proc Natl Acad Sci U S A 2003; 100:4429-34. [PMID: 12682295 PMCID: PMC153572 DOI: 10.1073/pnas.0730832100] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2002] [Accepted: 02/11/2003] [Indexed: 11/18/2022] Open
Abstract
Plant viruses have a significant impact on agronomic losses worldwide. A new strategy for engineering virus-resistant plants by transgenic expression of a dominant interfering peptide is presented here. This peptide of 29 aa strongly interacts with the nucleocapsid proteins (N) of different tospoviruses. Transgenic Nicotiana benthamiana lines expressing the peptide fused to a carrier protein were challenged with five different tospoviruses that have a nucleocapsid protein interacting with the peptide. In the transgenic plants, strong resistance to tomato spotted wilt virus, tomato chlorotic spot virus, groundnut ring spot virus, and chrysanthemum stem necrosis virus was observed. This therefore demonstrates the feasibility of using peptide "aptamers" as an in vivo tool to control viral infection in higher plants.
Collapse
Affiliation(s)
- Christoph Rudolph
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | | | | |
Collapse
|
8
|
Target validation through protein-domain knockout – applications of intracellularly stable single-chain antibodies. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1477-3627(02)02172-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
9
|
Sandrock T, Poritz M, Kim M, Feldhaus MJ, Roth B, Caponigro G, Kamb A. Expression levels of transdominant peptides and proteins in Saccharomyces cerevisiae. Yeast 2002; 19:1-7. [PMID: 11754477 DOI: 10.1002/yea.795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
From libraries of peptides and protein fragments, several inhibitors that block pheromone response in Saccharomyces cerevisiae have been isolated previously. In many cases, the inhibitors are displayed as part of a scaffold, such as green fluorescent protein. Each of the inhibitors has a characteristic physiological strength or genetic penetrance. In this report, the roles of expression level and display scaffold on the activities of a subset of pheromone-response pathway inhibitors were examined. Special consideration was given to the relationship between expression levels of specific inhibitors, which may exceed 50 microM in some instances, and penetrance.
Collapse
Affiliation(s)
- Tanya Sandrock
- Deltagen Proteomics, Inc., 615 Arapeen Drive, Suite 300, Salt Lake City, UT 84108, USA.
| | | | | | | | | | | | | |
Collapse
|
10
|
Sandrock TM, Risley B, Richards BT, Poritz MA, Austin HA, Yoo S, Kim MK, Roth B, Repetny K, Hsu F, Stump M, Teng DH, Kamb A. Exogenous peptide and protein expression levels using retroviral vectors in human cells. Mol Ther 2001; 4:398-406. [PMID: 11708876 DOI: 10.1006/mthe.2001.0476] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Pseudotyped retroviral vectors combine the advantages of broad host range, high expression, stable chromosomal integration, and ease of preparation. These vectors greatly facilitate delivery into mammalian cells of sequences encoding individual peptide inhibitors-including those with therapeutic utility-and inhibitor libraries. However, retroviral vectors vary in behavior, particularly with respect to expression levels in different cell lines. Expression level is especially important in transdominant experiments because the concentration of an inhibitor (for example, an expressed peptide) is one of the key determinants in the degree of complex formation between the inhibitor and its target. Thus, inhibitor concentration should have an impact on the expressivity and/or penetrance of an induced phenotype. Here, we compare several retroviral vectors and human cell lines for relative expression levels using a green fluorescent protein reporter. We show for a subset of these lines that cellular protein concentrations produced by single-copy vectors range up to about 2 microM. We also examine other variables that contribute to expression level, such as the nature of the expressed protein's carboxy terminus. Finally, we test the effect of increased concentration on phenotype with a nine-amino-acid peptide derived from the human papilloma virus protein E7 which overcomes E7-mediated cell growth.
Collapse
Affiliation(s)
- T M Sandrock
- Deltagen Proteomics, 615 Arapeen Dr., Suite 300, Salt Lake City, UT 84108, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Abedi M, Caponigro G, Shen J, Hansen S, Sandrock T, Kamb A. Transcriptional transactivation by selected short random peptides attached to lexA-GFP fusion proteins. BMC Mol Biol 2001; 2:10. [PMID: 11580863 PMCID: PMC56998 DOI: 10.1186/1471-2199-2-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2001] [Accepted: 08/31/2001] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Transcriptional transactivation is a process with remarkable tolerance for sequence diversity and structural geometry. In studies of the features that constitute transactivating functions, acidity has remained one of the most common characteristics observed among native activation domains and activator peptides. RESULTS We performed a deliberate search of random peptide libraries for peptides capable of conferring transcriptional transactivation on the lexA DNA binding domain. Two libraries, one composed of C-terminal fusions, the other of peptide insertions within the green fluorescent protein structure, were used. We show that (i) peptide sequences other than C-terminal fusions can confer transactivation; (ii) though acidic activator peptides are more common, charge neutral and basic peptides can function as activators; and (iii) peptides as short as 11 amino acids behave in a modular fashion. CONCLUSIONS These results support the recruitment model of transcriptional activation and, combined with other studies, suggest the possibility of using activator peptides in a variety of applications, including drug development work.
Collapse
Affiliation(s)
- Majid Abedi
- Arcaris, Inc. (current name: Deltagen Proteomics, Inc.), 615 Arapeen Drive Suite 300, Salt Lake City, UT 84108, USA
| | - Giordano Caponigro
- Arcaris, Inc. (current name: Deltagen Proteomics, Inc.), 615 Arapeen Drive Suite 300, Salt Lake City, UT 84108, USA
| | - Jiaxiang Shen
- Arcaris, Inc. (current name: Deltagen Proteomics, Inc.), 615 Arapeen Drive Suite 300, Salt Lake City, UT 84108, USA
| | - Steven Hansen
- Arcaris, Inc. (current name: Deltagen Proteomics, Inc.), 615 Arapeen Drive Suite 300, Salt Lake City, UT 84108, USA
| | - Tanya Sandrock
- Arcaris, Inc. (current name: Deltagen Proteomics, Inc.), 615 Arapeen Drive Suite 300, Salt Lake City, UT 84108, USA
| | - Alexander Kamb
- Arcaris, Inc. (current name: Deltagen Proteomics, Inc.), 615 Arapeen Drive Suite 300, Salt Lake City, UT 84108, USA
| |
Collapse
|