1
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Asar MC, Franco A, Soendergaard M. Phage Display Selection, Identification, and Characterization of Novel Pancreatic Cancer Targeting Peptides. Biomolecules 2020; 10:biom10050714. [PMID: 32380649 PMCID: PMC7277971 DOI: 10.3390/biom10050714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
Pancreatic cancer is characterized by a 5-year survival rate of 3%, in part due to inadequate detection methods. The small size of peptides offers advantages regarding molecular targeting. Thus, peptides may be used in detection of pancreatic cancer. Here, peptides that target pancreatic cancer cells were selected using phage display technology using a 15-mer fUSE5 library. Phage were pre-cleared against immortalized pancreatic cells (hTERT-HPNE), followed by selections against pancreatic cancer (Mia Paca-2) cells. Next-generation sequencing identified two peptides, MCA1 and MCA2, with a Log2 fold change (Mia Paca-2/ hTERT-HPNE) >1.5. Modified ELISA and fluorescent microscopy showed that both peptides bound significantly higher to Mia Paca-2 cells, and not to hTERT-HPNE, embryonic kidney (HEK 293), ovarian (SKOV-3) and prostate cancer (LNCaP) cell lines. Further characterization of MCA1 and MCA2 revealed EC50 values of 16.11 µM (95% CI [9.69, 26.31 µM]) and 97.01 µM (95% CI [58.64, 166.30 µM]), respectively. Based on these results, MCA1 was selected for further studies. A competitive dose response assay demonstrated specific binding and an IC50 value of 2.15 µM (95% CI [1.28, 3.62 µM]). Taken together, this study suggests that MCA1 may be used as a pancreatic cancer targeting ligand for detection of the disease.
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Affiliation(s)
- Mallika C. Asar
- Department of Chemistry, Western Illinois University, 1 University Circle, Macomb, IL 61455, USA;
| | - April Franco
- Department of Biological Sciences, Western Illinois University, 1 University Circle, Macomb, IL 61455, USA;
| | - Mette Soendergaard
- Department of Chemistry, Western Illinois University, 1 University Circle, Macomb, IL 61455, USA;
- Correspondence: ; Tel.: +1-309-298-1714
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2
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GC K, To D, Jayalath K, Abeysirigunawardena S. Discovery of a novel small molecular peptide that disrupts helix 34 of bacterial ribosomal RNA. RSC Adv 2019; 9:40268-40276. [PMID: 35542650 PMCID: PMC9076165 DOI: 10.1039/c9ra07812f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Despite the advances in modern medicine, antibiotic resistance is a persistent and growing threat to the world. Thus, the discovery and development of novel antibiotics have become crucial to combat multi-drug resistant pathogens. The goal of our research is to discover a small molecular peptide that can disrupt the synthesis of new ribosomes. Using the phage display technique, we have discovered a 7-mer peptide that binds to the second strand of 16S h34 RNA with a dissociation constant in the low micromolar range. Binding of the peptide alters RNA structure and inhibits the binding of the ribosomal RNA small subunit methyltransferase C (RsmC) enzyme that methylates the exocyclic amine of G1207. The addition of this peptide also increases the lag phase of bacterial growth. Introduction of chemical modifications to increase the binding affinity of the peptide to RNA, its uptake and stability can further improve the efficacy of the peptide as an antibiotic agent against pathogenic bacteria. Discovery of a novel heptapeptide that disrupts RNA–RNA and RNA–protein interactions in bacterial ribosome.![]()
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Affiliation(s)
- Keshav GC
- Department of Chemistry and Biochemistry
- Kent State University
- Kent
- USA
| | - Davidnhan To
- Department of Chemistry and Biochemistry
- Kent State University
- Kent
- USA
| | - Kumudie Jayalath
- Department of Chemistry and Biochemistry
- Kent State University
- Kent
- USA
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3
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Post-Transcriptional Modifications of RNA: Impact on RNA Function and Human Health. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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4
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Sherman EM, Holmes S, Ye JD. Specific RNA-binding antibodies with a four-amino-acid code. J Mol Biol 2014; 426:2145-57. [PMID: 24631830 DOI: 10.1016/j.jmb.2014.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 01/23/2023]
Abstract
Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function of these non-coding RNAs. As demonstrated for protein antigens, specific antibodies may aid in RNA crystal structure elucidation or the development of diagnostic tools and therapeutic drugs targeting disease-causing RNAs. Recent success and limitation of RNA antibody development has made it imperative to generate an effective antibody library specifically targeting RNA molecules. Adopting the reduced chemical diversity design and further restricting the interface diversity to tyrosines, serines, glycines, and arginines only, we have constructed a RNA-targeting Fab library. Phage display selection and downstream characterization showed that this library yielded high-affinity Fabs for all three RNA targets tested. Using a quantitative specificity assay, we found that these Fabs are highly specific, possibly due to the alternate codon design we used to avoid consecutive arginines in the Fab interface. In addition, the effectiveness of the minimal Fab library may challenge our view of the protein-RNA binding interface and provide a unique solution for future design of RNA-binding proteins.
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Affiliation(s)
- Eileen M Sherman
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
| | - Sean Holmes
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
| | - Jing-Dong Ye
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA.
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5
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Spears JL, Xiao X, Hall CK, Agris PF. Amino acid signature enables proteins to recognize modified tRNA. Biochemistry 2014; 53:1125-33. [PMID: 24483944 PMCID: PMC3985708 DOI: 10.1021/bi401174h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
Human tRNALys3UUU is the primer for HIV replication.
The HIV-1 nucleocapsid protein, NCp7, facilitates htRNALys3UUU recruitment from the host cell by binding to and remodeling
the tRNA structure. Human tRNALys3UUU is post-transcriptionally
modified, but until recently, the importance of those modifications
in tRNA recognition by NCp7 was unknown. Modifications such as the
5-methoxycarbonylmethyl-2-thiouridine at anticodon wobble position-34
and 2-methylthio-N6-threonylcarbamoyladenosine,
adjacent to the anticodon at position-37, are important to the recognition
of htRNALys3UUU by NCp7. Several short peptides
selected from phage display libraries were found to also preferentially
recognize these modifications. Evolutionary algorithms (Monte Carlo
and self-consistent mean field) and assisted model building with energy
refinement were used to optimize the peptide sequence in silico, while fluorescence assays were developed and conducted to verify
the in silico results and elucidate a 15-amino acid
signature sequence (R-W-Q/N-H-X2-F-Pho-X-G/A-W-R-X2-G, where X can be most amino acids, and Pho is hydrophobic)
that recognized the tRNA’s fully modified anticodon stem and
loop domain, hASLLys3UUU. Peptides of this sequence
specifically recognized and bound modified htRNALys3UUU with an affinity 10-fold higher than that of the starting
sequence. Thus, this approach provides an effective means of predicting
sequences of RNA binding peptides that have better binding properties.
Such peptides can be used in cell and molecular biology as well as
biochemistry to explore RNA binding proteins and to inhibit those
protein functions.
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Affiliation(s)
- Jessica L Spears
- The RNA Institute, University at Albany-SUNY , Life Sciences Research Building, Albany, New York 12222, United States
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6
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Graham WD, Barley-Maloney L, Stark CJ, Kaur A, Stolyarchuk K, Sproat B, Leszczynska G, Malkiewicz A, Safwat N, Mucha P, Guenther R, Agris PF. Functional recognition of the modified human tRNALys3(UUU) anticodon domain by HIV's nucleocapsid protein and a peptide mimic. J Mol Biol 2011; 410:698-715. [PMID: 21762809 PMCID: PMC3662833 DOI: 10.1016/j.jmb.2011.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/06/2011] [Accepted: 04/11/2011] [Indexed: 11/27/2022]
Abstract
The HIV-1 nucleocapsid protein, NCp7, facilitates the use of human tRNA(Lys3)(UUU) as the primer for reverse transcription. NCp7 also remodels the htRNA's amino acid accepting stem and anticodon domains in preparation for their being annealed to the viral genome. To understand the possible influence of the htRNA's unique composition of post-transcriptional modifications on NCp7 recognition of htRNA(Lys3)(UUU), the protein's binding and functional remodeling of the human anticodon stem and loop domain (hASL(Lys3)) were studied. NCp7 bound the hASL(Lys3)(UUU) modified with 5-methoxycarbonylmethyl-2-thiouridine at position-34 (mcm(5)s(2)U(34)) and 2-methylthio-N(6)-threonylcarbamoyladenosine at position-37 (ms(2)t(6)A(37)) with a considerably higher affinity than the unmodified hASL(Lys3)(UUU) (K(d)=0.28±0.03 and 2.30±0.62 μM, respectively). NCp7 denatured the structure of the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) more effectively than that of the unmodified hASL(Lys3)(UUU). Two 15 amino acid peptides selected from phage display libraries demonstrated a high affinity (average K(d)=0.55±0.10 μM) and specificity for the ASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37) comparable to that of NCp7. The peptides recognized a t(6)A(37)-modified ASL with an affinity (K(d)=0.60±0.09 μM) comparable to that for hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37), indicating a preference for the t(6)A(37) modification. Significantly, one of the peptides was capable of relaxing the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) structure in a manner similar to that of NCp7, and therefore could be used to further study protein recognition of RNA modifications. The post-transcriptional modifications of htRNA(Lys3)(UUU) have been found to be important determinants of NCp7's recognition prior to the tRNA(Lys3)(UUU) being annealed to the viral genome as the primer of reverse transcription.
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Affiliation(s)
- William D. Graham
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
| | - Lise Barley-Maloney
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
| | - Caren J. Stark
- Te RNA Institute, Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Amarpreet Kaur
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
| | - Khrystyna Stolyarchuk
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
| | - Brian Sproat
- Integrated DNA Technologies BVBA, Interleuvenlaan 12A, B-3001 Leuven, Belgium
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Technical University, Żeromskiego 116, 90-924, ŁódŸ, Poland
| | - Andrzej Malkiewicz
- Institute of Organic Chemistry, Technical University, Żeromskiego 116, 90-924, ŁódŸ, Poland
| | - Nedal Safwat
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
| | - Piotr Mucha
- Department of Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk, Poland
| | - Richard Guenther
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh NC 27695, USA
| | - Paul F. Agris
- Te RNA Institute, Biological Sciences, University at Albany, Albany, NY 12222, USA
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7
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Lamichhane TN, Abeydeera ND, Duc ACE, Cunningham PR, Chow CS. Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries. Molecules 2011; 16:1211-39. [PMID: 21278676 PMCID: PMC6259748 DOI: 10.3390/molecules16021211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 01/13/2023] Open
Abstract
Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.
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Affiliation(s)
- Tek N. Lamichhane
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | | | | | - Philip R. Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel: +1-313-577-2594; Fax: +1-313-577-8822
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8
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Scheunemann AE, Graham WD, Vendeix FAP, Agris PF. Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA. Nucleic Acids Res 2010; 38:3094-105. [PMID: 20110260 PMCID: PMC2875026 DOI: 10.1093/nar/gkp1253] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome’s subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy, calorimetry and NMR. The unmodified E. coli H69 hairpin exhibited a significantly higher affinity for neomycin B and tobramycin than for paromomycin (Kds = 0.3 ± 0.1, 0.2 ± 0.2 and 5.4 ± 1.1 µM, respectively). The binding of streptomycin was too weak to assess. In contrast to the E. coli H69, the human 28S rRNA H69 had a considerable decrease in affinity for the antibiotics, an important validation of the bacterial target. The three conserved pseudouridine modifications (Ψ1911, Ψ1915, Ψ1917) occurring in the loop of the E. coli H69 affected the dissociation constant, but not the stoichiometry for the binding of paromomycin (Kd = 2.6 ± 0.1 µM). G1906 and G1921, observed by NMR spectrometry, figured predominantly in the aminoglycoside binding to H69. The higher affinity of the E. coli H69 for neomycin B and tobramycin, as compared to paromomycin and streptomycin, indicates differences in the efficacy of the aminoglycosides.
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Affiliation(s)
- Ann E Scheunemann
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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9
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Llano-Sotelo B, Klepacki D, Mankin AS. Selection of small peptides, inhibitors of translation. J Mol Biol 2009; 391:813-9. [PMID: 19576904 DOI: 10.1016/j.jmb.2009.06.069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/25/2009] [Accepted: 06/26/2009] [Indexed: 11/30/2022]
Abstract
Identification of small molecular weight compounds targeting specific sites in the ribosome can accelerate development of new antibiotics and provide new tools for ribosomal research. We demonstrate here that antibiotic-size short peptides capable of inhibiting protein synthesis can be selected by using specific elements of ribosomal RNA as a target. The 'h18' pseudoknot encompassing residues 500-545 of the small ribosomal subunit RNA was used as a target in screening a heptapeptide phage-display library. Two of the selected peptides could efficiently interfere with both bacterial and eukaryotic translation. One of these inhibitory peptides exhibited a high-affinity binding to the isolated small ribosomal subunit (K(d) of 1.1 microM). Identification of inhibitory peptides that likely target a specific rRNA structure may pave new ways for validating new antibiotic sites in the ribosome. The selected peptides can be used as a tool in search of novel site-specific inhibitors of translation.
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Affiliation(s)
- Beatriz Llano-Sotelo
- Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, 60607, USA
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10
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Burns VA, Bobay BG, Basso A, Cavanagh J, Melander C. Targeting RNA with cysteine-constrained peptides. Bioorg Med Chem Lett 2007; 18:565-7. [PMID: 18065222 DOI: 10.1016/j.bmcl.2007.11.096] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 11/20/2007] [Accepted: 11/20/2007] [Indexed: 11/29/2022]
Abstract
A combined approach for targeting RNA with novel, biologically active ligands has been developed using a cyclic peptide library and in silico modeling. This approach has successfully identified novel cyclic peptide constructs that can target bTAR RNA. Subsequently, RNA/peptide interactions were effectively modeled using the HADDOCK docking program.
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Affiliation(s)
- Virginia A Burns
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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11
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Eshete M, Marchbank MT, Deutscher SL, Sproat B, Leszczynska G, Malkiewicz A, Agris PF. Specificity of Phage Display Selected Peptides for Modified Anticodon Stem and Loop Domains of tRNA. Protein J 2007; 26:61-73. [PMID: 17237992 DOI: 10.1007/s10930-006-9046-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein recognition of RNA has been studied using Peptide Phage Display Libraries, but in the absence of RNA modifications. Peptides from two libraries, selected for binding the modified anticodon stem and loop (ASL) of human tRNA(LyS3) having 2-thiouridine (s(2)U34) and pseudouridine (psi39), bound the modified human ASL(Lys3)(s(2)U34;psi39) preferentially and had significant homology with RNA binding proteins. Selected peptides were narrowed to a manageable number using a less sensitive, but inexpensive assay before conducting intensive characterization. The affinity and specificity of the best binding peptide (with an N-terminal fluorescein) were characterized by fluorescence spectrophotometry. The peptide exhibited the highest binding affinity for ASL(LYS3)(s(2)U34; psi39), followed by the hypermodified ASL(Lys3) (mcm(5)s(2) U34; ms(2)t(6)A37) and the unmodified ASL(Lys3), but bound poorly to singly modified ASL(Lys3) constructs (psi39, ms(2)t(6)A37, s(2)34), ASL(Lys1,2) (t(6)A37) and Escherichia coli ASL(Glu) (s(2)U34). Thus, RNA modifications are potentially important recognition elements for proteins and can be targets for selective recognition by peptides.
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Affiliation(s)
- Matthewos Eshete
- Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Campus Box 7622, Raleigh, NC, 27695-7622, USA
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12
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Zou J, Dickerson MT, Owen NK, Landon LA, Deutscher SL. Biodistribution of filamentous phage peptide libraries in mice. Mol Biol Rep 2005; 31:121-9. [PMID: 15293788 DOI: 10.1023/b:mole.0000031459.14448.af] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In vivo phage display is a new approach to acquire peptide molecules that bind stably to a given target. Phage peptide display libraries have been selected in mice and humans and numerous vasculature-targeting peptides have been reported. However, in vivo phage display has not typically produced molecules that extravasate to target specific organ or tumor antigens. Phage selections in animals have been performed for very short times without optimization for biodistribution or clearance rates to a particular organ. It is hypothesized that peptides that home to a desired antigen/organ can be obtained from in vivo phage experiments by optimization of incubation times, phage extraction and propagation procedures. To accomplish this goal, one must first gain a better understanding of the in vivo biodistribution and rate of clearance of engineered phage peptide display libraries. While the fate of wild type phage in rodents has been reported, the in vivo biodistribution of the commonly used engineered fd-tet M13 phage peptide display libraries (such as in the fUSE5 vector system) have not been well established. Here we report the biodistribution and clearance properties of fd-tet fifteen amino acid random peptide display libraries in fUSE5 phage in three common mouse models employed for drug discovery - CF-1, nude, and SCID mice.
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Affiliation(s)
- Jun Zou
- Department of Biochemistry, M743 Medical Sciences Bldg., University of Missouri, Columbia, MO 65212; 2ABC Laboratories, Columbia, MO 65204, USA
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13
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Mucha P, Szyk A, Rekowski P, Agris PF. Sequence-altered peptide adopts optimum conformation for modification-dependent binding of the yeast tRNAPhe anticodon domain. Protein J 2004; 23:33-8. [PMID: 15115180 DOI: 10.1023/b:jopc.0000016256.20648.0f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Amino acid contributions to protein recognition of naturally modified RNAs are not understood. Circular dichroism spectra and predictive software suggested that peptide tF2 (S1ISPW5GFSGL10 LRWSY15), selected from a phage display library to bind the modified anticodon domain of yeast tRNAPhe (ASL), adopted a beta-sheet structure. Ala residues incorporated at positions Pro4 and Gly6, both predicted to be involved in a turn, did not alter the peptide binding affinity for the ASLPhe, although major changes in the peptide's CD spectra were observed. Substitutions at three positions Pro4, Gly6, and Gly9, the latter not predicted to be in a turn, reduced the peptide's binding affinity to 4% of that of the unsubstituted tF2 and strongly influenced the peptide's secondary structure. The results suggest that peptides with different conformations, but similar affinities, adopt the optimal binding conformation, indicative of a structurally adaptive model of binding in which the modified RNA serves as a scaffold.
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Affiliation(s)
- Piotr Mucha
- Department of Chemistry, University of Gdansk, Sobieskiego 18, Gdansk 80-952, Poland.
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14
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Pustowka A, Dietz J, Ferner J, Baumann M, Landersz M, Königs C, Schwalbe H, Dietrich U. Identification of peptide ligands for target RNA structures derived from the HIV-1 packaging signal psi by screening phage-displayed peptide libraries. Chembiochem 2004; 4:1093-7. [PMID: 14523928 DOI: 10.1002/cbic.200300681] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anette Pustowka
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Strasse 42-44, 60596 Frankfurt, Germany
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15
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Stuart JW, Koshlap KM, Guenther R, Agris PF. Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe). J Mol Biol 2004; 334:901-18. [PMID: 14643656 DOI: 10.1016/j.jmb.2003.09.058] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Post-transcriptional modifications contribute chemistry and structure to RNAs. Modifications of tRNA at nucleoside 37, 3'-adjacent to the anticodon, are particularly interesting because they facilitate codon recognition and negate translational frame-shifting. To assess if the functional contribution of a position 37-modified nucleoside defines a specific structure or restricts conformational flexibility, structures of the yeast tRNA(Phe) anticodon stem and loop (ASL(Phe)) with naturally occurring modified nucleosides differing only at position 37, ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)), and ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)), were determined by NMR spectroscopy and restrained molecular dynamics. The ASL structures had similarly resolved stems (RMSD approximately 0.6A) of five canonical base-pairs in standard A-form RNA. The "NOE walk" was evident on the 5' and 3' sides of the stems of both RNAs, and extended to the adjacent loop nucleosides. The NOESY cross-peaks involving U(33) H2' and characteristic of tRNA's anticodon domain U-turn were present but weak, whereas those involving the U(33) H1' proton were absent from the spectra of both ASLs. However, ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) exhibited the downfield shifted 31P resonance of U(33)pGm(34) indicative of U-turns; ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)) did not. An unusual "backwards" NOE between Gm(34) and A(35) (Gm(34)/H8 to A(35)/H1') was observed in both molecules. The RNAs exhibited a protonated A(+)(38) resulting in the final structures having C(32).A(+)(38) intra-loop base-pairs, with that of ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) being especially well defined. A single family of low-energy structures of ASL(Phe)-(Cm(32),Gm(34), m(1)G(37),m(5)C(40)) (loop RMSD 0.98A) exhibited a significantly restricted conformational space for the anticodon loop in comparison to that of ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)) (loop RMSD 2.58A). In addition, the ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) average structure had a greater degree of similarity to that of the yeast tRNA(Phe) crystal structure. A comparison of the resulting structures indicates that modification of position 37 affects the accuracy of decoding and the maintenance of the mRNA reading frame by restricting anticodon loop conformational space.
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Affiliation(s)
- John W Stuart
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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Abstract
Studies of RNA-binding peptides, and recent combinatorial library experiments in particular, have demonstrated that diverse peptide sequences and structures can be used to recognize specific RNA sites. The identification of large numbers of sequences capable of binding to a particular site has provided extensive phylogenetic information used to deduce basic principles of recognition. The high frequency at which RNA-binding peptides are found in large sequence libraries suggests plausible routes to evolve sequence-specific binders, facilitating the design of new binding molecules and perhaps reflecting characteristics of natural evolution.
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Affiliation(s)
- Chandreyee Das
- Department of Biochemistry and Biophysics, 600 16th Street University of California, San Francisco, CA 94143-2280, USA
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Jin Y, Yu J, Yu YG. Identification of hNopp140 as a binding partner for doxorubicin with a phage display cloning method. CHEMISTRY & BIOLOGY 2002; 9:157-62. [PMID: 11880030 DOI: 10.1016/s1074-5521(02)00096-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Doxorubicin is a widely used anti-cancer drug. It is assumed to act by inhibiting DNA replication or transcription, although its precise targets and mechanism of cytotoxicity remain unresolved. A T7 phage library expressing human liver cDNA was screened against immobilized doxorubicin to isolate doxorubicin binding proteins. The selected phage contained the C-terminal region of nucleolar phosphoprotein hNopp140, an important factor in the biogenesis of the nucleolus. When the cloned sequence was expressed in E. coli, the recombinant protein was phosphorylated by casein kinase II and oligomerized in the presence of magnesium and fluoride ions, as occurs in vivo. Doxorubicin bound to the expressed protein with a dissociation constant of 4.5 x 10(-6) M, and this interaction was inhibited by the phosphorylation of hNopp140. These results suggested that doxorubicin might disrupt the cellular function of hNopp140.
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Affiliation(s)
- Youngnam Jin
- Structural Biology Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650, South Korea
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Mucha P, Szyk A, Rekowski P, Weiss PA, Agris PF. Anticodon domain methylated nucleosides of yeast tRNA(Phe) are significant recognition determinants in the binding of a phage display selected peptide. Biochemistry 2001; 40:14191-9. [PMID: 11714272 DOI: 10.1021/bi010978o] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The contributions of the natural modified nucleosides to RNA identity in protein/RNA interactions are not understood. We had demonstrated that 15 amino acid long peptides could be selected from a random phage display library using the criterion of binding to a modified, rather than unmodified, anticodon domain of yeast tRNA(Phe) (ASL(Phe)). Affinity and specificity of the selected peptides for the modified ASL(Phe) have been characterized by fluorescence spectroscopy of the peptides' tryptophans. One of the peptides selected, peptide t(F)2, exhibited the highest specificity and most significant affinity for ASL(Phe) modified with 2'-O-methylated cytidine-32 and guanosine-34 (Cm(32) and Gm(34)) and 5-methylated cytidine-40 (m(5)C(40)) (K(d) = 1.3 +/- 0.4 microM) and a doubly modified ASL(Phe)-Gm(34),m(5)C(40) and native yeast tRNA(Phe) (K(d) congruent with 2.3 and 3.8 microM, respectively) in comparison to that for the unmodified ASL(Phe) (K(d) = 70.1 +/- 12.3 microM). Affinity was reduced when a modification altered the ASL loop structure, and binding was negated by modifications that disfavored hairpin formation. Peptide t(F)2's higher affinity for the ASL(Phe)-Cm(32),Gm(34),m(5)C(40) hairpin and fluorescence resonance energy transfer from its tryptophan to the hypermodified wybutosine-37 in the native tRNA(Phe) placed the peptide across the anticodon loop and onto the 3'-side of the stem. Inhibition of purified yeast phenylalanyl-tRNA synthetase (FRS) catalyzed aminoacylation of cognate yeast tRNA(Phe) corroborated the peptide's binding to the anticodon domain. The phage-selected peptide t(F)2 has three of the four amino acids crucial to G(34) recognition by the beta-structure of the anticodon-binding domain of Thermus thermophilus FRS and exhibited circular dichroism spectral properties characteristic of beta-structure. Thus, modifications as simple as methylations contribute identity elements that a selected peptide specifically recognizes in binding synthetic and native tRNA and in inhibiting tRNA aminoacylation.
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Affiliation(s)
- P Mucha
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Kay BK. Mapping Protein-Protein Interactions with Combinatorial Peptides. Comp Funct Genomics 2001; 2:304-6. [PMID: 18629247 PMCID: PMC2448409 DOI: 10.1002/cfg.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2001] [Accepted: 07/27/2001] [Indexed: 11/28/2022] Open
Affiliation(s)
- Brian K. Kay
- Department of Pharmacology, 1300 University Ave., University of Wisconsin-Madison, Madison, WI 53706-1532, USA
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