1
|
Silva SAF, Silva FLB, Ribas AF, de Souza SGH, dos Santos TB. Genome-wide in silico analysis of SOD genes in common bean (Phaseolus vulgaris L.). ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s12892-020-00030-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
2
|
Nakayama N, Hagiwara K, Ito Y, Ijiro K, Osada Y, Sano KI. Superior cell penetration by a rigid and anisotropic synthetic protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2826-2832. [PMID: 25710086 DOI: 10.1021/la504494x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecules with structural anisotropy and rigidity, such as asbestos, demonstrate high cell-penetrating activity but also high toxicity. Here we synthesize a biodegradable, rigid, and fibrous artificial protein, CCPC 140, as a potential vehicle for cellular delivery. CCPC 140 penetrated 100% of cells tested in vitro, even at a concentration of 3.1 nM-superior to previously reported cell-penetrating peptides. The effects of cell-strain-dependency and aspect ratio on the cell-penetrating activity of CCPC 140 were also investigated.
Collapse
Affiliation(s)
- Norihisa Nakayama
- Graduate School of Environmental Symbiotic System Major and ‡Department of Innovative Systems Engineering, Nippon Institute of Technology , Miyashiro, Saitama 345-8501, Japan
| | | | | | | | | | | |
Collapse
|
3
|
Combinatorial contextualization of peptidic epitopes for enhanced cellular immunity. PLoS One 2014; 9:e110425. [PMID: 25343355 PMCID: PMC4208766 DOI: 10.1371/journal.pone.0110425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/13/2014] [Indexed: 11/25/2022] Open
Abstract
Invocation of cellular immunity by epitopic peptides remains largely dependent on empirically developed protocols, such as interfusion of aluminum salts or emulsification using terpenoids and surfactants. To explore novel vaccine formulation, epitopic peptide motifs were co-programmed with structural motifs to produce artificial antigens using our “motif-programming” approach. As a proof of concept, we used an ovalbumin (OVA) system and prepared an artificial protein library by combinatorially polymerizing MHC class I and II sequences from OVA along with a sequence that tends to form secondary structures. The purified endotoxin-free proteins were then examined for their ability to activate OVA-specific T-cell hybridoma cells after being processed within dendritic cells. One clone, F37A (containing three MHC I and two MHC II OVA epitopes), possessed a greater ability to evoke cellular immunity than the native OVA or the other artificial antigens. The sensitivity profiles of drugs that interfered with the F37A uptake differed from those of the other artificial proteins and OVA, suggesting that alteration of the cross-presentation pathway is responsible for the enhanced immunogenicity. Moreover, F37A, but not an epitopic peptide, invoked cellular immunity when injected together with monophosphoryl lipid A (MPL), and retarded tumor growth in mice. Thus, an artificially synthesized protein antigen induced cellular immunity in vivo in the absence of incomplete Freund's adjuvant or aluminum salts. The method described here could be potentially used for developing vaccines for such intractable ailments as AIDS, malaria and cancer, ailments in which cellular immunity likely play a crucial role in prevention and treatment.
Collapse
|
4
|
Tan X, Pecka JL, Tang J, Lovas S, Beisel KW, He DZZ. A motif of eleven amino acids is a structural adaptation that facilitates motor capability of eutherian prestin. J Cell Sci 2012; 125:1039-47. [PMID: 22399806 PMCID: PMC3311934 DOI: 10.1242/jcs.097337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2011] [Indexed: 11/20/2022] Open
Abstract
Cochlear outer hair cells (OHCs) alter their length in response to transmembrane voltage changes. This so-called electromotility is the result of conformational changes of membrane-bound prestin. Prestin-based OHC motility is thought to be responsible for cochlear amplification, which contributes to the exquisite frequency selectivity and sensitivity of mammalian hearing. Prestin belongs to an anion transporter family, the solute carrier protein 26A (SLC26A). Prestin is unique in this family in that it functions as a voltage-dependent motor protein manifested by two hallmarks, nonlinear capacitance and motility. Evidence suggests that prestin orthologs from zebrafish and chicken are anion exchangers or transporters with no motor function. We identified a segment of 11 amino acid residues in eutherian prestin that is extremely conserved among eutherian species but highly variable among non-mammalian orthologs and SLC26A paralogs. To determine whether this sequence represents a motif that facilitates motor function in eutherian prestin, we utilized a chimeric approach by swapping corresponding residues from the zebrafish and chicken with those of gerbil. Motility and nonlinear capacitance were measured from chimeric prestin-transfected human embryonic kidney 293 cells using a voltage-clamp technique and photodiode-based displacement measurement system. We observed a gain of motor function with both of the hallmarks in the chimeric prestin without loss of transport function. Our results show, for the first time, that the substitution of a span of 11 amino acid residues confers the electrogenic anion transporters of zebrafish and chicken prestins with motor-like function. Thus, this motif represents the structural adaptation that assists gain of motor function in eutherian prestin.
Collapse
Affiliation(s)
| | - Jason L. Pecka
- Department of Biomedical Sciences, Creighton University School of Medicine, 2500 California Plaza, Omaha, Nebraska, 68178, USA
| | - Jie Tang
- Department of Biomedical Sciences, Creighton University School of Medicine, 2500 California Plaza, Omaha, Nebraska, 68178, USA
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University School of Medicine, 2500 California Plaza, Omaha, Nebraska, 68178, USA
| | | | | |
Collapse
|
5
|
Murakami T, Kashiwagi K, Shiba K. Creation of novel signalling modulators from existing cytokine using scanning motif-programming. Chem Commun (Camb) 2011; 47:9357-9. [DOI: 10.1039/c1cc12214b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
6
|
Exploitation of peptide motif sequences and their use in nanobiotechnology. Curr Opin Biotechnol 2010; 21:412-25. [DOI: 10.1016/j.copbio.2010.07.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 12/18/2022]
|
7
|
Sano KI, Minamisawa T, Shiba K. Autonomous silica encapsulation and sustained release of anticancer protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:2231-2234. [PMID: 20085330 DOI: 10.1021/la9045226] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We present a novel method for preparing a silica carrier for the sustained release of a proteinaceous pharmaceutical. This method makes use of the silicification activity of the protein itself, which autonomously formed a protein-silica composite upon simple incubation with a silica precursor. The composite was dissolved, and the encapsulated protein was released into a culture medium, thereby sustaining the protein's activity for a long period of time.
Collapse
Affiliation(s)
- Ken-ichi Sano
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo 135-8550, Japan
| | | | | |
Collapse
|
8
|
Shiba K. Natural and artificial peptide motifs: their origins and the application of motif-programming. Chem Soc Rev 2010; 39:117-26. [DOI: 10.1039/b719081f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
9
|
|
10
|
Abstract
Motif-programming is a method for creating artificial proteins by combining functional peptide motifs in a combinatorial manner. Motifs are often short amino acid sequences within natural proteins that are associated with particular biological functions. Motifs also can be created de novo using molecular engineering. In particular, peptide aptamers, which have been isolated as specific binders against various targets, are believed to be promising motif blocks for creating novel biomaterials through motif-programming. It is now known, however, that simple arithmetic addition does not always work with motif-programming-e.g., simple conjugation of motifs-A and -B does not always result in a bifunctional peptide-AB. To solve this nonlinearity in motif-programming, we have been employing a combinatorial approach, which we called MolCraft. In MolCraft, we prepare a library of artificial proteins that contain multiple motifs in various numbers and orders, from which clones having the desired functions are selected. In MolCraft, a microgene is first rationally designed so that the encoded peptides contain motifs, and then tandemly polymerized with insertion or deletion mutations at the junctions between microgene units. Because of junctional perturbations, proteins translated from a single microgene polymer are molecularly diverse, originating from the combinatorics of three reading frames, and are thus combinatorial polymers of three peptides. By embedding functional motifs into different reading frames of a single microgene, combinatorial polymers of functional motifs are easily prepared. Notably, repetitiousness retained in the overall structure of proteins contributes to the formation of ordered structures, and enhances the chances of reconstituting biological activity. This method is particularly well suited for developing liaison molecules that interface between cells and inorganic materials. Examples of multifunctional artificial proteins created from this method will be introduced.
Collapse
Affiliation(s)
- Kiyotaka Shiba
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan.
| |
Collapse
|
11
|
Patwardhan P, Shiba K, Gordon C, Craddock BP, Tamiko M, Miller WT. Synthesis of functional signaling domains by combinatorial polymerization of phosphorylation motifs. ACS Chem Biol 2009; 4:751-8. [PMID: 19627099 DOI: 10.1021/cb900059f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The adaptor protein Cas contains a core substrate domain with multiple YXXP motifs that are phosphorylated by Src and other tyrosine kinases. Here, we used a synthetic strategy to determine the importance of the arrangement, spacing, and identity of the YXXP motifs. By polymerizing short DNA sequences encoding two phosphorylation motifs, we created a panel of Cas mutants in which the entire substrate domain was replaced by synthetic domains containing random numbers and arrangements of the motifs. Most of these synthetic Cas variants were recognized and phosphorylated by Src in vitro and in intact mammalian cells. The random polymer mutants also restored migration activity to Cas knockout cells; even artificial proteins containing a single motif retained some biological function. Our results suggest that the arrangement of Cas motifs is not critical for signaling. This method could be used to identify the minimal functional units in other signaling proteins.
Collapse
Affiliation(s)
- Parag Patwardhan
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Chris Gordon
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Minamisawa Tamiko
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
| |
Collapse
|
12
|
Chirila TV, Minamisawa T, Keen I, Shiba K. Effect of Motif-Programmed Artificial Proteins on the Calcium Uptake in a Synthetic Hydrogel. Macromol Biosci 2009; 9:959-67. [DOI: 10.1002/mabi.200900096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
13
|
Kashiwagi K, Tsuji T, Shiba K. Directional BMP-2 for functionalization of titanium surfaces. Biomaterials 2008; 30:1166-75. [PMID: 19022501 DOI: 10.1016/j.biomaterials.2008.10.040] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 10/17/2008] [Indexed: 11/16/2022]
Abstract
Efficient immobilization of biomacromolecules on material surfaces is a key to development in areas of regenerative medicine and tissue engineering. However, strong and irreversible immobilization of cytokines on surfaces often diminishes their biological functionality. A destructive hydrophobic interaction between the material surface and the biomolecule may underlie this inactivation. Alternatively, dissociation of the cytokine from the material may be necessary for signal transduction. Here we propose a new method for immobilizing cytokines on material surfaces: a material-binding artificial peptide is used to mediate reversible interaction between the cytokine and the material surface. We created artificial proteins that contained three copies of a Ti-binding motif, and fused them to the N-terminal of BMP-2. The engineered BMP-2 showed reversible binding to Ti surfaces and induced BMP signaling activity. When a hydrophobic protein devoid of the Ti-binding motif was fused to BMP-2, the protein tightly bound to Ti surfaces but showed little BMP activity, confirming the importance of the mode of immobilization.
Collapse
Affiliation(s)
- Kenji Kashiwagi
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, 3-10-6 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | | | | |
Collapse
|
14
|
Direct transformation from amorphous to crystalline calcium phosphate facilitated by motif-programmed artificial proteins. Proc Natl Acad Sci U S A 2008; 105:16866-70. [PMID: 18957547 DOI: 10.1073/pnas.0804277105] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An animal's hard tissue is mainly composed of crystalline calcium phosphate. In vitro, small changes in the reaction conditions affect the species of calcium phosphate formed, whereas, in vivo, distinct types of crystalline calcium phosphate are formed in a well-controlled spatiotemporal-dependent manner. A variety of proteins are involved in hard-tissue formation; however, the mechanisms by which they regulate crystal growth are not yet fully understood. Clarification of these mechanisms will not only lead to the development of new therapeutic regimens but will also provide guidance for the application of biomineralization in bionanotechnology. Here, we focused on the peptide motifs present in dentin matrix protein 1 (DMP1), which was previously shown to enhance hydroxylapatite (HAP) formation when immobilized on a glass substrate. We synthesized a set of artificial proteins composed of combinatorial arrangements of these motifs and successfully obtained clones that accelerated formation of HAP without immobilization. Time-resolved static light-scattering analyses revealed that, in the presence of the protein, amorphous calcium phosphate (ACP) particles increased their fractal dimension and molecular mass without increasing their gyration radii during a short period before precipitation. The protein thus facilitated reorganization of the internal structure of amorphous particles into ordered crystalline states, i.e., the direct transformation of ACP to HAP, thereby acting as a nucleus for precipitation of crystalline calcium phosphate. Without the protein, the fractal dimension, molecular mass, and gyration radii of ACP particles increased concurrently, indicating heterogeneous growth transformation.
Collapse
|
15
|
Shiba K. Functionalization of carbon nanomaterials by evolutionary molecular engineering: Potential application in drug delivery systems. J Drug Target 2008; 14:512-8. [PMID: 17046797 DOI: 10.1080/10611860600845033] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
By virtue of the progress made in evolutionary molecular engineering, peptide aptamers that specifically recognize target molecules are now routinely created using a peptide phage display system. The system was originally developed for isolating peptides that specifically recognized biomacromolecules (e.g. proteinous receptors), but are now also being used to acquire peptide motifs that bind to inorganic materials, such as semiconductors, metals and carbon nanomaterials. We have created the peptide aptamer against carbon nanohorns, a vesicular carbon nanomaterial whose size is 80-100 nm in diameter. By combining the peptide motif that has affinity to the surfaces of carbon nanohorns with peptide aptamers that can target specific organs, we can functionalize the carbon nanomaterial to provide novel types of carriers for drug delivery systems.
Collapse
Affiliation(s)
- Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, CREST/JST, Tokyo, Japan.
| |
Collapse
|
16
|
Kokubun K, Kashiwagi K, Yoshinari M, Inoue T, Shiba K. Motif-programmed artificial extracellular matrix. Biomacromolecules 2008; 9:3098-105. [PMID: 18826322 DOI: 10.1021/bm800638z] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motif-programming is a method for creating artificial proteins by combining functional peptide motifs in a combinatorial manner. This method is particularly well suited for developing liaison molecules that interface between cells and inorganic materials. Here we describe our creation of artificial proteins through the programming of two motifs, a natural cell attachment motif (RGD) and an artificial Ti-binding motif (minTBP-1). The created proteins were found to reversibly bind Ti and to bind MC3T3-E1 osteoblast-like cells. Moreover, although the interaction with Ti was not covalent, the proteins recapitulated several functions of fibronectin, and thus, could serve as an artificial ECM on Ti materials. Because this motif-programming system could be easily extended to create artificial proteins having other biological functions and material specificities, it should be highly useful for application to tissue engineering and regenerative medicine.
Collapse
Affiliation(s)
- Katsutoshi Kokubun
- Department of Clinical Pathophysiology, Division of Oral Implants Research and Oral Health Science Center, Tokyo Dental College, 1-2-2, Masago, Mihama-ku, Chiba, 261-8501 Japan
| | | | | | | | | |
Collapse
|
17
|
Tsuji T, Nagata T, Yanagawa H. N- and C-terminal Fragments of a Globular Protein Constructed by Elongation of Modules as a Units Associated for Functional Complementation. J Biochem 2008; 144:513-21. [DOI: 10.1093/jb/mvn099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
18
|
Initiation of the microgene polymerization reaction with non-repetitive homo-duplexes. Biochem Biophys Res Commun 2008; 368:606-13. [PMID: 18243133 DOI: 10.1016/j.bbrc.2008.01.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Accepted: 01/24/2008] [Indexed: 10/22/2022]
Abstract
Microgene Polymerization Reaction (MPR) is used as an experimental system to artificially simulate evolution of short, non-repetitive homo-duplex DNA into multiply-repetitive products that can code for functional proteins. Blunt-end ligation by DNA polymerase is crucial in expansion of homo-duplexes (HDs) into head-to-tail multiple repeats in MPR. The propagation mechanism is known, but formation of the initial doublet (ID) by juxtaposing two HDs and polymerization through the gap has been ambiguous. Initiation events with pairs of HDs using Real-Time PCR were more frequent at higher HD concentrations and slightly below the melting temperature. A process molecularity of about 3.1, calculated from the amplification efficiency and the difference in PCR cycles at which propagation was detected at varying HD concentrations, led to a simple mechanism for ID formation: the gap between two HDs is bridged by a third. Considering thermodynamic aspects of the presumed intermediate "nucleation complex" can predict relative propensity for the process with other HDs.
Collapse
|
19
|
Saito H, Minamisawa T, Yamori T, Shiba K. Motif-programmed artificial protein induces apoptosis in several cancer cells by disrupting mitochondria. Cancer Sci 2008; 99:398-406. [PMID: 18271938 PMCID: PMC11158330 DOI: 10.1111/j.1349-7006.2007.00697.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
By combinatorially assembling two natural motifs, respectively, associated with protein transduction (PTD) and induction of apoptosis (BH3), we previously synthesized an artificial protein (#284) that is taken up into cells, where it induces apoptosis. Here we used cluster analysis of GI(50) (average concentration required for 50% growth inhibition), as well as immunohistochemical and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling analyses to further characterize the capacity of #284 to induce apoptosis in a panel of 39 cancer cell lines. Our results showed that #284 preferentially inhibited the growth of several cancer cells with a GI(50) of approximately 5 microM, which is in the range of conventional anticancer drugs such as cisplatin and etoposide. In breast cancer HBC-4 cells, #284 caused mitochondrial aggregation and induced apoptosis in a BH3 motif-dependent manner. Moreover, transfection of the artificial gene that encodes #284 led to effective expression of the artificial protein within cells, which in turn caused apoptosis at a level similar to that seen in naturally occurring apoptosis inducers, Noxa/Bax transfectants. These findings suggest that synthetic proteins created by reprogramming peptide motifs have the potential to serve as novel agents useful in the treatment of cancer.
Collapse
Affiliation(s)
- Hirohide Saito
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | | | | | | |
Collapse
|
20
|
Saito H, Kashida S, Inoue T, Shiba K. The role of peptide motifs in the evolution of a protein network. Nucleic Acids Res 2007; 35:6357-66. [PMID: 17881369 PMCID: PMC2095796 DOI: 10.1093/nar/gkm692] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Naturally occurring proteins in cellular networks often share peptide motifs. These motifs have been known to play a pivotal role in protein interactions among the components of a network. However, it remains unknown how these motifs have contributed to the evolution of the protein network. Here we addressed this issue by a synthetic biology approach. Through the motif programming method, we have constructed an artificial protein library by mixing four peptide motifs shared among the Bcl-2 family proteins that positively or negatively regulate the apoptosis networks. We found one strong pro-apoptotic protein, d29, and two proteins having moderate, but unambiguous anti-apoptotic functions, a10 and d16, from the 28 tested clones. Thus both the pro- and anti-apoptotic modulators were present in the library, demonstrating that functional proteins with opposing effects can emerge from a single pool prepared from common motifs. Motif programming studies have exhibited that the annotated function of the motifs were significantly influenced by the context that the motifs embedded. The results further revealed that reshuffling of a set of motifs realized the promiscuous state of protein, from which disparate functions could emerge. Our finding suggests that motifs contributed to the plastic evolvability of the protein network.
Collapse
Affiliation(s)
- Hirohide Saito
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- *To whom correspondence should be addressed. +81 3 3570 0489+81 3 3570 0461 Correspondence may also be addressed to Hirohide Saito. +81 75 753 3997+81 75 753 3996
| | - Shunnichi Kashida
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Tan Inoue
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- *To whom correspondence should be addressed. +81 3 3570 0489+81 3 3570 0461 Correspondence may also be addressed to Hirohide Saito. +81 75 753 3997+81 75 753 3996
| |
Collapse
|
21
|
Shiba K, Minamisawa T. A Synthesis Approach to Understanding Repeated Peptides Conserved in Mineralization Proteins. Biomacromolecules 2007; 8:2659-64. [PMID: 17665949 DOI: 10.1021/bm700652b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We created artificial proteins that contained repeats of a short peptide motif, Asn-Gly-Asx. In nature this motif is repeated within shell proteins as an idiosyncratic domain, while in vitro it has been shown to suppress calcification. The motif was embedded within peptide sequences that did or did not have the ability to form secondary structures, which provided the motif with a variety of physicochemical properties. Although a short synthetic peptide containing the motif did not inhibit calcification in vitro, some of the artificial proteins carrying repeats of the motif did show robust suppression of calcification. Artificial proteins lacking the motif did not exhibit suppressive activity. Likewise, one construct containing multiple repeats of the motifs also did not exert an inhibitory effect on calcification. Apparently, carrying the Asn-Gly-Asx motif is not, by itself, sufficient for expression of its cryptic activity; instead, certain physicochemical properties of the polypeptides mediate its manifestation. We anticipate that syntheses using "motif programming", such as the one described here, will shed light on the origin of repetitive sequences as well as on the evolution of biomineralization proteins.
Collapse
Affiliation(s)
- Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Koto-ku, Tokyo 135-8550, Japan. kshiba@ jfcr.or.jp
| | | |
Collapse
|
22
|
Saito H, Minamisawa T, Shiba K. Motif programming: a microgene-based method for creating synthetic proteins containing multiple functional motifs. Nucleic Acids Res 2007; 35:e38. [PMID: 17287291 PMCID: PMC1874597 DOI: 10.1093/nar/gkm017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The presence of peptide motifs within the proteins provides the synthetic biologist with the opportunity to fabricate novel proteins through the programming of these motifs. Here we describe a method that enables one to combine multiple peptide motifs to generate a combinatorial protein library. With this method, a set of sense and antisense oligonucleotide primers were prepared. These primers were mixed and polymerized, so that the resultant DNA consisted of combinatorial polymers of multiple microgenes created from the stochastic assembly of the sense and antisense primers. With this motif-mixing method, we prepared a protein library from the BH1-4 motifs shared among Bcl-2 family proteins. Among the 41 clones created, 70% of clones had a stable, presumably folded expression product in human cells, which was detectable by immunohistochemistry and western blot. The proteins obtained varied with respect to both the number and the order of the four motifs. The method enables homology-independent polymerization of DNA blocks that coded motif sequences, and the frequency of each motif within a library can be adjusted in a tailor-made manner. This motif programming has a potential for creating a library with a large proportion of folded/functional proteins.
Collapse
Affiliation(s)
- Hirohide Saito
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan and CREST, Japan Science and Technology Agency (JST), c/o Cancer Institute
| | - Tamiko Minamisawa
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan and CREST, Japan Science and Technology Agency (JST), c/o Cancer Institute
| | - Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan and CREST, Japan Science and Technology Agency (JST), c/o Cancer Institute
- *To whom correspondence should be addressed. +81 3 3570 0489+81 3 3570 0461
| |
Collapse
|
23
|
Privé GG, Melnick A. Specific peptides for the therapeutic targeting of oncogenes. Curr Opin Genet Dev 2006; 16:71-7. [PMID: 16377176 DOI: 10.1016/j.gde.2005.12.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Accepted: 12/07/2005] [Indexed: 02/03/2023]
Abstract
Tumors are dependent on oncogenic proteins for their maintenance and survival. The ideal cancer therapy would include drugs that specifically target these proteins. Many such proteins function through interfaces that can be difficult to target effectively with small molecules. However, recent advances in cell-permeable peptide technology, improving cellular penetration and stability, raise the possibility that specific peptide interference of oncogenic proteins could be successfully translated to the clinic. Several active anti-tumor peptides were recently described. For example, a stable peptide inhibitor of the Hsp90 ATP-binding pocket killed a wide range of tumors in vitro and in vivo, and a peptide inhibitor of the BCL6 oncoprotein was active in B-cell lymphomas; both peptides functioned without toxicity to normal tissues.
Collapse
Affiliation(s)
- Gilbert G Privé
- Department of Medical Biophysics, University of Toronto, Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, 610 University Avenue, Toronto, Ontario, M5G 2M9, Canada
| | | |
Collapse
|
24
|
Kashiwagi K, Isogai Y, Nishiguchi KI, Shiba K. Frame shuffling: a novel method for in vitro protein evolution. Protein Eng Des Sel 2006; 19:135-40. [PMID: 16415043 DOI: 10.1093/protein/gzj008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe 'frame shuffling', a novel method for preparing artificial protein libraries. With this method, a Y-family DNA polymerase known to introduce frame shift mutations at high rates is utilized to scramble the reading frames of a parental gene. The resultant progeny produce mutant proteins having segmental sequence changes. Such frame-shuffled mutant proteins exhibit physicochemical properties that differ from those of proteins obtained using conventional mutagenesis.
Collapse
Affiliation(s)
- Kenji Kashiwagi
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Ariake, Koto-ku, Tokyo, Japan
| | | | | | | |
Collapse
|
25
|
Fischer R, Fotin-Mleczek M, Hufnagel H, Brock R. Break on through to the Other Side-Biophysics and Cell Biology Shed Light on Cell-Penetrating Peptides. Chembiochem 2005; 6:2126-42. [PMID: 16254940 DOI: 10.1002/cbic.200500044] [Citation(s) in RCA: 212] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cell-penetrating peptides (CPPs) have become widely used vectors for the cellular import of molecules in basic and applied biomedical research. Despite the broad acceptance of these molecules as molecular carriers, the details of the mode of cellular internalization and membrane permeation remain elusive. Within the last two years endocytosis has been demonstrated to be a route of uptake shared by several CPPs. These findings had a significant impact on CPP research. State-of-the-art cell biology is now required to advance the understanding of the intracellular fate of the CPP and cargo molecules. Owing to their presumed ability to cross lipid bilayers, CPPs also represent highly interesting objects of biophysical research. Numerous studies have investigated structure-activity relationships of CPPs with respect to their ability to bind to a lipid bilayer or to cross this barrier. Endocytosis route only relocates the membrane permeation from the cell surface to endocytic compartments. Therefore, biophysical experiments are key to a mechanistic molecular understanding of the cellular uptake of CPPs. However, biophysical investigations have to consider the molecular environment encountered by a peptide inside and outside a cell. In this contribution we will review biophysical and cell-biology data obtained for several prominent CPPs. Furthermore, we will summarize recent findings on the cell-penetrating characteristics of antimicrobial peptides and the antimicrobial properties of CPPs. Peptides of both groups have overlapping characteristics. Therefore, both fields may greatly benefit from each other. The review will conclude with a perspective of how biophysics and cell biology may synergize even more efficiently in the future.
Collapse
Affiliation(s)
- Rainer Fischer
- Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen,, Germany
| | | | | | | |
Collapse
|