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Biomedical subjects

Kiyotaka Shiba

Publications and source records attributed to Kiyotaka Shiba.

At least 19 recordsLinked to original sources
PubMed2006

Utilization of the pleiotropy of a peptidic aptamer to fabricate heterogeneous nanodot-containing multilayer nanostructures.

Peptide aptamers (=binders) against inorganic materials often show a capacity for mineralization of their target atoms; thus they are able to function both as binding molecules and as mediators for mineralization. Although the mechanisms underlying these two properties of peptide aptamers are not yet fully understood, they have been used separately to fabricate various nanostructures. Here, we present a novel method of nanofabrication, in which binding and mineralization by a peptide aptamer are alternately utilized to assemble multilayered nanostructures comprised of metal loaded cage proteins ornamented with Ti-binding peptides.

Amino Acid Sequence↗
PubMed2006

Frame shuffling: a novel method for in vitro protein evolution.

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.

Amino Acid Sequence↗
PubMed2006

Mechanism underlying specificity of proteins targeting inorganic materials.

Adhesion force analysis using atomic force microscopy clearly revealed for the first time the mechanism underlying the specific binding between a titanium surface and ferritin possessing the sequence of Ti-binding peptide in its N-terminal domain. Our results proved that the specific binding is due to double electrostatic bonds between charged residue and surface groups of the substrate. Furthermore, it is also demonstrated that the accretion of surfactant reduces nonspecific interactions, dramatically enhancing the selectivity and specificity of Ti-binding peptide.

Amino Acid Sequence↗
PubMed2006

Functionalization of carbon nanomaterials by evolutionary molecular engineering: potential application in drug delivery systems.

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.

Biomedical Engineering↗
PubMed2006

[Carbon nanohorns as a novel drug carrier].

Carbon nanohorns are nanostructured spherical aggregates of graphitic tubes whose sizes are 80-100 nm in diameter. They have extensive surface area and don't need metal catalyst for their synthesis. The oxidization or acid treatment makes nano windows on their walls, through which distinct set of small molecules have been shown to infiltrate into their inner space. These unique properties of carbon nanohorns suggest the possible use of the nanomaterials as a novel carrier in drug delivery systems.

Carbon↗
PubMed2005

Probing the conformational features of a phage display polypeptide sequence directed against single-walled carbon nanohorn surfaces.

Single-walled carbon nanohorns (SWNHs) are interesting carbon nanostructures that have applications to science and technology. Using M13 phage display technology, polypeptides directed again SWNHs surfaces have been created for a number of nanotechnology and pharmaceutical purposes, yet the molecular mechanism of polypeptide sequence interaction and binding to SWNHs surfaces is not known. Recently, we identified a linear 12-AA M13 phage pIII sequence, NH-12-5-2 (DYFSSPYYEQLF), that binds with high affinity to SWNHs surfaces. To probe the structure of this pIII tail polypeptide further, we investigated the conformation of a model peptide representing the 12 AA NH-12-5-2 sequence. At neutral pH, the NH-12-5-2 model polypeptide is conformationally labile and exhibits two-state conformational exchange involving the D1-S5 N-terminal segment. Simultaneous with this conformational exchange process is the observation that the P6 residue exhibits imido ring conformational variation. In the presence of the structure-stabilizing solvent, TFE, or at pH 2.5, both the exchange process and Pro ring motion phenomena disappear, indicating that the structure of this peptide sequence can be stabilized by extrinsic factors. Interestingly, we observe NMR parameters (ROEs, (3)J coupling constants) for NH-12-5-2 in 90% v/v TFE that are consistent with the presence of a partial helical structure, similar to what was observed at low pH in our earlier CD experiments. We conclude that the NH-12-5-2 model polypeptide sequence possesses an inherent conformational instability that involves the D1-S5 sequence segment and the P6 residue but that this instability can be offset by extrinsic factors (e.g., charge neutralization, imido ring interconversion, and hydrophobic-hydrophobic interactions). These nonbonding interactions may play a role in the recognition and binding of this phage sequence region to SWNHs surfaces.

Amino Acid Sequence↗
PubMed2005

Specificity and biomineralization activities of Ti-binding peptide-1 (TBP-1).

Numerous peptide aptamers that recognize inorganic materials have been isolated using in vitro peptide evolution systems. However, it remains unknown how peptides interact with inorganic materials or how specific those interactions are. We, therefore, assessed the target specificities of the peptide aptamer TBP-1 (RKLPDAPGMHTW) by monitoring its ability to bind 10 different metals. We found that phages displaying TBP-1 bound to Ti, Si, and Ag surfaces but not to Au, Cr, Pt, Sn, Zn, Cu, or Fe. As previously seen with Ti, binding to Si and Ag was diminished by R1A, P4A, or D5A mutation, suggesting that the same molecular mechanism underlies TBP-1 binding to all three materials. We also observed that a synthetic TBP-1 peptide mediated mineralization of both silica and Ag. It, thus, appears that although the overall chemical characteristics of Ti, Si, and Ag surfaces are dissimilar, they share a common subnanometric structure that is recognized by TBP-1.

Carrier Proteins↗
PubMed2004

Designer ribozymes: programming the tRNA specificity into flexizyme.

Fx3 is an artificial ribozyme with the ability to aminoacylate various tRNAs with phenylalanine and its nonnatural derivatives. Herein we report a simple strategy to build tRNA specificity into the generic Fx3, by appending to its 3'-end a tRNA-specific sequence (TSS), which is complementary to the acceptor stem of the cognate tRNA. This new designer ribozyme, referred to as Fx10, is able to recognize its cognate tRNA via a 10-base-pair interaction that is formed after the invasion of the tRNA acceptor stem by the TSS. We have demonstrated that Fx10 can aminoacylate its cognate tRNA with a high degree of specificity and also discriminate against the noncognate tRNAs. Because the tRNA specificity can be easily programmed into Fx10, it is a custom-made catalyst to generate nonnatural aminoacyl-tRNAs.

Acylation↗
PubMed2004

Synthesis of functional proteins by mixing peptide motifs.

Here, we describe a synthetic approach for generating artificial proteins by the assemblage of naturally occurring peptide motifs. Two motifs respectively related to apoptosis induction and protein transduction were encrypted into different reading frames of an artificial gene (microgene), which was then polymerized; random frame shifts at the junctions between the microgene units yielded combinatorial polymers of three reading frames. Among the proteins created, #284 was found to penetrate through cell membranes and exert a strong apoptotic effect on several cancer cell lines. Because a simple linkage of these motifs was not sufficient to construct a bifunctional peptide, and the successful reconstitution was dependent on how they were joined together, the combinatorial strategy is important for reconstituting functions from mixtures of motifs. This microgene-based approach represents a novel system for creating proteins with desired functions.

Amino Acid Motifs↗
PubMed2004

Cellular distribution of Lysyl-tRNA synthetase and its interaction with Gag during human immunodeficiency virus type 1 assembly.

Lysyl-tRNA synthetase (LysRS) is packaged into human immunodeficiency virus type 1 (HIV-1) via its interaction with Gag, and this enzyme facilitates the selective packaging of tRNA(3)(Lys), the primer for initiating reverse transcription, into HIV-1. The Gag/LysRS interaction is detected at detergent-resistant membrane but not in membrane-free cell compartments that contain Gag and LysRS. LysRS is found (i). in the nucleus, (ii). in a cytoplasmic high-molecular-weight aminoacyl-tRNA synthetase complex (HMW aaRS complex), (iii). in mitochondria, and (iv). associated with plasma membrane. The cytoplasmic form of LysRS lacking the mitochondrial import signal was previously shown to be efficiently packaged into virions, and in this report we also show that LysRS compartments in nuclei, in the HMW aaRS complex, and at the membrane are also not required as a primary source for viral LysRS. Exogenous mutant LysRS species unable to either enter the nucleus or bind to the cell membrane are still incorporated into virions. Many HMW aaRS components are not packaged into the virion along with LysRS, and the interaction of LysRS with p38, a protein that binds tightly to LysRS in the HMW aaRS complex, is not required for the incorporation of LysRS into virions. These data indicate that newly synthesized LysRS may interact rapidly with Gag before the enzyme has the opportunity to move to the above-mentioned cellular compartments. In confirmation of this idea, we found that newly synthesized LysRS is associated with Gag after a 10-min pulse with [(35)S]cysteine/methionine. This observation is also supported by previous work indicating that the incorporation of LysRS into HIV-1 is very sensitive to the inhibition of new synthesis of LysRS.

Cell Line↗
PubMed2004

Construction and characterization of chimeric proteins composed of type-1 and type-2 periplasmic binding proteins MglB and ArgT.

The respective type-1 and type-2 periplasmic binding proteins (PBPs) MglB and ArgT are believed to have evolved from a common ancestor into siblings showing topological differences in their main chain connectivity. At first glance, they show similar structure. But, more detailed examination reveals that the chain connectivity of ArgT is more convoluted than that of MglB. Reflecting that complexity, the folding of ArgT is complicated and involves intermediate folds. On the other hand, the folding of MglB is a simple two-state transition. In the present study, we constructed and characterized several chimeras made up of various subdomains of MglB and ArgT with the aim of gaining insight into the evolution of protein folding and protein structure. Although these chimeras did not fold as compactly as their parental proteins, some did exhibit cooperative folding, which suggests that novel proteins with new connectivity and new folding pathways could have emerged at a fairly high rate throughout the evolution of proteins.

Circular Dichroism↗
PubMed2003

Distinct macroscopic structures developed from solutions of chemical compounds and periodic proteins.

By controlling the growth of inorganic crystals, macro-biomolecules, including proteins, play pivotal roles in modulating biomineralization. Natural proteins that promote biomineralization are often composed of simple repeats of peptide sequences; however, the relationship between these repetitive structures and their functions remains largely unknown. Here we show that an artificial protein containing a repeated peptide sequence allows NaCl, KCl, CuSO(4) and sucrose to form a variety of macroscopic structures, as represented by their dendritic configurations. Mutational analyses revealed that the physicochemical characteristics of the protein, not the peptide sequence per se, were responsible for formation of the dendritic structures. This suggests that proteins that modulate crystal growth may have evolved as repeat-containing forms at a relatively high rate. These observations could serve as the basis for developing new genetic programming systems for creation of artificial proteins able to modulate crystal growth from inorganic compounds, and may thus provide a new tool for nano-biotechnology.

Crystallization↗
PubMed2003

Characterization of folding pathways of the type-1 and type-2 periplasmic binding proteins MglB and ArgT.

The family of periplasmic binding proteins (PBPs) is believed to have arisen from a common ancestor and to have differentiated into two types. At first approximation, both types of PBPs have the same fold pattern, reflecting their common origin. However, the connection between the main chains of a type 2 PBP is more complicated than a type 1 PBP's. We have been interested in the possibility that such structural changes affect the folding of PBPs. In this study, we have characterized the folding pathways of MglB (a type 1 PBP) and ArgT (a type 2 PBP) by using urea gradient gel electrophoresis, fast protein size-exclusion liquid chromatography and hydrophobic dye ANS binding assay. We found a distinct difference in folding between these two proteins. The folding of MglB followed a simple two-state transition model, whereas the folding of ArgT was more complicated.

Biological Transport, Active↗
PubMed2003

Translated products of tandem microgene repeats exhibit diverse properties also seen in natural proteins.

Repetitiousness is often observed in the primary and tertiary structures of proteins. We are intrigued by the potential role played by periodicity in the evolution of proteins and have created artificial repetitious proteins from repeats of short DNA sequences (microgenes). In this paper we characterize the physicochemical properties of six such artificially created proteins, which are the translated products of repeats of three microgenes. Three of the six proteins contain beta-sheet-like structures and are rather hydrophobic in nature. These proteins form macroscopic membranous structures in the presence of monovalent cationic ions, suggesting they have the capacity to promote strong intermolecular interactions. Of the other three proteins, one is comprised of alpha-helices and two have disordered structures. Small angle X-ray scattering analysis indicates that the artificial proteins do not fold as tightly as natural proteins, but are more compact than if completely denatured. One alpha-helical protein whose microgene unit was designed from coiled coil proteins was crystallized, demonstrating that repetitious artificial proteins can undergo transition to a more ordered state under appropriate conditions. Application of this approach to the development of a novel protein engineering system is discussed.

Amino Acid Sequence↗