[Searching the origin of life by in vitro evolution system].
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Acylation↗
Biomedical subjects
Kimitsuna Watanabe
Publications and source records attributed to Kimitsuna Watanabe.
Crystal structure of d(GCGAAAGCT) containing parallel-stranded duplex with homo base pairs and anti-parallel duplex with Watson-Crick base pairs.
A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized under a slightly acidic condition, and its crystal structure has been determined at 2.5A resolution. In the first half of the oligomer, the sequence CGAA forms a parallel duplex with another symmetry-related half through the homo base pairs, C2:C2+ (semi-protonated between the Watson-Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The second halves of the parallel duplex are split away in the different direction, and extended to form an anti-parallel B-form duplex with another second half.
Base Pairing↗
S-peptide as a potent peptidyl linker for protein cross-linking by microbial transglutaminase from Streptomyces mobaraensis.
We have found that ribonuclease S-peptide can work as a novel peptidyl substrate in protein cross-linking reactions catalyzed by microbial transglutaminase (MTG) from Streptomyces mobaraensis. Enhanced green fluorescent protein tethered to S-peptide at its N-terminus (S-tag-EGFP) appeared to be efficiently cross-linked by MTG. As wild-type EGFP was not susceptible to cross-linking, the S-peptide moiety is likely to be responsible for the cross-linking. A site-directed mutation study assigned Gln15 in the S-peptide sequence as the sole acyl donor. Mass spectrometric analysis showed that two Lys residues (Lys5 and Lys11) in the S-peptide sequence functioned as acyl acceptors. We also succeeded in direct monitoring of the cross-linking process by virtue of fluorescence resonance energy transfer (FRET) between S-tag-EGFP and its blue fluorescent color variant (S-tag-EBFP). The protein cross-linking was tunable by either engineering S-peptide sequence or capping the S-peptide moiety with S-protein, the partner protein of S-peptide for the formation of ribonuclease A. The latter indicates that S-protein can be used as a specific inhibitor of S-peptide-directed protein cross-linking by MTG. The controllable protein cross-linking of S-peptide as a potent substrate of MTG will shed new light on biomolecule conjugation.
Amino Acid Sequence↗
Analysis of relative positions of ribonucleotide bases in a crystal structure of ribosome.
Relative positions of bases to bases in a crystal structure of ribosome were analyzed extensively. It was found that there is no clear relation between bases apart more than 15 A and, thus, the relative location of bases can be analyzed within 15 A of the reference bases. As for base pairing, major positioning was found to be due to the Watson-Crick type base pairs. Some other positions corresponding to non-Watson-Crick type base pairs were also found in some extents. As for base-base stacking, it was observed that the bases stacked to adenine base are dispersive. It was found that less non-Watson-Crick base pairs was found close to the protein binding site, suggesting that the protein components have a tendency to bind to the regular stem structures. The database of relative location of bases must be useful for improvement of structural determination and structural modeling systems.
Algorithms↗