Akio Nishimura

Refined Crystal Structure of Samia cynthia ricini Silk Fibroin Revealed by Solid-State NMR Investigations

Samia cynthia ricini is one of the wild silkworms and its silk fibroin (SF) consists of alternatively repeating poly-l-alanine (PLA) sequences as crystalline domain and glycine-rich sequences as noncrystalline domain; the structure is similar to those of spider silk and other wild silkworm silks. In this paper, we proposed a new staggered model for the packing arrangement of the PLA sequence through the use of the Cambridge Serial Total Energy Package program and a comparison of the observed and calculated chemical shifts of the PLA sequence with the Gauge Including Projector Augmented Wave method. The new model was supported by the interatomic distance information from the cross peaks of Ala Cβ dipolar-assisted rotational resonance (DARR) spectrum of the PLA sequences in S. c. ricini SF fiber. In addition, three 13C NMR peaks observed in the β-sheet region were assigned to the carbons with different environments in the same model, but not assigned to different β-sheet structures.

Effect of Water on The Structure and Dynamics of Regenerated [3-13C] Ser, [3-13C] Tyr and [3-13C] Ala-Bombyx mori Silk Fibroin Studied with 13C Solid-State NMR.

The effects of water on the structure and dynamics of natural and regenerated silk fibroin (SF) samples were studied using 13C solid-state nuclear magnetic resonance (NMR) spectroscopy. We prepared different types of SF materials, sponges, and fibers with different preparation methods and compared their NMR spectra in the dry and hydrated states. Three kinds of 13C NMR techniques, r-INEPT, CP/MAS, and DD/MAS, coupled with 13C isotope labeling of Ser, Tyr, and Ala residues were used. In the hydrated sponges, several conformations, that is, Silk I* and two kinds of β-sheets, A and B, random coil, and highly mobile hydrated random coil were observed, and the fractions were determined. The fractions were remarkably different among the three sponges but with only small differences among the regenerated and native fibers. The increase in the fraction of β-sheet B might be one of the structural factors for preparing stronger regenerated SF fiber.

Unusual Dynamics of Alanine Residues in Polyalanine Regions with Staggered Packing Structure of Samia Cynthia Ricini Silk Fiber in Dry and Hydrated States Studied by 13C Solid-State NMR and Molecular Dynamics Simulation

Recently, the wild silkworm and spider dragline silks have been paid considerable attention as potentially valuable biomedical materials. Samia cynthia ricini is one of the wild silkworms and the primary structure of the silk fibroin (SF) consists of tandemly repeated polyalanine (poly-A:(A)12,13). Here, we report the unusual dynamical character observed in Ala Cβ groups in the poly-A region which forms an antiparallel-β-sheet structure with a staggered packing arrangement. The 13C spin-lattice relaxation ( T1s) and spin-spin relaxation times ( T2s) of Ala Cβ peaks in S. c. ricini SF fibers were observed in dry and hydrated states. The lowest field peak in Ala Cβ of the poly-A region showed 2 times longer T1 value and shorter correlation time than the other Ala Cβ peaks of the staggered packing structure, suggesting unusually fast hopping in methyl groups. Molecular dynamics simulations indicated that two of the Ala Cβ carbons out of eight existing in the unit cell of the staggered packing structure exhibited the fastest hopping motion in spite of the shortest Cβ-Cβ distance, indicating a geared hopping motion. T2 values of the hydrated and dry Ala Cβ peaks showed a similar value, indicating that the backbone motion of S. c. ricini SF fiber is not significantly affected by hydration.

Stretched exponential relaxation process of onion structures under various oscillatory shears with analysis using Shannon entropy

Hirokazu Maruoka, ∗ Akio Nishimura, Makoto Yoshida, Hideharu Ushiki, † and Keisuke Hatada 3, ‡ United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan Department Chemie, Physikalische Chemie, Ludwig-Maximilians-Universität München, Haus E2.033, Butenandtstrasse 11, 81377 München, Germany Physics Division, School of Science and Technology, Università di Camerino, via Madonna delle Carceri 9, I-62032 Camerino (MC), Italy (Dated: October 4, 2018)

Dynamics of a dry-rebounding drop: observations, simulations, and modeling

Abstract Dynamics of a dry-rebounding drop was studied experimentally, numerically, and theoretically. Experimental results were reproduced by our computational fluid dynamics simulations, from which time series of kinetic energy, potential energy, and surface energy were obtained. The time series of these energies quantitatively clarified the energy conversion and loss during the dry-rebound. These results were interpreted by using an imaginary spring model and a spherical harmonic analysis. The spring model explained the vertical deformation of the drop, however, could not completely explain the energy loss; the timings of the energy loss did not match. From a viewpoint of the spherical harmonic deformation of a drop, the deformation of the drop after the impact was found to be a combination of two vibrational motions. One of the two vibrational motions is an inertial motion derived from the free-fall and the another is a pressure-induced motion derived from a pressure surge due to the sudden stop of the bottom part of the drop at the impact. The existence of the pressure surge at the impact was confirmed in the simulated results. The pressure-induced motion resists the inertial motion and consequently dumps the kinetic energy of the drop.

Packing Arrangements and Intersheet Interaction of Alanine Oligopeptides As Revealed by Relaxation Parameters Obtained from High-Resolution 13C Solid-State NMR

Alanine oligopeptides provide a key structure of the crystalline domains of the silks from spiders and wild silkworm and also the sequences included in proteins such as antifreeze proteins and amyloids. In this paper, the local dynamics of alanine oligopeptides, (Ala)3, (Ala)4, and (Ala)6 were examined by high-resolution 13C solid-state NMR. The 13C spin-lattice relaxation times (T1s) for the Cβ4 carbons of antiparallel (AP)-β-sheet (Ala)4 significantly prolonged and the correlation time was estimated as 3.6 × 10-11 s which was shorter than those of other carbons in the AP-β-sheet (Ala)4 (2.8 × 10-10 s). The T1 values for the Cβ carbons of (Ala)6 showed significantly longer correlation time (8.8 × 10-9 s) than those of AP-β-sheet (Ala)4. It is thus revealed that AP-β-sheet (Ala)6 exhibited stronger intersheet interaction than those of AP-β-sheet (Ala)4. The 13C spin-spin relaxation times (T2s) for the Cβ4 carbons showed longer than those of the other Cβ1-3 carbons of AP-β-sheet (Ala)4. T2 values of Cβ carbons reflect the slow time-scale (∼70 kHz) backbone motions. The C-terminal forms strong hydrogen bonds with water molecules and thus the backbone motion is slower than ∼70 kHz, while the central backbone motions are faster than ∼70 kHz in the AP-β-sheet (Ala)4.