Experimental Approaches of NMR Spectroscopy by The Nuclear Magnetic Resonance Society of Japan

Author:The Nuclear Magnetic Resonance Society of Japan
Language: eng
Format: epub
Publisher: Springer Singapore, Singapore

The (ϕ, φ) plots of the 25 closest data base matches predicted for the GAGSGAGA motif using TALOS-N are shown in Fig. 10.2b [6]. Here the motif, GAGSGAGA is a typical sequence of crystalline domain of SF and appears frequently in the primary structure [26]. It is noted that the angles (ϕ, φ) fall into well narrow regions for the (i + 1) residue in typical type II β-turn structures. Figure 10.2c shows the model constructed using the average torsion angles for the best matches (ϕ, φ) for the repeated GAGSGAG motif. This type II β-turn structure is essentially the same as Silk I* structure (type II β-turn) in the solid-state reported previously [17, 28–30].

We reported previously molecular dynamic (MD) simulations of three dipeptides, Ac-X-NHMe (X = G, A, S), in water to examine the favorable local conformation for the repeated sequence of the GAGSGA in water [31]. The conformational probability maps calculated for these three dipeptides indicate that the torsion angle of each Gly, Ala, and Ser residues in the repeated GAGSGA sequence with type II β-turn structure was basically in the energetically stable regions in water. The high possibility of the appearance of β-turn structure was also pointed out by the MD simulation of Ac-(AG)8-NHMe in water. This means that the time-averaged local structure of the silk fibroin in random coil form seems basically similar to those of type II β-turn structure in the solid-state. The amplitude and width of the structural fluctuations of these three residues are relatively large for random coil form in the diluted silk fibroin aqueous solution and such a fluctuation decreases by aggregation formation of the silk fibroin molecules with increasing the concentration [5]. The aggregates still keep high mobility as shown in Fig. 10.1 for SF stored in the silk gland of living silkworm. The generation of such aggregate of silk fibroin chain with type II β-turn conformation will be one of the origins of the nucleation to change the structure to β-sheet structure easily by external forces [22].

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