Conformational change of 13C-labeled 47-mer model peptides of Nephila clavipes dragline silk in poly(vinyl alcohol) film by stretching studied by 13C solid-state NMR and molecular dynamics simulation

Hydration‐Induced β‐Sheet Crosslinking of α‐Helical‐Rich Spider Prey‐Wrapping Silk

“…Two peaks are required to fit the Ala C β β ‐sheet resonance because of different side‐chain packing arrangements that have been proposed from studies on silk‐like model peptides. [ 20 ] This procedure, outlined in the supplemental section of our prior work, was applied. [ 13 ] These results show that the β‐sheet content for Ala increases from ≈30% for the native silk to ≈41% after wetting, and reaches a maximum of ≈53% after wet‐shear and drying (Figure 3a and Table 2).…”

Structure and Dynamics of Spider Silk Studied with Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulation

“…Spiders can be fed on an isotopically labeled diet, allowing isotopic labeling of silk within the silk gland: either uniformly or by feeding amino acids labeled at individual positions [27][28][29][30][31][32][34][35][36][37]40,[42][43][44][45][47][48][49][50][53][54][55][56]59,61]. In addition, synthetic peptides with isotopically labelings in specific positions have proved very useful model systems permitting site-specific structural information [33,38,39,41,46,51,52,60,[62][63][64][65]. The conformation-dependent 13 C chemical shift in the 13 C cross polarization and magic angle spinning (CP/MAS) NMR spectra of silks and the model peptides coupled with selective 13 C labeling can be used effectively for determination of local structure at secondary structure level in an amino acid-specific manner [66][67][68][69][70]…”

“…On the other hand, molecular dynamics (MD) simulation is very effective to understand the local conformation and dynamics of Nephila clavipes (N. clavipes) dragline silks theoretically and to verify the experimental results [56,58,62,63,65]. MD simulation can play a critical role in connecting experimental restraints with potentially plausible molecular structures.…”

“…Therefore, it has been also used to understand the structure and structural changes of silk fibroins including silk fiber formation mechanism and the chain dynamics [73][74][75][76][77][78][79][80][81][82][83][84][85]. Especially, combination of solid-state NMR and MD simulations was very strong analytical tools to understand the local conformation and dynamics of the spider dragline silk in atomic resolution [56,58,62,63,65].…”

Packing Structure of Antiparallel β-Sheet Polyalanine Region in a Sequential Model Peptide of Nephila clavipes Dragline Silk Studied Using 13C Solid-State NMR and MD Simulation

“…Details of the structures of the Gly-rich regions are still lacking. ,,− One of the major challenges encountered in efforts to elucidate the local structures of Gly-rich regions is the presence of irregular amino acid sequences, which lead to considerable variations in local conformations and molecular structures. − Therefore, it is not easy to reveal the local conformations of the individual residues directly from the spider silk fibers, although useful information on the local structures and dynamics has been revealed partially for stable isotope-labeled dragline silks in the dry and hydrated states using solid-state NMR. − One of the potentially excellent approaches to studying the local conformations of individual residues is using sequential model peptides with selective stable isotope labeling of the Gly-rich regions and studying them using solid-state NMR based on a 13 C conformation-dependent NMR chemical shift analysis. ,,− We previously synthesized a 13 C-labeled 47-mer peptide with the sequence [(E) 4 (A) 6 GGAGQG­GYGGLGSQG­AGRGGLGGQ­GAG­(A) 6 (E) 4 (Glu (E), Ala (A), Gly (G), Gln (Q), Tyr (Y), Leu (L), Ser (S), and Arg (R)] as a typical sequential model peptide for the Gly-rich region of N. clavipes dragline silk (Figure a). ,− Here, (Glu) 4 blocks are attached at both ends to make them water-soluble . The 13 C cross-polarization (CP)/magic-angle spinning (MAS) NMR spectra of the 47-mer peptide after low-pH treatment as the sequential model of spider silk fiber were analyzed to determine the fractions of the conformations of individual Gly and Ala residues in the Gly-rich region using 13 C conformation-dependent chemical shifts and peak deconvolution. , The (Ala) 6 regions at both ends formed an AP-β structure with the staggered packing arrangement.…”