Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

Gray, Geoffrey; Vaart, Arjan van der; Guo, Chengchen; Jones, Justin A.; Onofrei, David; Cherry, Brian R.; Lewis, Randolph V.; Yarger, Jeffery L.; Holland, Gregory P.

doi:10.3390/ijms17122023

Cited by 27 publications

(28 citation statements)

References 49 publications

(75 reference statements)

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“…In a recent investigation of Ma dragline silk fiber from the N. clavipes species, the X amino acids in the Gly-Gly-X repeats were isotopically enriched. [63] 13 C chemical shifts extracted for X in the Gly-Gly-X repeat stretch where X = Leu, Tyr, and Gln were a bit ambiguous, however, it was determined that they were not β-sheet or α-helical. A combination of ssNMR and molecular dynamics (MD) simulations were then used to illuminate the conformational structure of poly(Gly-Gly-X) and results gave new insight into the secondary structure of these segments, providing further support that these regions are disordered and primarily non-β-sheet.…”

Section: Spectroscopic Techniquesmentioning

confidence: 99%

Experimental Methods for Characterizing the Secondary Structure and Thermal Properties of Silk Proteins

McGill

Holland

Kaplan

2018

Macromol. Rapid Commun.

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Silk proteins are biopolymers produced by spinning organisms that have been studied extensively for applications in materials engineering, regenerative medicine, and devices due to their high tensile strength and extensibility. This remarkable combination of mechanical properties arises from their unique semi-crystalline secondary structure and block copolymer features. The secondary structure of silks is highly sensitive to processing, and can be manipulated to achieve a wide array of material profiles. Studying the secondary structure of silks is therefore critical to understanding the relationship between structure and function, the strength and stability of silk-based materials, and the natural fiber synthesis process employed by spinning organisms. However, silks present unique challenges to structural characterization due to high-molecular-weight protein chains, repetitive sequences, and heterogeneity in intra- and interchain domain sizes. Here, experimental techniques used to study the secondary structure of silks, the information attainable from these techniques, and the limitations associated with them are reviewed. Ultimately, the appropriate utilization of a suite of techniques discussed here will enable detailed characterization of silk-based materials, from studying fundamental processing-structure-function relationships to developing commercially useful quality control assessments.

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Section: Spectroscopic Techniquesmentioning

confidence: 99%

Experimental Methods for Characterizing the Secondary Structure and Thermal Properties of Silk Proteins

McGill

Holland

Kaplan

2018

Macromol. Rapid Commun.

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“…The solid-state NMR studies used a combination of approaches [66]. 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].…”

Section: Introductionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Asakura¹

2020

Molecules

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This review will introduce very recent studies using solid-state nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulation on the structure and dynamics of spider dragline silks conducted by the author’s research group. Spider dragline silks possess extraordinary mechanical properties by combining high tensile strength with outstanding elongation before breaking, and therefore continue to attract attention of researchers in biology, biochemistry, biophysics, analytical chemistry, polymer technology, textile technology, and tissue engineering. However, the inherently non-crystalline structure means that X-ray diffraction and electron diffraction methods provide only limited information because it is difficult to study the molecular structure of the amorphous region. The most detailed picture of the structure and dynamics of the silks in the solid state experimentally have come from solid-state NMR measurements coupled with stable isotope labeling of the silks and the related silk peptides. In addition, combination of solid-state NMR and MD simulation was very powerful analytical tools to understand the local conformation and dynamics of the spider dragline silk in atomic resolution. In this review, the author will emphasize how solid-state NMR and MD simulation have contributed to a better understanding of the structure and dynamics in the spider dragline silks.

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“…Structural self-assembly from their precursor structure is frequently modeled in proteins. In particular, the secondary structure of spider silk was modeled recently (Gray et al, 2016). The irreversible formation of oriented blocks was observed also in swollen polymers (Miyazaki et al, 2006;Peng N. et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Dynamic Responsive Formation of Nanostructured Fibers in a Hydrogel Network: A Molecular Dynamics Study

2020

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In an effort to study natural fiber formation, such as, e.g., spider silk, we present a model, which is capable of forming biomimetic fibrillar nanostructure from a hydrogel micellar network. The latter consists of interacting atomic groups which form cores of micelles, and of flexible chains forming the shells of the micelles. Micelles are connected in a compact network by linearly stretched chains. The structural elements of the network can be transformed during deformation from micellar into fibrillary type and their evolution is found to depend significantly on strain rate. Our model suggests a set of conditions suitable for the formation of nanostructured fibrillar network. It demonstrates that a fibrillar structure is only formed upon sufficiently fast stretching while, in contrast, the micellar gel structure is preserved, if the material is pulled slowly. We illustrate this key aspect by a minimalistic model of only four chains as part of the whole network, which provides a detailed view on the mechanism of fibril formation. We conclude that such a simplified structure has similar functionality and is probably responsible for the formation of nano-structured molecular fibrils in natural materials.

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Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

Cited by 27 publications

References 49 publications

Experimental Methods for Characterizing the Secondary Structure and Thermal Properties of Silk Proteins

Experimental Methods for Characterizing the Secondary Structure and Thermal Properties of Silk Proteins

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

Dynamic Responsive Formation of Nanostructured Fibers in a Hydrogel Network: A Molecular Dynamics Study

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