Thermodynamic Confinement and α-Helix Persistence Length in Poly(γ-benzyl-<scp>l</scp>-glutamate)-<i>b</i>-poly(dimethyl siloxane)-<i>b</i>-poly(γ-benzyl-<scp>l</scp>-glutamate) Triblock Copolymers

Papadopoulos, Periklis; Floudas, George; Schnell, Ingo; Lieberwirth, Ingo; Nguyen, Trong Q.; Klok, Harm‐Anton

doi:10.1021/bm050772t

Cited by 37 publications

(47 citation statements)

References 39 publications

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“…Using the bending stiffness, we estimate the persistence length of the AH protein (at T = 300 K) to approximately be 5.5 nm. This result agrees somewhat with experimental studies that found a persistence length of a AH structure on the order of 1-2 nm [Papadopoulos et al 2006]. The reason for this disagreement could, for example, be rate effects.…”

Section: The Sequence Of the Protein Considered Here Is Gly Ser Asn Gsupporting

confidence: 91%

Hierarchical chemo-nanomechanics of proteins: entropic elasticity, protein unfolding and molecular fracture

Buehler¹

2007

JOMMS

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Proteins are an integral part of nature's material design. Here we apply multiscale modeling capable of providing a bottom-up description of the nanomechanics of chemically complex protein materials under large deformation and fracture. To describe the formation and breaking of chemical bonds of different character, we use a new reactive force field approach that enables us to describe the unfolding dynamics while considering the breaking and formation of chemical bonds in systems that are comprised of several thousand atoms. We particularly focus on the relationship between secondary and tertiary protein structures and the mechanical properties of molecules under large deformation and fracture. Our research strategy is to systematically investigate the nanomechanics of three protein structures with increasing complexity, involving alpha helices, random coils and beta sheets. The model systems include an alpha helical protein from human vimentin, a small protein α-conotoxin PnIB from conus pennaceus, and lysozyme, an enzyme that catalyzes breaking of glycosidic bonds. We find that globular proteins can feature extremely long unfolding paths of several tens of nanometers, displaying a characteristic sawtooth shape of the force-displacement curve. Our results suggest that the presence of disulfide crosslinks can significantly influence the mechanics of unfolding. Fibrillar proteins show shorter unfolding paths and continuous increase of forces until molecular rupture occurs. In the last part of the article we outline how a mesoscale representation of the alpha helical protein structure can be developed within the framework of hierarchical multiscale modeling, utilizing the results of atomistic modeling, without relying on empirical parameters. We apply this model to describe the competition between entropic and energetic elasticity in the mechanics of a single alpha helical protein molecule, at long time scales reaching several microseconds. We conclude with a discussion of hybrid reactive-nonreactive modeling that could help to overcome some of the computational limitations of reactive force fields.

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Section: The Sequence Of the Protein Considered Here Is Gly Ser Asn Gsupporting

confidence: 91%

Hierarchical chemo-nanomechanics of proteins: entropic elasticity, protein unfolding and molecular fracture

Buehler¹

2007

JOMMS

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“…26 Furthermore, the computed lamellar microstructure should be expected based on simple volume fraction rules, 1 but has not been experimentally observed. This deviation from experiment is believed to arise due to three factors: (1) monodisperse chain lengths, (2) strong segregation brought about by the repulsive PDMS/PBLG interactions, and (3) short spatial length scale.…”

Section: Resultsmentioning

confidence: 93%

Coarse-Grained Modeling of Peptidic/PDMS Triblock Morphology

2014

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The morphology and chain packing structures in block copolymers strongly impact their mechanical response; therefore, to design and develop high performance materials that utilize block copolymers, it is imperative to have an understanding of their self-assembly behavior. In this research, we utilize coarse-grained (CG) molecular dynamics to study the effects of peptidic volume fraction and secondary structure on the morphological development and chain assembly of the triblocks poly(γ-benzyl-L-glutamate)-b-poly(dimethylsiloxane)-b-poly(γ-benzyl-L-glutamate) (GSG) and poly(dimethylsiloxane)-b-poly(γ-benzyl-L-glutamate)-b-poly(dimethylsiloxane) (SGS). This necessitated developing a complete coarse-grained parameter set for poly(dimethylsiloxane) that closely captures the radial pair distribution of a united atom model and the experimental density at 300 K. These parameters are combined with the MARTINI amino acid CG force field and validated against prior reported values of domain spacing and peptide chain packing for GSG. The combined CG parameter set is then used to model SGS, a triblock currently in development for nature-inspired mechanically enhanced hybrid materials. The results reveal that the peptide side chain strongly influences the final morphology. For instance, lamellar or hexagonally packed cylindrical domain formation can result from the variation in side-chain interactions, namely, side-chain sterics preventing curved interface formation by increasing interfacial free volume. Ultimately, this research lays the foundation for future studies involving systems with dispersity, mixtures of secondary structures, and larger multiblock copolymers, such as polyurethanes and polyureas.

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“…It is hence useful to put our finding of the highly flexible nature of the Smc2-Smc4 coiled coils (L P ∼4 nm) into perspective. While a single alpha helix is very flexible (L P ∼1 nm; Papadopoulos et al., 2006 ), coiled coils are in general significantly more stiff. Theoretically, the persistence length of a coiled coil formed by two alpha helixes has been predicted to be as high as 200 nm ( Yogurtcu et al., 2010 ).…”

Section: Discussionmentioning

confidence: 99%

Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic

et al. 2016

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SummaryStructural maintenance of chromosomes (SMC) protein complexes, including cohesin and condensin, play key roles in the regulation of higher-order chromosome organization. Even though SMC proteins are thought to mechanistically determine the function of the complexes, their native conformations and dynamics have remained unclear. Here, we probe the topology of Smc2-Smc4 dimers of the S. cerevisiae condensin complex with high-speed atomic force microscopy (AFM) in liquid. We show that the Smc2-Smc4 coiled coils are highly flexible polymers with a persistence length of only ∼4 nm. Moreover, we demonstrate that the SMC dimers can adopt various architectures that interconvert dynamically over time, and we find that the SMC head domains engage not only with each other, but also with the hinge domain situated at the other end of the ∼45-nm-long coiled coil. Our findings reveal structural properties that provide insights into the molecular mechanics of condensin complexes.

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Thermodynamic Confinement and α-Helix Persistence Length in Poly(γ-benzyl-l-glutamate)-b-poly(dimethyl siloxane)-b-poly(γ-benzyl-l-glutamate) Triblock Copolymers

Cited by 37 publications

References 39 publications

Hierarchical chemo-nanomechanics of proteins: entropic elasticity, protein unfolding and molecular fracture

Hierarchical chemo-nanomechanics of proteins: entropic elasticity, protein unfolding and molecular fracture

Coarse-Grained Modeling of Peptidic/PDMS Triblock Morphology

Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic

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