Shear-Flow-Induced Unfolding of Polymeric Globules

Alexander‐Katz, Alfredo; Schneider, Mat­thias; Schneider, Stefan W.; Wixforth, Achim; Netz, Roland R.

doi:10.1103/physrevlett.97.138101

Cited by 152 publications

(246 citation statements)

References 15 publications

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“…Linear fits to the data in Fig. 2(b) yield the collapse points of~c % 0:6 AE 0:1 (N ¼ 50) and~c % 0:5 AE 0:1 (N ¼ 100), in good agreement with previous studies [19].…”

supporting

confidence: 78%

Internal Friction and Nonequilibrium Unfolding of Polymeric Globules

2009

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The stretching response of a single collapsed homopolymer is studied using Brownian dynamic simulations. The irreversibly dissipated work is found to be dominated by internal friction effects below the collapse temperature, and the internal viscosity grows exponentially with the effective cohesive strength between monomers. These results explain friction effects of globular DNA and are relevant for dissipation at intermediate stages of protein folding. DOI: 10.1103/PhysRevLett.103.028102 PACS numbers: 87.15.Àv, 62.40.+i, 82.37.Àj Conformational kinetics are crucial for the function of biopolymers: e.g., the muscle protein titin unfolds at a particular loading force in a highly dissipative manner, irreversibly converting most of the mechanical work into heat [1], while in myoglobin ligand dissociation induces a global conformational change of the protein [2][3][4]. Such transitions involve spatial protein reorganization, and thus internal dissipation mechanisms on different conformational levels in addition to solvent viscosity become important in determining the dynamic response to a given stimulus.Different contributions to internal polymeric friction have experimentally been distinguished [5]: On the smallest length scale are conformational molecular transitions involving torsional bond degrees of freedom [6,7]. For polymer solutions above the overlap concentration or for polymers in confined geometries, entanglement effects become important and contribute significantly [8]. Finally, for collapsed polymers or folded proteins, the continuous breakage and reformation of cohesive bonds gives rise to an extra contribution to the viscosity inside a globule [9,10]. The significant consequence particularly for protein science is that internal friction may dictate the rate of conformational kinetics and thus protein function dynamics. In all of these experimental studies, care is taken to isolate internal friction effects from the (in the present context uninteresting) hydrodynamic drag of the solvent by, for example, variation of the solvent viscosity [7].Coarse-grained stochastic models that involve activated hopping events in smooth and idealized energy landscapes nicely explain experimental titin unfolding force curves and provide insight into the dissipation mechanism involving two-step unfolding [11]. A different mechanism is expected for globular homopolymers, proteins in the molten globular state [12], and some disordered intermediates that occur during conformational protein transformations [13]. Here many near-optimal competing states exist, the energy landscape is rough, and structural changes occur gradually through a whole spectrum of intermediate states [14,15]. Many cohesive bonds are broken and reformed repeatedly during unfolding, and the concept of an internal effective viscosity naturally arises [9,10]. There have been quite a few simulation studies on the forced unfolding of bead-spring models for proteins [16] and globular polymers [17,18], but the concept of an internal viscosity has not been...

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“…Linear fits to the data in Fig. 2(b) yield the collapse points of~c % 0:6 AE 0:1 (N ¼ 50) and~c % 0:5 AE 0:1 (N ¼ 100), in good agreement with previous studies [19].…”

supporting

confidence: 78%

Internal Friction and Nonequilibrium Unfolding of Polymeric Globules

2009

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“…Hence, for collapsed vWF polymers we will use such value. For comparison purposes, we also study Y polymers, which correspond to u ¼ 0.41 k B T 19,20 . The monomers interact with the colloids at discrete binding sites on the colloid surfaces that mimic the actual GPIb-a receptor on the surface of platelets that specifically binds to the A1 domain of vWF [10][11][12] .…”

Section: Resultsmentioning

confidence: 99%

“…To control the solvent property of the polymers, we add a Lennard-Jones potential between each monomers with strength u. It has been shown that u ¼ 0.41 and 2.08 k B T are suitable choices for simulating polymers in the Y and bad solvent 19,20 . The monomers interact with the binding sites on the colloid surfaces (where each colloid has N b ¼ 64 binding sites on the surface) through the Bell model 21 .…”

Section: Methodsmentioning

confidence: 99%

Blood-clotting-inspired reversible polymer–colloid composite assembly in flow

et al. 2013

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Blood clotting is a process by which a haemostatic plug is assembled at the site of injury. The formation of such a plug, which is essentially a (bio)polymer-colloid composite, is believed to be driven by shear flow in its initial phase, and contrary to our intuition, its assembly is enhanced under stronger flowing conditions. Here, inspired by blood clotting, we show that polymer-colloid composite assembly in shear flow is a universal process that can be tailored to obtain different types of aggregates including loose and dense aggregates, as well as hydrodynamically induced 'log'-type aggregates. The process is highly controllable and reversible, depending mostly on the shear rate and the strength of the polymer-colloid binding potential. Our results have important implications for the assembly of polymercolloid composites, an important challenge of immense technological relevance. Furthermore, flow-driven reversible composite formation represents a new paradigm in non-equilibrium self-assembly.

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“…A Lennard-Jones potential is considered for each monomer with strength u to control the solvent properties of the polymers. It has been demonstrated that u = 0.41 and u = 2.08k B T are suitable choices for simulating polymers in the and bad solvent [73,78].…”

Section: A Simulation Of Clusters By Brownian Dynamicsmentioning

confidence: 99%

Micromechanical model for isolated polymer-colloid clusters under tension

et al. 2016

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Binary polymer-colloid (PC) composites form the majority of biological load-bearing materials. Due to the abundance of the polymer and particles, and their simple aggregation process, PC clusters are used broadly by nature to create biomaterials with a variety of functions. However, our understanding of the mechanical features of the clusters and their load transfer mechanism is limited. Our main focus in this paper is the elastic behavior of close-packed PC clusters formed in the presence of polymer linkers. Therefore, a micromechanical model is proposed to predict the constitutive behavior of isolated polymer-colloid clusters under tension. The mechanical response of a cluster is considered to be governed by a backbone chain, which is the stress path that transfers most of the applied load. The developed model can reproduce the mean behavior of the clusters and is not dependent on their local geometry. The model utilizes four geometrical parameters for defining six shape descriptor functions which can affect the geometrical change of the clusters in the course of deformation. The predictions of the model are benchmarked against an extensive set of simulations by coarse-grained-Brownian dynamics, where clusters with different shapes and sizes were considered. The model exhibits good agreement with these simulations, which, besides its relative simplicity, makes the model an excellent add-on module for implementation into multiscale models of nanocomposites.

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Shear-Flow-Induced Unfolding of Polymeric Globules

Cited by 152 publications

References 15 publications

Internal Friction and Nonequilibrium Unfolding of Polymeric Globules

Internal Friction and Nonequilibrium Unfolding of Polymeric Globules

Blood-clotting-inspired reversible polymer–colloid composite assembly in flow

Micromechanical model for isolated polymer-colloid clusters under tension

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