Globular structures of a helix-coil copolymer: Self-consistent treatment

Nowak, Christine; Rostiashvili, V. G.; Vilgis, Thomas A.

doi:10.1063/1.2403868

Cited by 3 publications

(3 citation statements)

References 40 publications

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“…This transition is also apparent in panels A and B of Figure . Complex coupling of coil-to-globule and helix–coil transitions has been observed for simplified models. − One may ask whether the artificially low temperatures coupled with explicit representation of counterions influence these results, but an analysis of both ion–ion and peptide–ion pair correlation functions indicates that ions remain largely inert with very little direct binding at all temperatures (see Figure S2, Supporting Information).…”

Section: Resultsmentioning

confidence: 99%

50 Years of Lifson–Roig Models: Application to Molecular Simulation Data

Vitalis

Caflisch

2011

J. Chem. Theory Comput.

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Simple helix-coil transition theories have been indispensable tools in the analysis of data reporting on the reversible folding of α-helical polypeptides. They provide a transferable means to not only characterize different systems but to also compare different techniques, viz., experimental probes monitoring helix-coil transitions in vitro or biomolecular force fields in silico. This article addresses several issues with the application of Lifson-Roig theory to helix-coil transition data. We use computer simulation to generate two sets of ensembles for the temperature-controlled, reversible folding of the 21-residue, alanine-rich FS peptide. Ensembles differ in the rigidity of backbone bond angles and are analyzed using two distinct descriptors of helicity. The analysis unmasks an underlying phase diagram that is surprisingly complex. The complexities give rise to fitted nucleation and propagation parameters that are difficult to interpret and that are inconsistent with the distribution of isolated residues in the α-helical basin. We show that enthalpies of helix formation are more robustly determined using van't Hoff analysis of simple measures of helicity rather than fitted propagation parameters. To overcome some of these issues, we design a simple variant of the Lifson-Roig model that recovers physical interpretability of the obtained parameters by allowing bundle formation to be described in simple fashion. The relevance of our results is discussed in relation to the applicability of Lifson-Roig models to both in silico and in vitro data.

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Section: Resultsmentioning

confidence: 99%

50 Years of Lifson–Roig Models: Application to Molecular Simulation Data

Vitalis

Caflisch

2011

J. Chem. Theory Comput.

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“…The Zimm-Bragg case μ = 1 is pathological in this respect. It produces coil segments without internal entropy as noted and commented on before [28].…”

Section: Order and Disordermentioning

confidence: 78%

Coil-helix transition of polypeptide at water-lipid interface

Sharma¹,

Reshetnyak²,

Andreev³

et al. 2015

J. Stat. Mech.

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Abstract. We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an α-helix conformation. The polypeptide is assumed to be adsorbed to the interface between a polar and a non-polar environment such as realized by water and the lipid bilayer of a membrane. The interfacial coilhelix transformation is the first stage in the folding process of helical membrane proteins. Depending on the values of model parameters, the conformation changes as a crossover, a discontinuous transition, or a continuous transition with helicity in the role of order parameter. Our model is constructed as a system of statistically interacting quasiparticles that are activated from the helix pseudo-vacuum. The particles represent links between adjacent residues in coil conformation that form a self-avoiding random walk in two dimensions. Explicit results are presented for helicity, entropy, heat capacity, and the average numbers and sizes of both coil and helix segments. arXiv:1405.2886v2 [cond-mat.soft] 8 Jan 2015Coil-helix transition of polypeptide at water-lipid interface 2

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“…Computer simulations of different models for single chains of multiblock copolymers were performed in [34,35,36,37,38,39,40,41] to study morphological transitions, in particular the collapse of flexible-semiflexible multiblock copolymers in selective solvents [36], the collapse of flexible AB-multiblock copolymers in selective solvents [35,37,38,39,40,41], and the phase transitions in protein-like AB- and HPmultiblock copolymers [34]. Furthermore, a self-consistent-field theory was developed in [42] to study transitions in a rod-coil multiblock globule, and three different possible morphologies were identified: cols, amorphous globules, and nematic Liquid-Crystalline (LC) globules. Our approach allows for the determination of the statistical mechanical equilibrium behavior of such polymers over an unprecedented range of temperatures, without resorting to a mean-field-like approximation.…”

Section: Introductionmentioning

confidence: 99%

Diagrams of States of Single Flexible-Semiflexible Multi-Block Copolymer Chains: A Flat-Histogram Monte Carlo Study

et al. 2019

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The combination of flexibility and semiflexibility in a single molecule is a powerful design principle both in nature and in materials science. We present results on the conformational behavior of a single multiblock-copolymer chain, consisting of equal amounts of Flexible (F) and Semiflexible (S) blocks with different affinity to an implicit solvent. We consider a manifold of macrostates defined by two terms in the total energy: intermonomer interaction energy and stiffness energy. To obtain diagrams of states (pseudo-phase diagrams), we performed flat-histogram Monte Carlo simulations using the Stochastic Approximation Monte Carlo algorithm (SAMC). We have accumulated two-Dimensional Density of States (2D DoS) functions (defined on the 2D manifold of macrostates) for a SF-multiblock-copolymer chain of length N = 64 with block lengths b = 4, 8, 16, and 32 in two different selective solvents. In an analysis of the canonical ensemble, we calculated the heat capacity and determined its maxima and the most probable morphologies in different regions of the state diagrams. These are rich in various, non-trivial morphologies, which are formed without any specific interactions, and depend on the block length and the type of solvent selectivity (preferring S or F blocks, respectively). We compared the diagrams with those for the non-selective solvent and reveal essential changes in some cases. Additionally, we implemented microcanonical analysis in the “conformational” microcanonical ( N V U , where U is the potential energy) and the true microcanonical ( N V E , where E is the total energy) ensembles with the aim to reveal and classify pseudo-phase transitions, occurring under the change of temperature.

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Globular structures of a helix-coil copolymer: Self-consistent treatment

Cited by 3 publications

References 40 publications

50 Years of Lifson–Roig Models: Application to Molecular Simulation Data

50 Years of Lifson–Roig Models: Application to Molecular Simulation Data

Coil-helix transition of polypeptide at water-lipid interface

Diagrams of States of Single Flexible-Semiflexible Multi-Block Copolymer Chains: A Flat-Histogram Monte Carlo Study

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