Microcanonical analyses of homopolymer aggregation processes

Chen, Tao; Lin, Xiangsong; Liu, Yuan; Lu, Teng; Liang, Haojun

doi:10.1103/physreve.78.056101

Cited by 16 publications

(10 citation statements)

References 32 publications

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“…The hydrophobicity of the side chains correlates with the aggregation rate [15,16], so it is an important physicochemical ingredient promoting the nucleation of fibrillar aggregates. The microcanonical analysis of the heteropolymer aggregation process has been performed [13,17] and supports the main idea that simple models encompassing hydrophobic interactions among monomers or segments present the overall aggregation phenomenon through a temperaturedriven first-order transition. A more comprehensive study on the properties of the aggregation phenomenon shows that the change in the aggregation rate depends on diverse factors, grouped into extrinsic or intrinsic factors [15,18].…”

Section: Introductionmentioning

confidence: 58%

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

Frigori

Rizzi

Alves

2013

The Journal of Chemical Physics

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The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.

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Section: Introductionmentioning

confidence: 58%

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

Frigori

Rizzi

Alves

2013

The Journal of Chemical Physics

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“…[20][21][22][23][24] As shown in Fig. In systems of finite size such as the NPA considered here, the microcanonical entropy loss together with the consequent "backbending effect" will be an important indicator for essential structural transitions.…”

Section: A First-order-like Transition In Adsorption Of Nongrafted Pmentioning

confidence: 97%

Canonical and microcanonical analysis of nongrafted homopolymer adsorption by an attractive substrate

Wang

Chen

Lin

et al. 2009

The Journal of Chemical Physics

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Using the off-lattice Monte Carlo simulation and replica-exchange method, we studied the behavior of nongrafted homopolymer adsorption by an attractive substrate from both the canonical and the microcanonical views. An adsorption transition is identified from the peak in canonical specific heat and compared with the conventional polymer adsorption with one end anchored on the surface of the substrate. Judging from the typical "backbending effect" and the negative specific heat in microcanonical ensemble, the transition is first-order-like when adsorption is relatively strong. However, it becomes second-order-like when the strength of adsorption becomes weak enough. Further study reveals that for a chain consisting of a limited number of monomers, the type of this transition becoming either first- or second-order-like depends not only on the interplay between monomer-monomer and monomer-substrate interaction, but also on the width of the gap in which it is confined.

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“…Refs. [19][20][21][22][23][24][25][26][27][28][29][30][33][34][35][36][37][38][39][40][41][43][44][45][46][47][48][49][50][51] ) to perform the microcanonical analysis directly from the conformational microcanonical ensemble, i.e., neglecting the kinetic energy contribution to E, thus performing the analysis based only on the conformational density of states Ω p (E p ). The conformational entropy of a system with fixed potential energy E p is then defined as 62 S p (E p ) = k B ln Ω p (E p ).…”

Section: F Conformational Microcanonical Ensemblementioning

confidence: 99%

“…Examples of computational studies include not only lattice [17][18][19][20][21][22][23][24] and magnetic models 25,26 , but also more sophisticated biopolymeric systems, in particular, models for peptide aggregation [27][28][29][30][31][32][33] , protein dimerization 34 , homopolymer collapse [35][36][37] , protein folding [38][39][40][41][42][43][44][45][46][47][48] , and polymer adsorption [49][50][51] .…”

Section: Introductionmentioning

confidence: 99%

Microcanonical characterization of first-order phase transitions in a generalized model for aggregation

Trugilho,

Rizzi

2021

Preprint

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Aggregation transitions in disordered mesoscopic systems play an important role in several areas of knowledge, from materials science to biology. The lack of a thermodynamic limit in systems that are intrinsically finite makes the microcanonical thermostatistics analysis, which is based on the microcanonical entropy, a suitable alternative to study the aggregation phenomena. Although microcanonical entropies have been used in the characterization of first-order phase transitions in many nonadditive systems, most of the studies are only done numerically with aid of advanced Monte Carlo simulations. Here we consider a semi-analytical approach to characterize aggregation transitions that occur in a generalized model related to the model introduced by Thirring. By considering an effective interaction energy between the particles in the aggregate, our approach allowed us to obtain scaling relations not only for the microcanonical entropies and temperatures, but also for the sizes of the aggregates and free-energy profiles. In addition, we test the approach commonly used in simulations which is based on the conformational microcanonical entropy determined from a density of states that is a function of the potential energy only. Besides the evaluation of temperature versus concentration phase diagrams, we explore this generalized model to illustrate how one can use the microcanonical thermostatistics as an analysis method to determine experimentally relevant quantities such as latent heats and free-energy barriers of aggregation transitions.

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Microcanonical analyses of homopolymer aggregation processes

Cited by 16 publications

References 32 publications

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

Canonical and microcanonical analysis of nongrafted homopolymer adsorption by an attractive substrate

Microcanonical characterization of first-order phase transitions in a generalized model for aggregation

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