Alternation of phases of regular and irregular dynamics in protein folding

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Alternation of phases of regular and irregular dynamics in protein folding. / Chekmarev, Sergei F.

In: Physical Review E, Vol. 99, No. 2, 022412, 19.02.2019.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{e8afa1aaea864e129220d86b87517e32,

title = "Alternation of phases of regular and irregular dynamics in protein folding",

abstract = "The regularity of the dynamics in different phases of protein folding is investigated for a set of proteins which undergo a cooperative, two-state folding transition. To determine the degree of regularity of the dynamics, the fractal dimension of probability fluxes is calculated on the basis of simulated folding trajectories. It has been found that the phases of regular and irregular dynamics alternate as follows. In the initial (collapse) phase of folding, the dynamics are essentially regular. Then, as the protein comes to the basin of semicompact states that precedes the transition state, the dynamics become irregular. At the transition state, the dynamics are regularized again but become less regular when the nativelike states are explored. Depending on the specific conditions at which the protein folding was considered, some phases of the dynamics could not be well resolved, but no significant deviation from this general picture has been observed. The regularization of the dynamics at the transition state is discussed in relation to the recent studies of the Hamiltonian dynamics of small clusters, where both regular and chaotic dynamics were observed depending on the flatness of the energy surface at the transition state.",

keywords = "CHAOTIC REACTION PATHS, FREE-ENERGY SURFACES, MOLECULAR-DYNAMICS, SMALL CLUSTERS, SIMULATION, COMPLEXITY, LANDSCAPE, THERMODYNAMICS, DISTRIBUTIONS, TRANSITIONS, Models, Molecular, Protein Folding, Thermodynamics, Proteins/chemistry, Kinetics",

author = "Chekmarev, {Sergei F.}",

note = "Publisher Copyright: {\textcopyright} 2019 American Physical Society.",

year = "2019",

month = feb,

day = "19",

doi = "10.1103/PhysRevE.99.022412",

language = "English",

volume = "99",

journal = "Physical Review E",

issn = "2470-0045",

publisher = "American Physical Society",

number = "2",

}

RIS

TY - JOUR

T1 - Alternation of phases of regular and irregular dynamics in protein folding

AU - Chekmarev, Sergei F.

PY - 2019/2/19

Y1 - 2019/2/19

N2 - The regularity of the dynamics in different phases of protein folding is investigated for a set of proteins which undergo a cooperative, two-state folding transition. To determine the degree of regularity of the dynamics, the fractal dimension of probability fluxes is calculated on the basis of simulated folding trajectories. It has been found that the phases of regular and irregular dynamics alternate as follows. In the initial (collapse) phase of folding, the dynamics are essentially regular. Then, as the protein comes to the basin of semicompact states that precedes the transition state, the dynamics become irregular. At the transition state, the dynamics are regularized again but become less regular when the nativelike states are explored. Depending on the specific conditions at which the protein folding was considered, some phases of the dynamics could not be well resolved, but no significant deviation from this general picture has been observed. The regularization of the dynamics at the transition state is discussed in relation to the recent studies of the Hamiltonian dynamics of small clusters, where both regular and chaotic dynamics were observed depending on the flatness of the energy surface at the transition state.

AB - The regularity of the dynamics in different phases of protein folding is investigated for a set of proteins which undergo a cooperative, two-state folding transition. To determine the degree of regularity of the dynamics, the fractal dimension of probability fluxes is calculated on the basis of simulated folding trajectories. It has been found that the phases of regular and irregular dynamics alternate as follows. In the initial (collapse) phase of folding, the dynamics are essentially regular. Then, as the protein comes to the basin of semicompact states that precedes the transition state, the dynamics become irregular. At the transition state, the dynamics are regularized again but become less regular when the nativelike states are explored. Depending on the specific conditions at which the protein folding was considered, some phases of the dynamics could not be well resolved, but no significant deviation from this general picture has been observed. The regularization of the dynamics at the transition state is discussed in relation to the recent studies of the Hamiltonian dynamics of small clusters, where both regular and chaotic dynamics were observed depending on the flatness of the energy surface at the transition state.

KW - CHAOTIC REACTION PATHS

KW - FREE-ENERGY SURFACES

KW - MOLECULAR-DYNAMICS

KW - SMALL CLUSTERS

KW - SIMULATION

KW - COMPLEXITY

KW - LANDSCAPE

KW - THERMODYNAMICS

KW - DISTRIBUTIONS

KW - TRANSITIONS

KW - Models, Molecular

KW - Protein Folding

KW - Thermodynamics

KW - Proteins/chemistry

KW - Kinetics

UR - http://www.scopus.com/inward/record.url?scp=85062475059&partnerID=8YFLogxK

U2 - 10.1103/PhysRevE.99.022412

DO - 10.1103/PhysRevE.99.022412

M3 - Article

C2 - 30934237

AN - SCOPUS:85062475059

VL - 99

JO - Physical Review E

JF - Physical Review E

SN - 2470-0045

IS - 2

M1 - 022412

ER -

ID: 18680334