Aging dynamics in globular proteins

Summary and analysis of experimental results and simulation by a modified trap model

Levente Herenyi, Krisztian Szigeti, J. Fidy, Tamas Temesvari, Jorg Schlichter, Josef Friedrich

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Recent results of spectral diffusion experiments by spectral hole-burning techniques carried out at cryogenic temperatures on various monomeric heme proteins unequivocally show interesting new features of conformational dynamics of globular proteins that were not emphasized in the literature until now. These new aspects of the protein dynamics are anomalous diffusion and the aging effect. Here, using the similarities between proteins and glassy systems, we present a model which can interpret the line broadening and-through this effect-the aging phenomenon as well. Leaving untouched the widely accepted energy landscape (EL) concept for the general description of protein dynamics, we concentrate on the bottom of the funnel-like EL, because this part corresponds to the native state(s) at low temperature. We suggest that the overall shape of the EL at the lowest energy range is rather smooth, but on a finer scale it consists of traps. The dynamics is defined by sequential jumps among these traps and the process is described by a Master equation, where the hopping rate only depends on the parameters of the starting state. This model was adapted to interpret the common results of spectral diffusion experiments. We tested our model in the simplest case by computer simulation, and it shows excellent agreement with the experimental data. To our knowledge this is the first work where a theoretical interpretation of the aging dynamics of proteins is directly and quantitatively related to the experimental observations. We also show that the model, after the generalization that the traps are hierarchically organized, is in accordance with the concept of other well-known EL models.

Original languageEnglish
Pages (from-to)68-75
Number of pages8
JournalEuropean Biophysics Journal
Volume33
Issue number1
DOIs
Publication statusPublished - Feb 2004

Fingerprint

Proteins
Hemeproteins
Temperature
Computer Simulation

Keywords

  • Anomalous diffusion
  • Energy landscape
  • Spectral diffusion
  • Spectral hole burning

ASJC Scopus subject areas

  • Biophysics

Cite this

Aging dynamics in globular proteins : Summary and analysis of experimental results and simulation by a modified trap model. / Herenyi, Levente; Szigeti, Krisztian; Fidy, J.; Temesvari, Tamas; Schlichter, Jorg; Friedrich, Josef.

In: European Biophysics Journal, Vol. 33, No. 1, 02.2004, p. 68-75.

Research output: Contribution to journalArticle

Herenyi, Levente ; Szigeti, Krisztian ; Fidy, J. ; Temesvari, Tamas ; Schlichter, Jorg ; Friedrich, Josef. / Aging dynamics in globular proteins : Summary and analysis of experimental results and simulation by a modified trap model. In: European Biophysics Journal. 2004 ; Vol. 33, No. 1. pp. 68-75.
@article{25d3083684b644a3bd1a035004d96885,
title = "Aging dynamics in globular proteins: Summary and analysis of experimental results and simulation by a modified trap model",
abstract = "Recent results of spectral diffusion experiments by spectral hole-burning techniques carried out at cryogenic temperatures on various monomeric heme proteins unequivocally show interesting new features of conformational dynamics of globular proteins that were not emphasized in the literature until now. These new aspects of the protein dynamics are anomalous diffusion and the aging effect. Here, using the similarities between proteins and glassy systems, we present a model which can interpret the line broadening and-through this effect-the aging phenomenon as well. Leaving untouched the widely accepted energy landscape (EL) concept for the general description of protein dynamics, we concentrate on the bottom of the funnel-like EL, because this part corresponds to the native state(s) at low temperature. We suggest that the overall shape of the EL at the lowest energy range is rather smooth, but on a finer scale it consists of traps. The dynamics is defined by sequential jumps among these traps and the process is described by a Master equation, where the hopping rate only depends on the parameters of the starting state. This model was adapted to interpret the common results of spectral diffusion experiments. We tested our model in the simplest case by computer simulation, and it shows excellent agreement with the experimental data. To our knowledge this is the first work where a theoretical interpretation of the aging dynamics of proteins is directly and quantitatively related to the experimental observations. We also show that the model, after the generalization that the traps are hierarchically organized, is in accordance with the concept of other well-known EL models.",
keywords = "Anomalous diffusion, Energy landscape, Spectral diffusion, Spectral hole burning",
author = "Levente Herenyi and Krisztian Szigeti and J. Fidy and Tamas Temesvari and Jorg Schlichter and Josef Friedrich",
year = "2004",
month = "2",
doi = "10.1007/s00249-003-0346-3",
language = "English",
volume = "33",
pages = "68--75",
journal = "European Biophysics Journal",
issn = "0175-7571",
publisher = "Springer Verlag",
number = "1",

}

TY - JOUR

T1 - Aging dynamics in globular proteins

T2 - Summary and analysis of experimental results and simulation by a modified trap model

AU - Herenyi, Levente

AU - Szigeti, Krisztian

AU - Fidy, J.

AU - Temesvari, Tamas

AU - Schlichter, Jorg

AU - Friedrich, Josef

PY - 2004/2

Y1 - 2004/2

N2 - Recent results of spectral diffusion experiments by spectral hole-burning techniques carried out at cryogenic temperatures on various monomeric heme proteins unequivocally show interesting new features of conformational dynamics of globular proteins that were not emphasized in the literature until now. These new aspects of the protein dynamics are anomalous diffusion and the aging effect. Here, using the similarities between proteins and glassy systems, we present a model which can interpret the line broadening and-through this effect-the aging phenomenon as well. Leaving untouched the widely accepted energy landscape (EL) concept for the general description of protein dynamics, we concentrate on the bottom of the funnel-like EL, because this part corresponds to the native state(s) at low temperature. We suggest that the overall shape of the EL at the lowest energy range is rather smooth, but on a finer scale it consists of traps. The dynamics is defined by sequential jumps among these traps and the process is described by a Master equation, where the hopping rate only depends on the parameters of the starting state. This model was adapted to interpret the common results of spectral diffusion experiments. We tested our model in the simplest case by computer simulation, and it shows excellent agreement with the experimental data. To our knowledge this is the first work where a theoretical interpretation of the aging dynamics of proteins is directly and quantitatively related to the experimental observations. We also show that the model, after the generalization that the traps are hierarchically organized, is in accordance with the concept of other well-known EL models.

AB - Recent results of spectral diffusion experiments by spectral hole-burning techniques carried out at cryogenic temperatures on various monomeric heme proteins unequivocally show interesting new features of conformational dynamics of globular proteins that were not emphasized in the literature until now. These new aspects of the protein dynamics are anomalous diffusion and the aging effect. Here, using the similarities between proteins and glassy systems, we present a model which can interpret the line broadening and-through this effect-the aging phenomenon as well. Leaving untouched the widely accepted energy landscape (EL) concept for the general description of protein dynamics, we concentrate on the bottom of the funnel-like EL, because this part corresponds to the native state(s) at low temperature. We suggest that the overall shape of the EL at the lowest energy range is rather smooth, but on a finer scale it consists of traps. The dynamics is defined by sequential jumps among these traps and the process is described by a Master equation, where the hopping rate only depends on the parameters of the starting state. This model was adapted to interpret the common results of spectral diffusion experiments. We tested our model in the simplest case by computer simulation, and it shows excellent agreement with the experimental data. To our knowledge this is the first work where a theoretical interpretation of the aging dynamics of proteins is directly and quantitatively related to the experimental observations. We also show that the model, after the generalization that the traps are hierarchically organized, is in accordance with the concept of other well-known EL models.

KW - Anomalous diffusion

KW - Energy landscape

KW - Spectral diffusion

KW - Spectral hole burning

UR - http://www.scopus.com/inward/record.url?scp=1042267273&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=1042267273&partnerID=8YFLogxK

U2 - 10.1007/s00249-003-0346-3

DO - 10.1007/s00249-003-0346-3

M3 - Article

VL - 33

SP - 68

EP - 75

JO - European Biophysics Journal

JF - European Biophysics Journal

SN - 0175-7571

IS - 1

ER -