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A new concept to reveal protein dynamics based on energy dissipation.

ABSTRACT: Protein dynamics is essential for its function, especially for intramolecular signal transduction. In this work we propose a new concept, energy dissipation model, to systematically reveal protein dynamics upon effector binding and energy perturbation. The concept is applied to better understand the intramolecular signal transduction during allostery of enzymes. The E. coli allosteric enzyme, aspartokinase III, is used as a model system and special molecular dynamics simulations are designed and carried out. Computational results indicate that the number of residues affected by external energy perturbation (i.e. caused by a ligand binding) during the energy dissipation process shows a sigmoid pattern. Using the two-state Boltzmann equation, we define two parameters, the half response time and the dissipation rate constant, which can be used to well characterize the energy dissipation process. For the allostery of aspartokinase III, the residue response time indicates that besides the ACT2 signal transduction pathway, there is another pathway between the regulatory site and the catalytic site, which is suggested to be the ?15-?K loop of ACT1. We further introduce the term "protein dynamical modules" based on the residue response time. Different from the protein structural modules which merely provide information about the structural stability of proteins, protein dynamical modules could reveal protein characteristics from the perspective of dynamics. Finally, the energy dissipation model is applied to investigate E. coli aspartokinase III mutations to better understand the desensitization of product feedback inhibition via allostery. In conclusion, the new concept proposed in this paper gives a novel holistic view of protein dynamics, a key question in biology with high impacts for both biotechnology and biomedicine.

SUBMITTER: Ma CW

PROVIDER: S-EPMC3195717 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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A new concept to reveal protein dynamics based on energy dissipation.

Ma Cheng-Wei CW Xiu Zhi-Long ZL Zeng An-Ping AP

PloS one 20111017 10

Protein dynamics is essential for its function, especially for intramolecular signal transduction. In this work we propose a new concept, energy dissipation model, to systematically reveal protein dynamics upon effector binding and energy perturbation. The concept is applied to better understand the intramolecular signal transduction during allostery of enzymes. The E. coli allosteric enzyme, aspartokinase III, is used as a model system and special molecular dynamics simulations are designed and ...[more]

PMID: 22022616

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Project description:Many different molecular species have been observed in the interstellar medium. These range from simple diatomic species to saturated organic molecules with several carbon atoms. The latter molecules are assumed to be formed predominantely on the surface of interstellar dust grains. All surface reactions that can proceed under the low interstellar temperatures are exothermic. Their exothermicity can be as high as a few electron volts, which is considerable compared to the thermal energy of the molecules at 10 K. It is postulated that this exothermicity can be used for the desorption of reaction products from the grain. In previous studies, we have shown that translational excitation can lead to desorption, whereas vibrational and rotational excitations are much less efficient in the desorption of surface products. Vibrational excitation is however much more likely upon bond formation than translational excitation. The present study follows energy dissipation upon translational, vibrational, or rotational excitation of admolecules on a surface and its conversion, or lack thereof, to different energy contributions. To this end, thousands of molecular dynamics simulations were performed with an admolecule on top of a surface that received a fixed amount of energy, vibrational, rotational, or translational. Three different surface species have been considered, CO2, H2O, and CH4, spanning a range in binding energies, the number of internal degrees of freedom, and molecular weights. A fast exchange of energy between vibrational stretches is observed, but only very limited exchange to rotational or translation excitation has been found. For the dissipation of energy to the surface, excitation of the surface-admolecule bond is critical. Astrochemical models often assume instantaneous equipartition of energy after a reaction process to estimate the amount of available energy for chemical desorption. Based on the present study, we conclude that this assumption is not justified.

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A new concept to reveal protein dynamics based on energy dissipation.

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A new concept to reveal protein dynamics based on energy dissipation.

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