Ab initio study of alanine polypeptide chain twisting

Ilia Solov'yov, Alexander V. Yakubovich, Andrey V. Solov'yov, Walter Greiner

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles ph$ and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.
OriginalsprogEngelsk
TidsskriftPhysical Review E
Vol/bind73
Sider (fra-til)021916-(1-10)
ISSN2470-0045
StatusUdgivet - 2006

Fingeraftryk

polypeptides
twisting
alanine
Potential Energy Surface
potential energy
Conformation
proteins
amino acids
Amino Acids
data bases
Protein
Angle
Energy Landscape
Protein Folding
helices
folding
Secondary Structure
Helix
Density Functional
degrees of freedom

Citer dette

Solov'yov, I., Yakubovich, A. V., Solov'yov, A. V., & Greiner, W. (2006). Ab initio study of alanine polypeptide chain twisting. Physical Review E, 73, 021916-(1-10).
Solov'yov, Ilia ; Yakubovich, Alexander V. ; Solov'yov, Andrey V. ; Greiner, Walter. / Ab initio study of alanine polypeptide chain twisting. I: Physical Review E. 2006 ; Bind 73. s. 021916-(1-10).
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title = "Ab initio study of alanine polypeptide chain twisting",
abstract = "We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles ph$ and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.",
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Solov'yov, I, Yakubovich, AV, Solov'yov, AV & Greiner, W 2006, 'Ab initio study of alanine polypeptide chain twisting', Physical Review E, bind 73, s. 021916-(1-10).

Ab initio study of alanine polypeptide chain twisting. / Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.; Greiner, Walter.

I: Physical Review E, Bind 73, 2006, s. 021916-(1-10).

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Ab initio study of alanine polypeptide chain twisting

AU - Solov'yov, Ilia

AU - Yakubovich, Alexander V.

AU - Solov'yov, Andrey V.

AU - Greiner, Walter

PY - 2006

Y1 - 2006

N2 - We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles ph$ and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

AB - We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles ph$ and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

M3 - Journal article

VL - 73

SP - 021916-(1-10)

JO - Physical Review E

JF - Physical Review E

SN - 2470-0045

ER -

Solov'yov I, Yakubovich AV, Solov'yov AV, Greiner W. Ab initio study of alanine polypeptide chain twisting. Physical Review E. 2006;73:021916-(1-10).