Conformational changes in glycine tri- and hexapeptide

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

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within 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 the 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 the glycine 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
TidsskriftThe European Physical Journal D: Atomic, Molecular, Optical and Plasma Physics
Vol/bind39
Sider (fra-til)23-34
ISSN1434-6060
StatusUdgivet - 2006

Fingeraftryk

glycine
Potential energy surfaces
Amino acids
potential energy
Conformations
Polypeptides
polypeptides
proteins
amino acids
Proteins
Protein folding
Energy barriers
data bases
Potential energy
helices
folding
Density functional theory
degrees of freedom
Thermodynamics
density functional theory

Citer dette

Yakubovich, Alexander V. ; Solov'yov, Ilia ; Solov'yov, Andrey V. ; Greiner, Walter. / Conformational changes in glycine tri- and hexapeptide. I: The European Physical Journal D: Atomic, Molecular, Optical and Plasma Physics. 2006 ; Bind 39. s. 23-34.
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title = "Conformational changes in glycine tri- and hexapeptide",
abstract = "We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within 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 the 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 the glycine 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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Conformational changes in glycine tri- and hexapeptide. / Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter.

I: The European Physical Journal D: Atomic, Molecular, Optical and Plasma Physics, Bind 39, 2006, s. 23-34.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Conformational changes in glycine tri- and hexapeptide

AU - Yakubovich, Alexander V.

AU - Solov'yov, Ilia

AU - Solov'yov, Andrey V.

AU - Greiner, Walter

PY - 2006

Y1 - 2006

N2 - We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within 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 the 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 the glycine 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 glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within 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 the 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 the glycine 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 - 39

SP - 23

EP - 34

JO - The European Physical Journal D: Atomic, Molecular, Optical and Plasma Physics

JF - The European Physical Journal D: Atomic, Molecular, Optical and Plasma Physics

SN - 1434-6060

ER -