Toward direct determination of conformations of protein building units from multidimensional NMR experiments III

A theoretical case study of For-L-Phe-NH2

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Abstract

Chemical shielding anisotropy tensors have been determined, within the GIAO-RHF formalism using a smaller [6-31+G(d)] and two medium-size basis sets [6-311++G(d,p) and TZ2P], for all elements of the conformational library (altogether 27 structures) of the hydrophobic model peptide For L-Phc-NH2. The individual chemical shifts and their conformational averages have been compared to their experimental counterparts taken from the BioMagnetic Resonance Bank (BMRB). At the highest level of theory applied, for all nuclei but the amide proton, deviations between statistically averaged theoretical and experimental chemical shifts are as low as a few percent. One-dimensional (1D) chemical shift - structure plots do not allow unambiguous identification of backbone conformations. On the other hand, on chemical shift chemical shift plots of selected nuclei, e.g., 1HN with 15N or 15N with 13Cα, regions corresponding to major conformational motifs have been found, providing basis for the identification of peptide conformers solely from NMR shift data. The 2D 1Hα-13Cα as well as the 3D 1Hα-13Cα-13C β chemical shift chemical shift plots appear to be of special importance for direct determination of conformations of protein building units from multidimensional NMR experiments. 48 pairs of 1Hα-13Cα data for phenylalanine residues have been extracted from 18 selected proteins and compared to relevant ab initio results, supporting the calculated results. Thus, the appealing idea of establishing backbone folding information of peptides and proteins from chemical shift information alone, obtained from selected multiple-pulse NMR experiments (e.g., 2D-HSQC, 2D-HMQC, and 3D-HNCA), has received further support.

Original languageEnglish
Pages (from-to)513-530
Number of pages18
JournalEuropean Physical Journal D
Volume20
Issue number3
DOIs
Publication statusPublished - Sep 2002

Fingerprint

chemical equilibrium
proteins
nuclear magnetic resonance
peptides
plots
nuclei
phenylalanine
folding
amides
shielding
tensors
formalism
deviation
anisotropy
protons
shift
pulses

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Atomic and Molecular Physics, and Optics

Cite this

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title = "Toward direct determination of conformations of protein building units from multidimensional NMR experiments III: A theoretical case study of For-L-Phe-NH2",
abstract = "Chemical shielding anisotropy tensors have been determined, within the GIAO-RHF formalism using a smaller [6-31+G(d)] and two medium-size basis sets [6-311++G(d,p) and TZ2P], for all elements of the conformational library (altogether 27 structures) of the hydrophobic model peptide For L-Phc-NH2. The individual chemical shifts and their conformational averages have been compared to their experimental counterparts taken from the BioMagnetic Resonance Bank (BMRB). At the highest level of theory applied, for all nuclei but the amide proton, deviations between statistically averaged theoretical and experimental chemical shifts are as low as a few percent. One-dimensional (1D) chemical shift - structure plots do not allow unambiguous identification of backbone conformations. On the other hand, on chemical shift chemical shift plots of selected nuclei, e.g., 1HN with 15N or 15N with 13Cα, regions corresponding to major conformational motifs have been found, providing basis for the identification of peptide conformers solely from NMR shift data. The 2D 1Hα-13Cα as well as the 3D 1Hα-13Cα-13C β chemical shift chemical shift plots appear to be of special importance for direct determination of conformations of protein building units from multidimensional NMR experiments. 48 pairs of 1Hα-13Cα data for phenylalanine residues have been extracted from 18 selected proteins and compared to relevant ab initio results, supporting the calculated results. Thus, the appealing idea of establishing backbone folding information of peptides and proteins from chemical shift information alone, obtained from selected multiple-pulse NMR experiments (e.g., 2D-HSQC, 2D-HMQC, and 3D-HNCA), has received further support.",
author = "A. Perczel and A. Cs{\'a}sz{\'a}r",
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AU - Perczel, A.

AU - Császár, A.

PY - 2002/9

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N2 - Chemical shielding anisotropy tensors have been determined, within the GIAO-RHF formalism using a smaller [6-31+G(d)] and two medium-size basis sets [6-311++G(d,p) and TZ2P], for all elements of the conformational library (altogether 27 structures) of the hydrophobic model peptide For L-Phc-NH2. The individual chemical shifts and their conformational averages have been compared to their experimental counterparts taken from the BioMagnetic Resonance Bank (BMRB). At the highest level of theory applied, for all nuclei but the amide proton, deviations between statistically averaged theoretical and experimental chemical shifts are as low as a few percent. One-dimensional (1D) chemical shift - structure plots do not allow unambiguous identification of backbone conformations. On the other hand, on chemical shift chemical shift plots of selected nuclei, e.g., 1HN with 15N or 15N with 13Cα, regions corresponding to major conformational motifs have been found, providing basis for the identification of peptide conformers solely from NMR shift data. The 2D 1Hα-13Cα as well as the 3D 1Hα-13Cα-13C β chemical shift chemical shift plots appear to be of special importance for direct determination of conformations of protein building units from multidimensional NMR experiments. 48 pairs of 1Hα-13Cα data for phenylalanine residues have been extracted from 18 selected proteins and compared to relevant ab initio results, supporting the calculated results. Thus, the appealing idea of establishing backbone folding information of peptides and proteins from chemical shift information alone, obtained from selected multiple-pulse NMR experiments (e.g., 2D-HSQC, 2D-HMQC, and 3D-HNCA), has received further support.

AB - Chemical shielding anisotropy tensors have been determined, within the GIAO-RHF formalism using a smaller [6-31+G(d)] and two medium-size basis sets [6-311++G(d,p) and TZ2P], for all elements of the conformational library (altogether 27 structures) of the hydrophobic model peptide For L-Phc-NH2. The individual chemical shifts and their conformational averages have been compared to their experimental counterparts taken from the BioMagnetic Resonance Bank (BMRB). At the highest level of theory applied, for all nuclei but the amide proton, deviations between statistically averaged theoretical and experimental chemical shifts are as low as a few percent. One-dimensional (1D) chemical shift - structure plots do not allow unambiguous identification of backbone conformations. On the other hand, on chemical shift chemical shift plots of selected nuclei, e.g., 1HN with 15N or 15N with 13Cα, regions corresponding to major conformational motifs have been found, providing basis for the identification of peptide conformers solely from NMR shift data. The 2D 1Hα-13Cα as well as the 3D 1Hα-13Cα-13C β chemical shift chemical shift plots appear to be of special importance for direct determination of conformations of protein building units from multidimensional NMR experiments. 48 pairs of 1Hα-13Cα data for phenylalanine residues have been extracted from 18 selected proteins and compared to relevant ab initio results, supporting the calculated results. Thus, the appealing idea of establishing backbone folding information of peptides and proteins from chemical shift information alone, obtained from selected multiple-pulse NMR experiments (e.g., 2D-HSQC, 2D-HMQC, and 3D-HNCA), has received further support.

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