Toward Direct Determination of Conformations of Protein Building Units from Multidimensional NMR Experiments I. A Theoretical Case Study of For-Gly-NH2 and For-L-Ala-NH2

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Abstract

NMR chemical shielding anisotropy tensors have been computed, employing several basis sets and the GIAO-RHF and GIAO-MP2 formalisms of electronic structure theory, for all the atoms of the five and nine typical backbone conformers of For-Gly-NH2 and For-L-Ala-NH2, respectively. Multidimensional chemical shift plots, as a function of the respective backbone fold, have been generated for both peptide models. On the 2D 1HNH-15NNH and 15NNH-13Cα plots the most notable feature is that at all levels of theory studied the backbone conformers cluster in different regions. Computed chemical shifts, as well as their averages, have been compared to relevant experimental values taken from the BioMagnetic Resonance Bank (BMRB). At the highest levels of theory, for all nuclei but the amide protons, deviations between statistically averaged theoretical and experimental shifts are as low as 1-3%. These results indicate that chemical shift information from selected multiple-pulse NMR experiments (e.g., 2D-HSQC and 3D-HNCA) could directly be employed to extract folding information for polypeptides and proteins.

Original languageEnglish
Pages (from-to)882-900
Number of pages19
JournalJournal of Computational Chemistry
Volume21
Issue number10
Publication statusPublished - Jul 30 2000

Fingerprint

Chemical shift
Conformation
Conformations
Backbone
Nuclear magnetic resonance
Proteins
Protein
Unit
Experiment
Peptides
Experiments
Polypeptides
Amides
Shielding
Electronic structure
Tensors
Protons
Electronic Structure
Anisotropy
Folding

Keywords

  • Multidimensional NMR experiments
  • Protein building units
  • Theoretical case study

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

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title = "Toward Direct Determination of Conformations of Protein Building Units from Multidimensional NMR Experiments I. A Theoretical Case Study of For-Gly-NH2 and For-L-Ala-NH2",
abstract = "NMR chemical shielding anisotropy tensors have been computed, employing several basis sets and the GIAO-RHF and GIAO-MP2 formalisms of electronic structure theory, for all the atoms of the five and nine typical backbone conformers of For-Gly-NH2 and For-L-Ala-NH2, respectively. Multidimensional chemical shift plots, as a function of the respective backbone fold, have been generated for both peptide models. On the 2D 1HNH-15NNH and 15NNH-13Cα plots the most notable feature is that at all levels of theory studied the backbone conformers cluster in different regions. Computed chemical shifts, as well as their averages, have been compared to relevant experimental values taken from the BioMagnetic Resonance Bank (BMRB). At the highest levels of theory, for all nuclei but the amide protons, deviations between statistically averaged theoretical and experimental shifts are as low as 1-3{\%}. These results indicate that chemical shift information from selected multiple-pulse NMR experiments (e.g., 2D-HSQC and 3D-HNCA) could directly be employed to extract folding information for polypeptides and proteins.",
keywords = "Multidimensional NMR experiments, Protein building units, Theoretical case study",
author = "A. Perczel and A. Cs{\'a}sz{\'a}r",
year = "2000",
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AU - Perczel, A.

AU - Császár, A.

PY - 2000/7/30

Y1 - 2000/7/30

N2 - NMR chemical shielding anisotropy tensors have been computed, employing several basis sets and the GIAO-RHF and GIAO-MP2 formalisms of electronic structure theory, for all the atoms of the five and nine typical backbone conformers of For-Gly-NH2 and For-L-Ala-NH2, respectively. Multidimensional chemical shift plots, as a function of the respective backbone fold, have been generated for both peptide models. On the 2D 1HNH-15NNH and 15NNH-13Cα plots the most notable feature is that at all levels of theory studied the backbone conformers cluster in different regions. Computed chemical shifts, as well as their averages, have been compared to relevant experimental values taken from the BioMagnetic Resonance Bank (BMRB). At the highest levels of theory, for all nuclei but the amide protons, deviations between statistically averaged theoretical and experimental shifts are as low as 1-3%. These results indicate that chemical shift information from selected multiple-pulse NMR experiments (e.g., 2D-HSQC and 3D-HNCA) could directly be employed to extract folding information for polypeptides and proteins.

AB - NMR chemical shielding anisotropy tensors have been computed, employing several basis sets and the GIAO-RHF and GIAO-MP2 formalisms of electronic structure theory, for all the atoms of the five and nine typical backbone conformers of For-Gly-NH2 and For-L-Ala-NH2, respectively. Multidimensional chemical shift plots, as a function of the respective backbone fold, have been generated for both peptide models. On the 2D 1HNH-15NNH and 15NNH-13Cα plots the most notable feature is that at all levels of theory studied the backbone conformers cluster in different regions. Computed chemical shifts, as well as their averages, have been compared to relevant experimental values taken from the BioMagnetic Resonance Bank (BMRB). At the highest levels of theory, for all nuclei but the amide protons, deviations between statistically averaged theoretical and experimental shifts are as low as 1-3%. These results indicate that chemical shift information from selected multiple-pulse NMR experiments (e.g., 2D-HSQC and 3D-HNCA) could directly be employed to extract folding information for polypeptides and proteins.

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