Toward direct determination of conformations of protein building units from multidimensional NMR experiments VI. Chemical shift analysis of his to gain 3D structure and protonation state information

Péter Hudáky, A. Perczel

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4 Citations (Scopus)

Abstract

NMR-chemical shift structure correlations were investigated by using GIAO-RB3LYP/6-311 + +G(2d,2p) formalism. Geometries and chemical shifts (CSI values) of 103 different conformers of N′-formyl-L-histidinamide were determined including both neutral and charged protonation forms. Correlations between amino acid torsional angle values and chemical shifts were investigated for the first time for an aromatic and polar amino acid residue whose side chain may carry different charges. Linear correlation coefficients of a significant level were determined between chemical shifts and dihedral angles for CSI[ 1Hα]/φ, CSI[13Cα]/φ, and CS/[13Cα]/ψ. Protonation of the imidazole ring induces the upfield shift of CSI[13Cα] for positively charged histidines and an opposite effect for the negative residue. We investigated the correspondence of theoretical and experimental 13Cα, 13Cβ, and 1Hα chemical shifts and the nine basic conformational building units characteristic for proteins. These three chemical shift values allow the identification of conformational building units at 80% accuracy. These results enable the prediction of additional regular secondary structural elements (e.g., polyProlinell, inverse γ-turns) and loops beyond the assignment of chemical shifts to α-helices and β-pleated sheets. Moreover, the location of the His residue can be further specified in a β-sheet. It is possible to determine whether the appropriate residue is located at the middle or in a first/last β-strand within a β-sheet based on calculated CSI values. Thus, the attractive idea of establishing local residue specific backbone folding parameters in peptides and proteins by employing chemical shift information (e.g., 1Hα and 13Cα) obtained from selected heteronuclear correlation NMR experiments (e.g., 2D-HSQC) is reinforced.

Original languageEnglish
Pages (from-to)1307-1317
Number of pages11
JournalJournal of Computational Chemistry
Volume26
Issue number13
DOIs
Publication statusPublished - Oct 2005

Fingerprint

Protonation
Chemical shift
Conformation
Conformations
Nuclear magnetic resonance
Proteins
Protein
Unit
Experiment
Experiments
Amino Acids
Amino acids
Dihedral angle
Correlation Structure
Helix
Folding
Backbone
Histidine
Peptides
Correlation coefficient

Keywords

  • ab initio
  • Chemical shift
  • Conformational building unit
  • GIAO
  • Histidine
  • Model peptide
  • NMR
  • Prediction
  • Quantum chemical calculation
  • Structure

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 VI. Chemical shift analysis of his to gain 3D structure and protonation state information",
abstract = "NMR-chemical shift structure correlations were investigated by using GIAO-RB3LYP/6-311 + +G(2d,2p) formalism. Geometries and chemical shifts (CSI values) of 103 different conformers of N′-formyl-L-histidinamide were determined including both neutral and charged protonation forms. Correlations between amino acid torsional angle values and chemical shifts were investigated for the first time for an aromatic and polar amino acid residue whose side chain may carry different charges. Linear correlation coefficients of a significant level were determined between chemical shifts and dihedral angles for CSI[ 1Hα]/φ, CSI[13Cα]/φ, and CS/[13Cα]/ψ. Protonation of the imidazole ring induces the upfield shift of CSI[13Cα] for positively charged histidines and an opposite effect for the negative residue. We investigated the correspondence of theoretical and experimental 13Cα, 13Cβ, and 1Hα chemical shifts and the nine basic conformational building units characteristic for proteins. These three chemical shift values allow the identification of conformational building units at 80{\%} accuracy. These results enable the prediction of additional regular secondary structural elements (e.g., polyProlinell, inverse γ-turns) and loops beyond the assignment of chemical shifts to α-helices and β-pleated sheets. Moreover, the location of the His residue can be further specified in a β-sheet. It is possible to determine whether the appropriate residue is located at the middle or in a first/last β-strand within a β-sheet based on calculated CSI values. Thus, the attractive idea of establishing local residue specific backbone folding parameters in peptides and proteins by employing chemical shift information (e.g., 1Hα and 13Cα) obtained from selected heteronuclear correlation NMR experiments (e.g., 2D-HSQC) is reinforced.",
keywords = "ab initio, Chemical shift, Conformational building unit, GIAO, Histidine, Model peptide, NMR, Prediction, Quantum chemical calculation, Structure",
author = "P{\'e}ter Hud{\'a}ky and A. Perczel",
year = "2005",
month = "10",
doi = "10.1002/jcc.20266",
language = "English",
volume = "26",
pages = "1307--1317",
journal = "Journal of Computational Chemistry",
issn = "0192-8651",
publisher = "John Wiley and Sons Inc.",
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TY - JOUR

T1 - Toward direct determination of conformations of protein building units from multidimensional NMR experiments VI. Chemical shift analysis of his to gain 3D structure and protonation state information

AU - Hudáky, Péter

AU - Perczel, A.

PY - 2005/10

Y1 - 2005/10

N2 - NMR-chemical shift structure correlations were investigated by using GIAO-RB3LYP/6-311 + +G(2d,2p) formalism. Geometries and chemical shifts (CSI values) of 103 different conformers of N′-formyl-L-histidinamide were determined including both neutral and charged protonation forms. Correlations between amino acid torsional angle values and chemical shifts were investigated for the first time for an aromatic and polar amino acid residue whose side chain may carry different charges. Linear correlation coefficients of a significant level were determined between chemical shifts and dihedral angles for CSI[ 1Hα]/φ, CSI[13Cα]/φ, and CS/[13Cα]/ψ. Protonation of the imidazole ring induces the upfield shift of CSI[13Cα] for positively charged histidines and an opposite effect for the negative residue. We investigated the correspondence of theoretical and experimental 13Cα, 13Cβ, and 1Hα chemical shifts and the nine basic conformational building units characteristic for proteins. These three chemical shift values allow the identification of conformational building units at 80% accuracy. These results enable the prediction of additional regular secondary structural elements (e.g., polyProlinell, inverse γ-turns) and loops beyond the assignment of chemical shifts to α-helices and β-pleated sheets. Moreover, the location of the His residue can be further specified in a β-sheet. It is possible to determine whether the appropriate residue is located at the middle or in a first/last β-strand within a β-sheet based on calculated CSI values. Thus, the attractive idea of establishing local residue specific backbone folding parameters in peptides and proteins by employing chemical shift information (e.g., 1Hα and 13Cα) obtained from selected heteronuclear correlation NMR experiments (e.g., 2D-HSQC) is reinforced.

AB - NMR-chemical shift structure correlations were investigated by using GIAO-RB3LYP/6-311 + +G(2d,2p) formalism. Geometries and chemical shifts (CSI values) of 103 different conformers of N′-formyl-L-histidinamide were determined including both neutral and charged protonation forms. Correlations between amino acid torsional angle values and chemical shifts were investigated for the first time for an aromatic and polar amino acid residue whose side chain may carry different charges. Linear correlation coefficients of a significant level were determined between chemical shifts and dihedral angles for CSI[ 1Hα]/φ, CSI[13Cα]/φ, and CS/[13Cα]/ψ. Protonation of the imidazole ring induces the upfield shift of CSI[13Cα] for positively charged histidines and an opposite effect for the negative residue. We investigated the correspondence of theoretical and experimental 13Cα, 13Cβ, and 1Hα chemical shifts and the nine basic conformational building units characteristic for proteins. These three chemical shift values allow the identification of conformational building units at 80% accuracy. These results enable the prediction of additional regular secondary structural elements (e.g., polyProlinell, inverse γ-turns) and loops beyond the assignment of chemical shifts to α-helices and β-pleated sheets. Moreover, the location of the His residue can be further specified in a β-sheet. It is possible to determine whether the appropriate residue is located at the middle or in a first/last β-strand within a β-sheet based on calculated CSI values. Thus, the attractive idea of establishing local residue specific backbone folding parameters in peptides and proteins by employing chemical shift information (e.g., 1Hα and 13Cα) obtained from selected heteronuclear correlation NMR experiments (e.g., 2D-HSQC) is reinforced.

KW - ab initio

KW - Chemical shift

KW - Conformational building unit

KW - GIAO

KW - Histidine

KW - Model peptide

KW - NMR

KW - Prediction

KW - Quantum chemical calculation

KW - Structure

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U2 - 10.1002/jcc.20266

DO - 10.1002/jcc.20266

M3 - Article

C2 - 15999335

AN - SCOPUS:24144439154

VL - 26

SP - 1307

EP - 1317

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 13

ER -