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LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics
Published on: April 9, 2017
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Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.
David Punihaole1, Zhenmin Hong1, Ryan S Jakubek1
1Department of Chemistry, University of Pittsburgh , 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States.
The Journal of Physical Chemistry. B
|September 23, 2015
Summary
We identified specific vibrational spectral markers for glutamine (Gln) and asparagine (Asn) side chains. These markers, linked to dihedral angles, offer new insights into protein structures in solution and fibrils.
Area of Science:
- Biophysics
- Spectroscopy
- Computational Chemistry
Background:
- Glutamine (Gln) and asparagine (Asn) are crucial amino acids involved in protein structure and function.
- Understanding the conformational dynamics of Gln and Asn side chains is essential for deciphering protein behavior.
Purpose of the Study:
- To identify and characterize vibrational spectral markers that report on the side chain structures of Gln and Asn.
- To correlate spectral properties with specific dihedral angles (χ3 for Gln, χ2 for Asn) and explore their dependence on protein backbone structure.
Main Methods:
- Density Functional Theory (DFT) calculations to model vibrational properties.
- UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally measure spectral bands.
- Analysis of the Protein Data Bank (PDB) to study angle distributions in peptides.
Main Results:
- Identified Amide III(P) (AmIII(P)) vibrations as sensitive markers for Gln and Asn side chain dihedral angles.
- Established a correlation between AmIII(P) band frequency and the OCCC dihedral angle (χ3 for Gln, χ2 for Asn).
- Demonstrated that AmIII(P) band line shapes can quantify angle distributions, influenced by peptide backbone Ramachandran angles.
Conclusions:
- The AmIII(P) spectral marker provides a novel method for probing Gln and Asn side chain conformations in various protein contexts.
- This technique offers valuable insights into protein structure in solution, including Gln/Asn-rich amyloid fibrils and prions.
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