NMR, Crystallographic and Quantum Chemical Studies of Amino Acids in Peptides and Proteins
Sun, Haihong
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https://hdl.handle.net/2142/85444
Description
Title
NMR, Crystallographic and Quantum Chemical Studies of Amino Acids in Peptides and Proteins
Author(s)
Sun, Haihong
Issue Date
2005
Doctoral Committee Chair(s)
Oldfield, Eric
Department of Study
Biophysics and Computational Biology
Discipline
Biophysics and Computational Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biophysics, General
Language
eng
Abstract
"In this work we combined the ab initio methods, NMR and X-ray crystallography techniques to investigate the qualitative and quantitative relationships between chemical shift and geometry of amino acids in protein. First, we used ab initio quantum chemical techniques to compute the Back-bone Calpha and Cbeta NMR chemical shielding of 20 amino acids in their most populous conformations. The computed tensor element and orientation surfaces as functions of back-bone torsion angle (phi,Psi), Where -pi < phi < pi, and -pi < Psi < pi, are reported on our web (feh.scs.uiuc.edu). The calculated tensor elements and tensor orientations of Ala, Val, Leu, Met and Phe were validated by the experimental data measured by Solid State NMR. Using the chemical shifts and tensor orientation measured, we can predict the back-bone torsion angles and sidechain conformation with accuracy of 5.8 degrees by using Z-surface approaching. Second we extended our investigations to compute sidechain C13 a of aliphatic and aromatic amino acid, such as Ile, Trp and His, both in peptides and protein. The computed model and method were validated by experimental chemical shift data and high-resolution x-ray crystallographic structural information. The Trp Cgamma shifts are shown to be correlated with the sidechain torsion angles chi1 and chi 2 and appear to arise from gamma-gauche interactions with the backbone C' and NH atoms. That helps solve the problem of the chemical shift non-equivalences of non-protonated aromatic carbons in proteins first identified over thirty years ago. In histidine-contained peptides, there is no such strong correlation between the aromatic 13C chemical shift and the side chain geometry, however, incorporation of near-neighbor residues in a fully quantum mechanical ""supermolecule"" calculation provided much improved predictions. The Cepsilon1 shifts appear to be dominated by electrostatic interactions with hydrogen-bond partner molecules, knowledge of Cgamma and Cdelta2 shifts enables in most cases good predictions of tautomeric state. These results open up the way to analyzing 13C NMR chemical shifts, tautomer states (from Cdelta2, Cepsilon1 shifts) and electrostatics (from Cepsilon1 shifts) of histidine residue in proteins, and should be applicable to imidazole-containing drug molecules bound to proteins."
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