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Molecular recognition and dynamics in proteins studied by NMR

Wallerstein, Johan LU (2019)
Abstract
Knowledge of dynamics in protein is very important in the description of protein function and molecular recognition. The thesis investigates protein dynamics on time-scales from milli- to sub-nanosecond, with focus on the latter, using NMR spin relaxation experiments on two proteins, the 138-residue carbohydrate recognition domain of galectin-3 (Gal3C) and the 56-residue B1 domain of bacterial protein G (PGB1). Fives studies are presented.

By measuring the exchange contribution to R2-relaxation, as a function of pH, using 13C-CPMG-experiments directed on the side-chain carbonyls of glutamic and aspartic acid in PGB1, we could determine site specific protonation rate constants k(on), and deprotonation rate constants k(off). A... (More)
Knowledge of dynamics in protein is very important in the description of protein function and molecular recognition. The thesis investigates protein dynamics on time-scales from milli- to sub-nanosecond, with focus on the latter, using NMR spin relaxation experiments on two proteins, the 138-residue carbohydrate recognition domain of galectin-3 (Gal3C) and the 56-residue B1 domain of bacterial protein G (PGB1). Fives studies are presented.

By measuring the exchange contribution to R2-relaxation, as a function of pH, using 13C-CPMG-experiments directed on the side-chain carbonyls of glutamic and aspartic acid in PGB1, we could determine site specific protonation rate constants k(on), and deprotonation rate constants k(off). A linear free-energy relationship between log k(on) and pKa is found, which provides information on the free-energy landscape of the protonation reaction, showing that the variability among residues in these rates arises from charge stabilization of the deprotonated state.

Dimethyl sulfoxide (DMSO) is often used for dissolving nonpolar ligands in protein-ligand studies. DMSO change the viscosity, which is proportional to rotational correlation time. The correlation time of PGB1 and Gal3C was determined for different DMSO-concentrations. Effects of minute additions of DMSO in samples used in spin-relaxation experiments were examined for the case of 2H-methyl side chain model-free studies. Chemical shift perturbations studies on apo-Gal3C show uniform changes of chemical shifts, indicating DMSO has a minor impact on the hydration layer.

15N-backbone and 2H-methyl side chain NMR order parameters (S2) are determined for three Gal3C complexes using the Lipari-Szabo model-free formalism developed in the 80s. Minor changes in ligand structure generate differences in the conformational entropy. Specifically, the radial distribution of conformational entropy, with ligand in the centre reveals how entropy varies between consecutive shells within the protein. The study combines NMR relaxation with isothermal titration calorimetry (ITC), X-ray crystallography, and computational approaches.

The structure–thermodynamic relationship for halogen bonds C–X (X=F, Cl, Br, and I) between the ligand substituents and the backbone C=O of a glycine in Gal3C was studied with NMR, ITC, X-ray crystallography and computational approaches. The sigma-hole associated with the halogen bond affects the electron density of surrounding 15N nuclei in amides, and consequently the chemical shift of these nuclei. There is a correlation between ITC-determined enthalpy of binding vs amide chemical shift.

In Gal3C bound to natural substrate lactose, the chemical shifts changes of the 13C-E1 in histidine side chains are traced as a function of pH using 1H-13C HSQC-experiments. The experiment helps in determination of the tautomeric state in the proteins four histidines. The histidine in the binding site is in tautomer ND1, another is in tautomer NE2 and two are partly charged. Neutron diffraction studies at pH 7.5 confirms the NMR-studies.
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author
supervisor
opponent
  • Professor Wolf-Watz, Magnus, University of Umeå, Umeå.
organization
alternative title
Molekylär igenkänning och dynamik hos proteiner studerat med NMR
publishing date
type
Thesis
publication status
published
subject
keywords
Chemical exchange, Conformational entropy, Entropy, Galectin-3, Isothermal Titration Calorimetry, ITC, Model-free formalism, Molecular recognition, Nuclear Magnetic Resonance, NMR, PGB1, Protein dynamics, Protein–ligand interactions, Proton-transfer reactions, Spin relaxation, Viscosity, Chemical exchange, Conformational entropy, Entropy, Galectin-3, Isothermal Titration Calorimetry, ITC, Model-free formalism, Molecular recognition, Nuclear Magnetic Resonance, NMR, PGB1, Protein dynamics, Protein–ligand interactions, Proton-transfer reactions, Spin relaxation, Viscosity
pages
214 pages
publisher
Department of Biophysical Chemistry, Lund University
defense location
Lecture hall KC:F, Kemicentrum, Naturvetarvägen 14, Faculty of Engineering LTH, Lund
defense date
2019-11-20 13:00:00
ISBN
9789174226959
9789174226942
language
English
LU publication?
yes
id
b693f1ba-7c8e-44a7-bc52-1099acf4131a
date added to LUP
2019-10-24 11:51:36
date last changed
2019-10-25 12:21:44
@phdthesis{b693f1ba-7c8e-44a7-bc52-1099acf4131a,
  abstract     = {Knowledge of dynamics in protein is very important in the description of protein function and molecular recognition. The thesis investigates protein dynamics on time-scales from milli- to sub-nanosecond, with focus on the latter, using NMR spin relaxation experiments on two proteins, the 138-residue carbohydrate recognition domain of galectin-3 (Gal3C) and the 56-residue B1 domain of bacterial protein G (PGB1). Fives studies are presented.<br/><br/>By measuring the exchange contribution to R2-relaxation, as a function of pH, using 13C-CPMG-experiments directed on the side-chain carbonyls of glutamic and aspartic acid in PGB1, we could determine site specific protonation rate constants k(on), and deprotonation rate constants k(off). A linear free-energy relationship between log k(on) and pKa is found, which provides information on the free-energy landscape of the protonation reaction, showing that the variability among residues in these rates arises from charge stabilization of the deprotonated state.<br/><br/>Dimethyl sulfoxide (DMSO) is often used for dissolving nonpolar ligands in protein-ligand studies. DMSO change the viscosity, which is proportional to rotational correlation time. The correlation time of PGB1 and Gal3C was determined for different DMSO-concentrations. Effects of minute additions of DMSO in samples used in spin-relaxation experiments were examined for the case of 2H-methyl side chain model-free studies. Chemical shift perturbations studies on apo-Gal3C show uniform changes of chemical shifts, indicating DMSO has a minor impact on the hydration layer.<br/><br/>15N-backbone and 2H-methyl side chain NMR order parameters (S2) are determined for three Gal3C complexes using the Lipari-Szabo model-free formalism developed in the 80s. Minor changes in ligand structure generate differences in the conformational entropy. Specifically, the radial distribution of conformational entropy, with ligand in the centre reveals how entropy varies between consecutive shells within the protein. The study combines NMR relaxation with isothermal titration calorimetry (ITC), X-ray crystallography, and computational approaches.<br/><br/>The structure–thermodynamic relationship for halogen bonds C–X (X=F, Cl, Br, and I) between the ligand substituents and the backbone C=O of a glycine in Gal3C was studied with NMR, ITC, X-ray crystallography and computational approaches. The sigma-hole associated with the halogen bond affects the electron density of surrounding 15N nuclei in amides, and consequently the chemical shift of these nuclei. There is a correlation between ITC-determined enthalpy of binding vs amide chemical shift.<br/><br/>In Gal3C bound to natural substrate lactose, the chemical shifts changes of the 13C-E1 in histidine side chains are traced as a function of pH using 1H-13C HSQC-experiments. The experiment helps in determination of the tautomeric state in the proteins four histidines. The histidine in the binding site is in tautomer ND1, another is in tautomer NE2 and two are partly charged. Neutron diffraction studies at pH 7.5 confirms the NMR-studies.<br/>},
  author       = {Wallerstein, Johan},
  isbn         = {9789174226959},
  language     = {eng},
  month        = {10},
  publisher    = {Department of Biophysical Chemistry, Lund University},
  school       = {Lund University},
  title        = {Molecular recognition and dynamics in proteins studied by NMR},
  url          = {https://lup.lub.lu.se/search/ws/files/71016467/JohanW_kappa_LUB.pdf},
  year         = {2019},
}