1. First Principle Calculation of Nuclear Magnetic Resonance (NMR) chemical shift Kanchan Sonkar Center of Biomedical Magnetic Resonance SGPGIMS-Campus, Lucknow, India 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

2. Overview Introduction to NMR spectroscopy Membrane proteins structure calculation Problems associated Application to be ported 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

3. Basic principle of NMR spectroscopy Relies on magnetic properties of nuclei, which behave like tiny bar magnets BoBo 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

4. Resonance frequency is directly proportional to – Gyromagnetic ratio – Applied magnetic field At B=11.7 T (tesla, 10 4 Gauss) the resonant frequency for 1 H is 500 MHz 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

5. 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

6. Other useful nuclei used in NMR 1 H 1/2 99.98 1.00 1.00 100.000 2 H 1 1.5x10 -2 9.65x10 -3 1.45x10 -6 15.351 13 C 1/2 1.108 1.59x10 -2 1.76x10 -4 25.144 14 N 1 99.63 1.01x10 -3 1.01x10 -3 7.224 15 N 1/2 0.37 1.04x10 -3 3.85x10 -6 10.133 19 F 1/2 100 0.83 0.83 94.077 23 Na 3/2 100 9.25x10 -2 9.25x10 -2 26.451 31 P 1/2 100 6.63x10 -2 6.63x10 -2 40.481 113 Cd 1/2 12.26 1.09x10 -2 1.33x10 -3 22.182 isotopeIabundance(%) sensitivity (relative) sensitivity (absolute) Frequency (MHz) at 2.3488 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

7. Applications of NMR Three-dimensional structural studies – Proteins, Protein-ligand complexes – DNA, RNA, Protein/DNA complexes – Natural product chemistry – Synthetic organic chemistry Study of dynamic processes – reaction kinetics – study of equilibrium (chemical or structural) Drug Design Medicine: MRI, Metabonomics 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

8. NMR spectrometer 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

9. Spectrum acquisition Spin in a magnetic field B 0 Magnetization lies along z- axis 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

10. rf pulse application on z-magnetization Spectrum acquisition 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

11. Spectrum acquisition Relaxation process – Transverse relaxation – Longitudinal relaxation 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

12. Signal recorded in the form of Free Induction Decay (FID) FID (time domain signal)Spectrum (frequency domain signal) 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

13. Interpretation of NMR spectrum Chemical shift – Nuclei resonate at different Larmor frequencies – Larmor frequency depends upon Local environment Presence of other magnetic nuclei Shielding tensor Chemical shift 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

14. Chemical shift can be calculated as Some reference compounds: ● 1H, 13C, 29Si → tetramethylsilane (TMS) ● 15N → liquid NH3 ● 17O → liquid H2O ● 19F → liquid CFCl3 ● 27Al → AlCl3 in D2O ● 43Ca → CaCl2(aq) 1 mol/L 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

15. Chemical shift range 1H 13C 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

16. Chemical shift The origin of the chemical shift are the orbital currents induced by the external magnetic field Gives information of local environment 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

17. Solid state NMR Molecules in liquids move very fast – Giving sharp NMR lines (isotropic chemical shift) In solids – No movement is possible Hence, broad NMR peaks (anisotropy) No averaging of spin interaction-broader lines Poly crystalline line shape 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

18. Averaging of spin interactions Some interactions depend on – Magic angle spinning spin the sample at the magic angle ~ 54.74° 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

19. Effect of Magic Angle Spinning on Glycine 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

20. Proteins Most important biological molecule Perform various functions – Tissue regeneration – Immune responses for human body – Cellular signalling and molecular transport Specialized protein classes for various processes 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

21. Membrane proteins Most abundant proteins Involve in almost all cellular processes GPCR-richest receptor target for drug discovery 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

22. Types Peripheral membrane proteins Integral membrane proteins Spectrin Accessory Glycoprotein 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

23. Integral membrane proteins 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

24. Structure calculation methods X-ray crystallography – Protein must be in crystallized form Atomic force method – Provides only surface information Solution NMR – Unsuitable for membrane proteins Solid state NMR – Most promising techniques 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

25. Solid state NMR of membrane proteins Capable of determining the three-dimensional structures of proteins in their native functional environments 15N chemical shift and 15N–1H dipolar coupling gives the structural information Pulse sequences for 2D PISEMA experiments 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

26. Protein Sci. 2003 12: 403-411 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

27. J. Mol. Biol. (2004) 341, 869–879 Few examples representing PISEMA spectra 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

28. Problems associated Applicable for low molecular weight proteins Solution: – Design new pulse sequences – Use of another naturally occurring isotope 13C nuclei – Calculation of 13C chemical shift tensors in alpha- helix and beta sheets 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

29. Application to be ported – Installation and compilation of Quantum Espresso – Running examples on GRID infrastructure – Calculation of 13C chemical shift for glycine and N- Acetyl Valine – Requirements: Scientific Linux Quantum Espresso software C and Fortran compilers MPI-Libraries 2/17/2016 Asia 2 2011-Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng