First Principle Calculation of Nuclear Magnetic Resonance (NMR) chemical shift Kanchan Sonkar Center of Biomedical Magnetic Resonance SGPGIMS-Campus, Lucknow,

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Presentation transcript:

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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

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

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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

Other useful nuclei used in NMR 1 H 1/ H 1 1.5x x x C 1/ x x N x x N 1/ x x F 1/ Na 3/ x x P 1/ x x Cd 1/ x x isotopeIabundance(%) sensitivity (relative) sensitivity (absolute) Frequency (MHz) at /17/2016 Asia Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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

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

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

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

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

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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

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

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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

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

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

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

Protein Sci : /17/2016 Asia Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng

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 Joint CHAIN/EU- IndiaGrid2/EPIKH School for Application Portng