Raman Spectroscopy and its Application in Biology CASR

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1 Raman Spectroscopy and its Application in Biology CASR Chandrabhas Narayana Chemistry and Physics of Materials Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore , India Lecture for TSU Seminar, February 19, 2013

2 Light Scattering Laboratory Raman Spectroscopy Study of Physical Properties of Material Brillouin Spectroscopy X-rays from Synchrotron Source

3 Light Scattering Laboratory Elastic/acoustic properties of Nano systems (Nanotubes, Graphene) and bulk systems (pyrochlore, topological insulators, Li-Plastics Battery) Vibrational properties of Graphenes, Fast Ionic conductors, multiferroics, Metal Organic Framework solids, Molecular Solids etc. Ultra high pressure studies (both vibrational and structural) of ionic conductors, semiconductors, molecular solids such as Hydrogen, Silane, binary nitrides, Aluminium, multiferroics. Drug-Protein interactions, diagnostics using surface enhanced Raman spectroscopy

4 What happens when light falls on a material? Transmission Reflection Absorption Luminescence Elastic Scattering Inelastic Scattering

5 Why are Sky and Sea Blue?

6 Why is this water not Blue?

7 Why is some parts of the water in swimming pool Blue/not Blue?

8 HCl H 2 O CASR Sym. Stretching Vibrations in Molecules 8086 cm n = 2991 cm -1-1 = 1 ev n = 4139 cm Room Temp = 25 mev -1 HF Asym. Stretching Sym. Bending n 1 = 3835 cm -1 n n 2 = 1648 cm -1 3 = 3939 cm -1 NH 3 n 1 = cm -1 n n 2 = 1022 cm -1 3 = cm -1 Asym. Bending n 4 = cm -1 SF 6 n 5 = cm -1 n n 6 = cm -1 2 = cm -1 n 1 = cm -1 n n 4 = cm -1 3 = cm -1

9 Classical Picture of Raman Induced Polarization Polarizability Taylor Series Expansion Stokes Raman Anti-Stokes Raman

10 Energy diagram and Quantum picture Virtual states Raman cross section photon S a,b <e g,p 2 H er p 2,e b > <e b,p 2 H ep p 1,e a > <e a,p 1 H er p 1,e g > E s -E b x E i -E a ex g Electronic states Vibrational states If E i = E a or E s = E b We have Resonance Raman effect

11 Raman spectra of CCl 4 Sym. Bending Sym. Stretching asym. Bending asym. Stretching

12 Raman spectra of CCl 4 Isotope effect Cl has two isotopes 35 Cl and 37 Cl Relative abundance is 3:1

13 Diamond spectra is similar to the crystalline Silicon and Germanium but is shifted to higher Raman frequency because of lighter weight and bond strength. RAMAN OF ISO-STRUCTURAL CRYSTALS

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15 Raman, Fluorescence and IR Scattering Absorption and emission Absorption

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17 Problems with Raman: a)very Weak for every 10 9 photons only 1 photon Raman a)resonant Raman not feasible with every sample. b)absorption a better process than scattering

18 How do we see color?

19 How do we see color?

20 How do we see color? Additive Substractive

21 Plasmons in Nanoparticles

22 Origin of Surface Enhanced Raman Spectroscopy Initially thought to be depended on Surface Area of the rough surface It was shown that the scattering cross section far exceeded the number of molecules on the rough surface. It was proposed that the origin was due to surface plasmons hence a truly nano phenomenon. Alkali and Ag the best, Au and Cu the next best, Al, In, Pt followed by transition metals and then bad conductors. Exciting wavelength, polarization, exact nature of the nanostructure also effect the SERS

23 Earlier SERS was thought to be due to creation of larger surface area Now we understand it to orignate from the surface plasmon of the nano structures

24 Surface Enhanced Raman Scattering (SERS) Raman signal intensity gets enhanced when molecules are adsorbed on metal nanoparticles, colloids, island films etc. Pathways for enhancement : Electromagnetic enhancement Enhanced local optical fields of metallic nanostructure Chemical enhancement Molecule-nanostructure system provide new energy states

25 Raman Spectrometers

26 US Patent No. US 8,179,525 B2 (2012), G.V. Pavan Kumar et al Current Science (2007) 93, 778. CASR Micro Raman setup Optical fiber Focusing lens CCD Monochromator Edge filter Camera Computer Dichroic Mirror LASER Objective lens Stage CASR

27 G.V. Pavan Kumar et al. J. Phys. Chem. C 111, 4388 (2007) Gayathri Kumari New Nanoparticle Architecture for SERS application Gayathri Kumari and Pavan Kumar G.V. Gayatri Kumari and C. Narayana J. Phys. Chem. Letters 3, 1130 (2012) CASR

28 G.V. Pavan Kumar et al. J. Phys. Chem. C 111, 4388 (2007) Ag Core Au Shell Nanoparticles with hot spots a) Au : Ag = 0.1 Au : Ag = 0.8 c) 100 nm 100 nm Au : Ag = nm b) d) CASR 28

29 Raman Intensity Raman Intensity SERS from Hot Spots Ad Adenine, TP Thiophenol, Imd Imidazole, ATP adenosine Triphosphate, Hb - Hemoglobin a) Ad Tp Imd ATP Hb b) Ad ATP TP Imd Hb Au : Ag Au : Ag G.V. Pavan Kumar et al. J. Phys. Chem. C 111, 4388 (2007) CASR 29

30 Gold Silica Silver Sandwich Structure The Silica layer between Gold and Silver can be the buffer layer. The SERS enhancement was possible by controlling the gold layer. Triple layer nanostructure: CASR Shoute, L. C. T. et al Applied Spectroscopy, 2009, 63, 133

31 Gayatri Kumari and C. Narayana J. Phys. Chem. Letters, 3, 1130 (2012) Ag CASR Gold Silica Silver Sandwich Nanoparticles SiO 2 Ag Au TEM images at the different stages of formation of sandwich nanoparticles (a) (b) (c) (d)

32 Gold Silica Silver Sandwich Nanoparticles FESEM picture of

33 SERS from Au-SiO 2 -Ag nanostructures CASR Gayatri Kumari and C. Narayana J. Phys. Chem. Letters, 3, 1130 (2012)

34 Gayatri Kumari and C. Narayana J. Phys. Chem. Letters, 3, 1130 (2012) SERS from Au-SiO 2 -Ag nanostructures 10-5 M of Thiophenol 10-7 M of Thiophenol Ag@SiO CASR SiO

35 Small Molecule Interaction with Oncogenic Kinases, Aurora A and Aurora B Soumik Sidhanth Tapas Kumar Kundu Dhanasekaran Karthigeyan Soumik Sidhanth, Partha P. Kundu, D. Karthikeyan, Tapas K. Kundu CASR Soumik Siddhanta et al, RSC Advances (2013) in press D. Karthigeyan et al, PNAS (USA) under Review

36 The relative localization of Aurora A and Aurora B in mitotic cells is shown above. The kinases play a role in cytokinesis too, where they are concentrated in the mid-body region.

37 Overexpression of Aurora A by gene amplification or other means, leads to aneuploidy, which in turn leads to oncogenesis. Mitotic progression is disrupted and normal spindle orientation of chromosomes is not achieved. The cell fails to undergo cytokinesis, producing tetraploid progeny.

38 J. M. Elkins et al, Journal of Medicinal Chemistry 55, (2012) Structure of Aurora A Kinase C-Terminal N-Terminal CASR

39 Structure of Aurora A Kinase CASR J. Nowakowski et al, Structure 10, (2002) Soumik Siddhanta et al, RSC Advances (2013) in press

40 Structure of Aurora A Kinase Aurora A and Aurora B are very much identical and have only 4 residues different in the catalytic part This makes it difficult to make specific Inhibitors for these molecules for these CASR

41 SERS of Aurora Kinase Aurora A kinase Aurora B kinase Tyrosine Phenylanaline Amide I SERS spectra of Aurora A kinase and Aurora B kinase in presence of silver nanoparticles. λ= nm; signal accumulation time = 30 s Soumik Siddhanta et al, RSC Advances (2013) in press

42 Effect of Denaturing of the Aurora A kinase Protein Aurora B kinase SERS spectra of Aurora A/Aurora B kinase (black) and denatured Aurora A/Aurora B kinase (red). Soumik Siddhanta et al, RSC Advances (2013) in press

43 Active sites of Aurora A kinase This Aurora A-adenosine complex shows the hinge region (green), Glycine rich loop(red) and activation loop (purple). Type I inhibitors bind to the ATP binding site through the formation of 1 3 hydrogen bonds to the kinase hinge residues and through hydrophobic interactions in and around the region occupied by the adenine ring of ATP. The position of a conserved Threonine residue, Thr-288, which is phosphorylated during activation of Aurora A, is shown by a star. CASR Type II inhibitors use the ATP-binding site, and also exploit unique hydrogen bonding and hydrophobic interactions made possible by the DFG residues of the activation loop being folded away from the conformation required for phosphate group transfer

44 Conclusions SERS can be used to validate the autodock and molecular dynamics simulations with the knowledge of the structure of the protein. SERS gives the interactions in the proteins in their active state, in physiological conditions. Thus helps in the derivatization of the small molecule for producing effective drug as well as fast screening of the potential molecules. With better control over molecular dynamics simulation, it opens up new avenues in the drug discoveries.

45 R. Dhanya Venkat Srinu Badram Soumik Sidhanth Gayathri K Partha Pratim Kundu Dr. Diptikanta Swain Dr. Gopal K Pradhan Dr. Pavan Kumar Dr. Kavitha G Dr. Md. Seikh Dr. Murugavel Dr. Navneeth Ms. Sonia Balan Dr. Nashiour Rohman Dr. Veena HG Acknowledgements POCE Students: Rangarajan Gayathri Nair Sruthi Vibha Collaborators Tapas Kundu Ranga Uday V. Nagaraja Hans Agren Funding sources: DST, DBT, JNCASR, Swedish Research Links