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अखिल भारतीय आयुर्विज्ञान संस्थान, नई दिल्ली
All India Institute Of Medical Sciences, New Delhi
कॉल सेंटर:  011-26589142

Dr. Ethayathulla Abdul Samath

Dr. Ethayathulla Abdul Samath

 

 

 

Research Interests

The research work is focused on TP53 tumor suppressor gene plays crucial role in suppression of cancer. But the mutation in p53 leads to tumour proliferation sometimes drug resistance cancer cells. The research focused on targeting mutant p53 with structure-based drug design to restore mutant p53 to functional like wild type. We do structure-based drug design by X-ray crystallography and for drug binding and functional studies we various biophysical techniques like ITC, CD, Fluorescence and cell based functional assay in p53 mutant cell lines.

The second major project in our lab is antimicrobial drug development against drug resistant bacterial pathogen. We work on bacterial cell division proteins particularly FtsZ and its associate proteins involved forming divisome protein complex assembly. We do structure-based drug design by X-ray crystallography, In silico drug screening and for drug binding studies we various biophysical techniques like ITC, CD, Fluorescence.

Any additional information  

Associate Professor (2017 - till date): Biophysics, AIIMS, New Delhi, India

Assistant Professor (2014 – 2017): Biophysics, AIIMS, New Delhi, India

Research Associate (2012-2014): Texas Tech University Health Science center, Texas, USA

Post doctoral Fellow (2007 - 2012):  University of California San Diego, California, USA.

Ph.D. (Biophysics, 2007: AllMS, New Delhi

Master of Science (Biophysics, 2002): University of Madras, Chennai

Bachelor of Science (Physics -2000): University of Madras, Chennai

Google scholar

https://scholar.google.com/citations?user=KZJOecsAAAAJ&hl=en

Pubmed

https://www.ncbi.nlm.nih.gov/pubmed/?term=Ethayathulla+AS%5BAuthor%5D

RCSB:

http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=C3644177&startAt=0&newsortfield=Release%20Date%20Descending

 

Email

यह ईमेल पता spambots से संरक्षित किया जा रहा है. आप जावास्क्रिप्ट यह देखने के सक्षम होना चाहिए.

Contact Number

011-26593351. 011-26593201

Awards and Honors

Senior Research Fellowship awarded by CSIR, New Delhi, India.

Senior Research Fellowship in the project from DST, New Delhi, India.

Junior Research Fellowship in the project from DST, New Delhi, India.

Junior Research Fellowship in the project from DBT, New Delhi, India.

Recent Publications

 

  1. Yadav P, Kumar M, Bansal R, Kaur P, Ethayathulla AS. Structure model of ferrochelatase from Salmonella Typhi elucidating metalation mechanism. Int J Biol Macromol. 2019 Apr 15;127:585-593.
  2. Bansal R, Haque MA, Yadav P, Gupta D, Ethayathulla AS, Hassan MI, Kaur P. Estimation of structure and stability of MurE ligase from Salmonella enterica serovar Typhi. Int J Biol Macromol. 2018 Apr 1;109:375-382.
  3. Gupta D, Sachdeva E, Haque MA, Rahman S, Bansal R, Ethayathulla AS, Hassan MI, Kaur P.Effect of chemical denaturants on the conformational stability of GyrB subunit of DNA gyrase from Salmonella enterica serovar Typhi.Int J Biol Macromol. 2017 May 9;103:165-174.
  4. Khan MI, Gupta AK, Kumar DR, Kumar M, Ethayathulla AS, Hariprasad G.Molecular modeling of Gly80 and Ser80 variants of human group IID phospholipase A2 and their receptor complexes: potential basis for weight loss in chronic obstructive pulmonary disease.J Mol Model. 2016 Sep;22(9):232.
  5. Ramos A, Tse PW, Wang J, Ethayathulla AS, Viadiu H. Sequence Variation in the Response Element Determines Binding by the Transcription Factor p73. Biochemistry. 2015 Dec 1;54(47):6961-72.
  6. Tikhonova EB, Ethayathulla AS, Su Y, Hariharan P, Xie S, Guan L. A transcription blocker isolated from a designed repeat protein combinatorial library by in vivo functional screen. Sci Rep. 2015 Jan 28;5:8070.
  7. Amin A, Ethayathulla AS, Guan L. Suppression of conformation-compromised mutants of Salmonella entericaserovar Typhimurium MelB. J Bacteriol. 2014;196(17):3134-9.
  8. Ethayathulla AS, Yousef MS, Amin A, Leblanc G, Kaback HR, Guan L. Structure-based mechanism for Na(+)/melibiose symport by MelB. Nat Commun. 2014;5:3009.
  9. Ciribilli Y, Monti P, Bisio A, Nguyen T, Ethayathulla AS, Ramos A, Foggetti G, Menichini P, Menendez D, Resnick M, Viadiu H, Fronza G, Inga A. Transactivation specificity is conserved among p53 family proteins and depends on a response element sequence code. Nucleic Acids Res. 2013 Oct;41(18):8637-53.
  10. Ethayathulla AS, Nguyen HT, Viadiu H. Crystal Structures of the DNA-binding Domain Tetramer of the p53 Tumor Suppressor Family Member p73 Bound to Different Full-site Response Elements. J Biol Chem. 2013; 288(7):4744-54.
  11. Ethayathulla AS, Tse P, Monti P, Nguyen S, Inga A, Fronza G, Viadiu H. Structure of p73 DNA-Binding Domain Tetramer Modulates p73 Transactivation. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6066-71.
  12. Soni BR, Hasan MI, Parmar A, Ethayathulla AS, Kumar RP, Singh NK, Sinha M, Kaur P, Yadav S, Sharma S, Madamwar D, Singh TP. Structure of the novel 14kDa fragment of alpha-subunit of phycoerythrin from the starving cyanobacterium Phormidium tenue. J Struct Biol. 2010 171(3):247-55
  13. Mishra P, Prem Kumar R, Ethayathulla AS, Singh N, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A, Bhakuni V, Singh TP. Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose. FEBS J. 2009 276(12):3392-402.
  14. Ethayathulla AS, Bessho Y, Shinkai A, Padmanabhan B, Singh TP, Kaur P, Yokoyama S. Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima. Acta Crystallogr Sect F. 2008 (64) 498-500.

Dr. Pradeep Sharma

Dr. Pradeep Sharma

 

Designation

Assistant Professor

Email

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Contact Number

+91-11-26594608 ; +91-11-26593201

Research Interests

Structural Biology ; Rational Structure based Drug Design ; Multidrug Resistant Bacterial Therapeutics

Awards and Honors

 

 

 

 

 

 

 

 

INSA Young Scientist Award

DST Inspire Faculty Award  

S V Talekar Medal for the best postgraduate of Department of Biophysics (AIIMS)

Ludo Frevel Crystallography Award, ICDD, USA

Summer Training Award at ESRF, Grenoble, France (European Commission)

Chaired, Society of Young Scientists, AIIMS, New Delhi (2009-10)

IUCr Travel award to attend IUCr meeting at Osaka, Japan

Awarded CSIR-Junior Research Fellowship

Awarded CSIR Senior Research Fellowship

Gold Medalist from Maharshi Dayanand University, Rohtak

Merit certificate awarded by Higher Education Department Haryana

National Merit Scholarship

Significant Publications

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  

 

 

 

 

 

 

 

 

 

 

Gupta A, Singh PK, Sharma P, Kaur P, Sharma S, Singh TP (2019) Structural and biochemical studies of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with dephospho-coenzyme A and coenzyme A. Int J Biol Macromol. 8130: 35145-35151.

Gupta A, Singh PK, Iqbal N, Sharma P, Baraigya HR, Kaur P, Umar MS, Ahmad F, Sharma A, Owais M, Sharma S, Singh TP (2019) Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii. Biochim Biophys Acta Proteins Proteom. 1867:537-547.

Chaudhary A, Kumar V, Singh PK, Sharma P, Bairagya HR, Kaur P, Sharma S, Chauhan SS, Singh TP (2018) A glycoprotein from mammary gland secreted during involution promotes apoptosis: Structural and biological studies. Arch Biochem Biophys. 644:72-80.

Kaushik S, Iqbal N, Singh N, Sikarwar JS, Singh PK, Sharma P, Kaur P, Sharma S, Owais M, Singh TP (2018) Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies. Biochem J.475:547-560.

Yadav SP, Singh PK, Sharma P, Iqbal N, Kaur P, Sharma S, Singh TP (2017) Structure and binding studies of proliferating cell nuclear antigen from Leishmania donovani. Biochim Biophys Acta Proteins Proteom. 1865:1395-1405.

Sirohi HV, Singh PK, Iqbal N, Sharma P, Singh AK, Kaur P, Sharma S, Singh TP (2017) Design of anti-thyroid drugs: Binding studies and structure determination of the complex of lactoperoxidase with 2-mercaptoimidazole at 2.30 Å resolution. Proteins. 85(10):1882-1890.

Iqbal N, Kumar M, Sharma P, Yadav SP, Kaur P, Sharma S, Singh TP (2017) Binding studies and structure determination of the recombinantly produced type-II 3-dehydroquinate dehydratase from Acinetobacter baumannii. Int J Biol Macromol.459-465.

Singh A, Kumar A, Gautam L, Sharma P, Sinha M, Bhushan A, Kaur P, Sharma S, Arora A, Singh TP (2014) Structural and binding studies of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa provide a platform for the structure-based inhibitor design against peptidyl-tRNA hydrolase. Biochem J. 463(3):329-37.

Sharma P, Dube D, Sinha M, Yadav S, Kaur P, Sharma S, & Singh TP (2013) Structural insights into the dual strategy of recognition by peptidoglycan recognition protein, PGRP-S: Structure of the ternary complex of PGRP-S with lipopolysaccharide and stearic acid. Plos One. 8(1):e53756. doi: 10.1371.

Sharma P, Yamini S, Dube D, Singh A, Mal G, Pandey N, Sinha M, Singh AK, Dey S, Kaur P, Mitra DK, Sharma S, & Singh TP (2013) Structural Basis of the Binding of Fatty Acids to Peptidoglycan Recognition Protein, PGRP-S. Arch Biochem Biophys. 529(1):1-10. doi: 10.1016.

Sharma P, Dube D, Sinha M, Dey S, Kaur P, Sharma S,& Singh TP (2012) Structural basis of heparin binding to camel peptidoglycan recognition protein-S. Int J Biochem Mol Biol. 3:86-94.

Sharma P, Dube D, Sinha M, Mishra B, Dey S, Mal G, Pathak KML, Kaur P, Mitra DK, Sharma S, & Singh TP (2011) Multi-ligand specificity of pathogen associated molecular pattern-binding site in peptidoglycan recognition protein. J Biol Chem 286:31723-30.

Sharma P, Dube D, Singh A, Mishra B, Singh N, Sinha M, Dey S, Kaur P, Mitra DK, Sharma S, & Singh TP (2011) Structural basis of recognition of pathogen associated molecular patterns and inhibition of proinflammatory cytokines by camel peptidoglycanrecognition protein. J Biol Chem 286, 16208-17.

Sharma P, Singh N, Sinha M, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A & Singh TP (2009) Tryptophan as a three-way switch in regulating the function of the secretory signalling glycoprotein (SPS-40) from mammary glands: structure of SPS-40 complexed with 2-methylpentane-2,4-diol at 1.6 Å resolution. Acta Cryst D 65, 375-8.

Sharma P, Singh N, Sinha M, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A & Singh TP (2008) Crystal structure of the peptidoglycan recognition protein at 1.8 Å resolution reveals dual strategy to combat infection through two independent functional homodimers. J Mol Biol 378, 923-32.    

M.D Biophysics Syllabus

M.D Biophysics Syllabus

PAPER I

Molecular Pharmacology: definition and determination of important pharmaco-kinetic parameters and pharmaco-dynamic parameters, pharmacokinetic basis of individual difference in response to drugs, pharmacokinetic properties, pharmacopore identification, influence of structural modifications on pharmacokinetic properties, mode of action of drugs, quantitative structure activity relationship, present and future aids to drug design, structure and confirmation of drugs and receptors, drug receptor binding forces, structural aspects of drug-nucleic acid interactions

Peptides-design, synthesis and applications: introduction to peptides, peptide design, synthesis of peptides (solution phase and solid phase), protection and deprotection of amino and carboxyl group, unnatural amino acids, conformation of peptides, purification and crystallization of peptides, determination of structure of small molecules (briefly), application of peptides

Biomechanics: Basic concepts of fluid dynamics, Bernoulli equation and its applications, streamline flow, Reynolds number, viscous flow, effects of gravity and external acceleration on circulation

Biostatistics: mean, median, mode, dispersion, standard deviation, correlation and regression, T-Test, chi-square test, F-test, ANOVA, how to enter data, edit and transform data, descriptive statistics ie. how to calculate mean, SD, range etc., frequency distribution, hypothesis tests for means and proportions, ANOVA, scatter plot, correlation matrix, regression, probability distribution.

Bioinformatics: Introduction, repositories, databases, pairwise sequence based alignment, relationship between sequence and structures, structural bioinformatics, genomics, proteomics, human genome project, software packages

Clinical proteomics

 

PAPER II

Spectroscopic techniques: Introduction to spectroscopy, basic principles, instrumentation and applications of UV-VIS absorption, infrared, Raman, atomic absorption, fluorescence, Circular dichroism, Laser spectroscopy, nuclear magnetic resonance, electron spin resonance, acoustic spectroscopy; solvent perturbation; difference spectroscopy; Fourier transform techniques; applications of Laser; mass spectroscopy.

Elementary crystallography: Introduction to crystallography, symmetry in crystals, lattices and unit cells, crystal systems, Bravais lattices, elements of symmetry- rotation axis, mirror planes and center of inversion, point group symmetry- monoaxial point groups, polyaxial point groups, translational symmetry- screw axis and glide planes, space group, equivalent points, X-ray diffraction and Bragg’s equation

X-ray diffraction methods: Scattering factor, structure factor expression, reciprocal lattice, Ewald’s sphere, electron density equation, phase problem, Patterson function, molecular replacement method, isomorphous replacement, refinement programs and interpretation of results, methods of data collection of crystal containing small molecule and large molecule, factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates.

Separation techniques: Basic principles and applications of electrophoresis-types of electrophoresis, estimation of molecular weight of proteins by logirthmic method; basic principles and applications of centrifugation-sedimentation, estimation of sedimentation rate by sedimentation velocity method and equilibrium method; basic principles and applications of chromatography-capacity factor of the gel, Kd value, α value.

Molecular modeling: Basic principle of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in cartesian space, molecular mechanics-basic principle, molecular dynamics basic principles

 

PAPER III

Cell biology: Organization and structure of prokaryotes and eukaryotes, nucleus, cytoplasm, plasma membrane, mitochondria-structure, function respiratory chain and ATP synthesis, endoplasmic reticulum, golgi apparatus, membranes, ribosomes, peroxisomes, lysozomes, transcription and translation, transport of proteins, cancer and its molecular genetics, oncogenes, tumor suppression gene

Molecular biology: central dogma, genetic code, gene and operon, structure of DNA and RNA, plasmids, selectable markers, agarose gel, PCR, Cloning PCR products, expression vectors, cell free translation, c- DNA libraries, genomic libraries, DNA micro arrays, DNA sequencing

Proteins, purification, structure and function: twenty amino acids: structure and function, the peptide bond, primary structure of a protein: methods of sequence determination, forces determining protein structure, secondary structure of a protein: β strands, β sheets (parallel and anti parallel), β turns, α helix, 310 helix and π helix (differences), tertiary structure of a protein: protein folds-all α helix motifs (Lone helix, helix-turn-helix, four helix bundle and eight helix bundle), protein folds-all β sheet motifs (β sandwich, β barrel, greek Key topology and β propellars), protein folds- α / β motifs (Tim barrel, Rosman fold, α/β horseshoe), quaternary structure of a protein: macromolecular assemblies, domains and domain swapping, membrane proteins, purification methods, studies of proteins with MALDI-TOF, enzymes and enzyme kinetics, G-proteins and G-protein coupled receptors(GPCRs), proteins as targets for rational structure based drug design

Principles of nucleic acid structure: nucleotide structure and properties: introduction to DNA, RNA, bases, sugars, phosphates, structure of nucleotide, nucleosides and polynucleotides and their nomenclature scheme. tautomerisation and ionization. genetic code. stereochemistry: nucleoside, torsion angles, sugar conformation, NMR study, DNA structure: different types of DNA and their structure, DNA motifs, DNA repeats and their significance, function and stability, spectroscpic study of DNA: dye binding, interaction, denaturation, and renaturation of DNA, thermal denaturation and Tm value, RNA: structure and properties, different forms of RNA and their significance, alkaline hydrolysis of RNA, how it differs from DNA, role of 2’OH group, structure of phenylalanine tRNA, enzymes involved in molecular biology: DNA polymerase, RNA polymerase, reverse transcriptase, restriction endonuclease. DNA interaction: protein, dye, drugs and carcinogens, DNA replication: DNA polymerization, mutation, and DNA repair, DNA transcription: RNA synthesis, types of RNA polymerase, DNA polymorphism: repeats of DNA and their significance, single nucleotide polymorphism, c-DNA, cloning and expression and purification

Membrane biology: Lipid structure and their organization, comparison of different membrane models, diffusions and permeability, different types of transport system across membranes, liposome and its applications

 

PAPER IV

Imaging techniques: Ultrasound, nuclear magnetic resonance, positron emission topography, computer axial tomography, whole body scanner, dose calibrators, gamma scintillation camera, digital imaging techniques, acquisition, analysis and processing of data from gamma camera, enhancement, topographic reconstruction, display and recording of image

Radiation biophysics: production and types of radiations, radiation measurement units, interaction of radiation with matter, detection of radiation by ionization chamber, G.M counter, proportional counter, liquid scintillation counter, radiation protection, molecular effects of radiation on membranes, cytoplasmic organelles, macromolecules, factors modifying effects of radiation, repairs of radiation induced damage

Radio pharmaceuticals: Production of radionuclides by reactors, cyclotrons and particle accelerators, use of radionuclide generators, elements of radiochemistry

Diagnostic use of radionuclides: In vivo imaging and functional studiesof brain, thyroid, heart, biliary tract, liver, kidney, spleen, tumors, bones and abscesses, use of imaging devices and external detectors for organ imaging, time dependent and differential functional studies, use of physiological gating techniques for functional studies, methodology and quality control of competitive binding and radio immunoassay, procedures for the measurement of peptide hormones, drugs and other biological substances, basic principles of radionuclide therapy in thyrotoxicosis and carcinoma thyroid

Bioelectric potentials: Principles and interpretations of electro-encephalogram, electro-cardiogram and electro-retionogram

Dynamics of non-linear Processes: Physico-mathematical foundations of the dynamics of non-linear processes, phase plane method, different modes of excitations, nearly sinusoidal oscillations, building up of oscillations, effect of third harmonic distortion, Liapounov criteria of stability, limit cycles

 

         

 

 

 

M.Sc. Biophysics Syllabus

M.Sc. Biophysics Syllabus

PAPER I

Cell biology: Organization and structure of prokaryotes and eukaryotes, nucleus, cytoplasm, plasma membrane, mitochondria-structure, function respiratory chain and ATP synthesis, endoplasmic reticulum, golgi apparatus, membranes, ribosomes, peroxisomes, lysozomes, transcription and translation, transport of proteins, cancer and its molecular genetics, oncogenes, tumor suppression gene

Molecular biology: central dogma, genetic code, gene and operon, structure of DNA and RNA, plasmids, selectable markers, agarose gel, PCR, cloning PCR products, expression vectors, cell free translation, c- DNA libraries, genomic libraries, DNA micro arrays, DNA sequencing

Bioinformatics: Introduction, repositories, databases, pairwise sequence based alignment, relationship between sequence and structures, structural bioinformatics, genomics, proteomics, human genome project, software packages

Numerical methods: Introduction to numerical methods, solutions to non-linear algebraic equations by the method of iteration and Newton aphson method, numerical integration by trapezoidal rule and simpson’s rule, numerical solution of ordinary differential equations by picard’s method of successive approximation, Euler’s method and Runge-Kutta method

Dynamics of non-linear processes: Physico-mathematical foundations of the dynamics of non-linear processes, phase plane method, different modes of excitations, nearly sinusoidal oscillations, building up of oscillations, effect of third harmonic distortion, Liapounov criteria of stability, limit cycles

PAPER II

Elementary crystallography: Introduction, symmetry in crystals, lattices and unit cells, crystal systems, Bravais lattices, elements of symmetry- rotation axis, mirror planes and center of inversion, point group symmetry- monoaxial point groups, polyaxial point groups, translational symmetry- screw axis and glide planes, space group, equivalent points, X-ray diffraction and Bragg equation 

X-ray diffraction methods: scattering factor, structure factor expression, reciprocal lattice, Ewald’s sphere, electron density equation, phase problem, Patterson function, molecular replacement method, isomorphous replacement, refinement programs and interpretation of results, methods of data collection of crystal containing small molecule and large molecule, factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates.

Proteins : Purification, structure and function: twenty amino acids: structure and function, the peptide bond, primary structure of a protein: methods of sequence determination, forces determining protein structure, secondary structure of a protein: β strands, β sheets (parallel and anti parallel), β turns, α helix, 3.10 helix and π helix (differences), tertiary structure of a protein: protein folds-all alpha helix motifs (Lone helix, helix-turn-helix, four helix bundle and eight helix bundle), protein folds-all β sheet motifs (β sandwich, β barrel, greek Key topology and β propellars), protein folds- α / β motifs (Tim barrel, Rosman fold, α/β horseshoe), quaternary structure of a protein: macromolecular assemblies, domains and domain swapping, membrane proteins, purification methods, studies of proteins with MALDI-TOF, enzymes and enzyme kinetics, G-proteins and G-protein coupled receptors(GPCRs), proteins as targets for rational structure based drug design

Principles of nucleic acid structure: nucleotide structure and properties: Introduction to DNA, RNA, bases, sugars, phosphates, structure of nucleotide, nucleosides and polynucleotides and their nomenclature scheme. tautomerisation and ionization. genetic code. stereochemistry: nucleoside, torsion angles, sugar confirmation, NMR study, DNA structure: different types of DNA and their structure, DNA motifs, DNA repeats and their significance, function and stability, spectroscpic study of DNA: dye binding, interaction, denaturation, and renaturation of DNA, thermal denaturation and Tm value, RNA: structure and properties, different forms of RNA and their significance, alkaline hydrolysis of RNA, how it differs from DNA, role of 2’OH group, structure of phenylalanine tRNA, enzymes involved in molecular biology: DNA polymerase, RNA polymerase, reverse transcriptase, restriction endonuclease. DNA interaction: protein, dye, drugs and carcinogens, DNA replication: DNA polymerization, mutation, and DNA repair, DNA transcription: RNA synthesis, types of RNA polymerase, DNA polymorphism: repeats of DNA and their significance, single nucleotide polymorphism, c-DNA, cloning and expression and purification

Membrane Biology: Lipid structure and their organization, comparison of different membrane models, diffusion and permeability, different types of transport systems across membranes, liposome and its applications

Peptides-design, synthesis and applications: Introduction to peptides, peptide design, synthesis of peptides (solution phase and solid phase), protection and deprotection of amino and carboxyl group, unnatural amino acids, conformation of peptides, purification and crystallization of peptides, determination of structure of small molecules (briefly), application of peptides

PAPER III

Mathematical methods and their applications in biological systems: Ordinary differential equations of the first degree and first order (variable separable method, linear equation), linear differential equations of the second order with constant coefficients, the Laplace Transform, Inverse Laplace transform, application of Laplace transform to solutions of differential equations, Fourier series and their applications.

Quantum biology and its uses: Classical mechanics, Newton, Lagrange and Hamilton’s equations, Schrodinger’s equation and its complete solution for S.H.O, central force and angular momentum

Quantum chemistry: Atomic orbital models, the wave equation, molecular orbitals, the LCAO method, the overlap method, coulomb and resonance integrals, the hydrogen molecule, charge distributions, approximate methods.

Theoretical modeling of biomolecular systems: Basic principles of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in cartesian space, molecular mechanics-basic principle, molecular dynamics basic principles

Spectroscopic techniques: Introduction to spectroscopy, basic principles, instrumentation and applications of UV-VIS absorption, infrared, Raman, atomic absorption, fluorescence, circular dichroism, Laser spectroscopy, nuclear magnetic resonance, electron spin resonance, acoustic spectroscopy; solvent perturbation; difference spectroscopy; Fourier transform techniques; applications of Laser; mass spectroscopy.

 

         

 

 

M.Sc. Biophysics Syllabus

PAPER I

Cell biology: Organization and structure of prokaryotes and eukaryotes, nucleus, cytoplasm, plasma membrane, mitochondria-structure, function respiratory chain and ATP synthesis, endoplasmic reticulum, golgi apparatus, membranes, ribosomes, peroxisomes, lysozomes, transcription and translation, transport of proteins, cancer and its molecular genetics, oncogenes, tumor suppression gene

Molecular biology: central dogma, genetic code, gene and operon, structure of DNA and RNA, plasmids, selectable markers, agarose gel, PCR, cloning PCR products, expression vectors, cell free translation, c- DNA libraries, genomic libraries, DNA micro arrays, DNA sequencing

Bioinformatics: Introduction, repositories, databases, pairwise sequence based alignment, relationship between sequence and structures, structural bioinformatics, genomics, proteomics, human genome project, software packages

Numerical methods: Introduction to numerical methods, solutions to non-linear algebraic equations by the method of iteration and Newton aphson method, numerical integration by trapezoidal rule and simpson’s rule, numerical solution of ordinary differential equations by picard’s method of successive approximation, Euler’s method and Runge-Kutta method

Dynamics of non-linear processes: Physico-mathematical foundations of the dynamics of non-linear processes, phase plane method, different modes of excitations, nearly sinusoidal oscillations, building up of oscillations, effect of third harmonic distortion, Liapounov criteria of stability, limit cycles

PAPER II

Elementary crystallography: Introduction, symmetry in crystals, lattices and unit cells, crystal systems, Bravais lattices, elements of symmetry- rotation axis, mirror planes and center of inversion, point group symmetry- monoaxial point groups, polyaxial point groups, translational symmetry- screw axis and glide planes, space group, equivalent points, X-ray diffraction and Bragg equation 

X-ray diffraction methods: scattering factor, structure factor expression, reciprocal lattice, Ewald’s sphere, electron density equation, phase problem, Patterson function, molecular replacement method, isomorphous replacement, refinement programs and interpretation of results, methods of data collection of crystal containing small molecule and large molecule, factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates.

Proteins : Purification, structure and function: twenty amino acids: structure and function, the peptide bond, primary structure of a protein: methods of sequence determination, forces determining protein structure, secondary structure of a protein: β strands, β sheets (parallel and anti parallel), β turns, α helix, 3.10 helix and π helix (differences), tertiary structure of a protein: protein folds-all alpha helix motifs (Lone helix, helix-turn-helix, four helix bundle and eight helix bundle), protein folds-all β sheet motifs (β sandwich, β barrel, greek Key topology and β propellars), protein folds- α / β motifs (Tim barrel, Rosman fold, α/β horseshoe), quaternary structure of a protein: macromolecular assemblies, domains and domain swapping, membrane proteins, purification methods, studies of proteins with MALDI-TOF, enzymes and enzyme kinetics, G-proteins and G-protein coupled receptors(GPCRs), proteins as targets for rational structure based drug design

Principles of nucleic acid structure: nucleotide structure and properties: Introduction to DNA, RNA, bases, sugars, phosphates, structure of nucleotide, nucleosides and polynucleotides and their nomenclature scheme. tautomerisation and ionization. genetic code. stereochemistry: nucleoside, torsion angles, sugar confirmation, NMR study, DNA structure: different types of DNA and their structure, DNA motifs, DNA repeats and their significance, function and stability, spectroscpic study of DNA: dye binding, interaction, denaturation, and renaturation of DNA, thermal denaturation and Tm value, RNA: structure and properties, different forms of RNA and their significance, alkaline hydrolysis of RNA, how it differs from DNA, role of 2’OH group, structure of phenylalanine tRNA, enzymes involved in molecular biology: DNA polymerase, RNA polymerase, reverse transcriptase, restriction endonuclease. DNA interaction: protein, dye, drugs and carcinogens, DNA replication: DNA polymerization, mutation, and DNA repair, DNA transcription: RNA synthesis, types of RNA polymerase, DNA polymorphism: repeats of DNA and their significance, single nucleotide polymorphism, c-DNA, cloning and expression and purification

Membrane Biology: Lipid structure and their organization, comparison of different membrane models, diffusion and permeability, different types of transport systems across membranes, liposome and its applications

Peptides-design, synthesis and applications: Introduction to peptides, peptide design, synthesis of peptides (solution phase and solid phase), protection and deprotection of amino and carboxyl group, unnatural amino acids, conformation of peptides, purification and crystallization of peptides, determination of structure of small molecules (briefly), application of peptides

PAPER III

Mathematical methods and their applications in biological systems: Ordinary differential equations of the first degree and first order (variable separable method, linear equation), linear differential equations of the second order with constant coefficients, the Laplace Transform, Inverse Laplace transform, application of Laplace transform to solutions of differential equations, Fourier series and their applications.

Quantum biology and its uses: Classical mechanics, Newton, Lagrange and Hamilton’s equations, Schrodinger’s equation and its complete solution for S.H.O, central force and angular momentum

Quantum chemistry: Atomic orbital models, the wave equation, molecular orbitals, the LCAO method, the overlap method, coulomb and resonance integrals, the hydrogen molecule, charge distributions, approximate methods.

Theoretical modeling of biomolecular systems: Basic principles of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in cartesian space, molecular mechanics-basic principle, molecular dynamics basic principles

Spectroscopic techniques: Introduction to spectroscopy, basic principles, instrumentation and applications of UV-VIS absorption, infrared, Raman, atomic absorption, fluorescence, circular dichroism, Laser spectroscopy, nuclear magnetic resonance, electron spin resonance, acoustic spectroscopy; solvent perturbation; difference spectroscopy; Fourier transform techniques; applications of Laser; mass spectroscopy.

 

         

 

 

Prof. Sujata Sharma

Prof. Sujata Sharma

 
Designation Professor
Email sujatasharma.aiims@gmail.com
Contact Number +91-11-26594608 ; +91-11-26593201
Research Interests Protein Structure Determination ; Rational Structure based Drug Design ; Multidrug Resistant Bacterial Therapeutics
Awards and Honors
National Bioscience Award for Career Development for the year 2011 (Department of Biotechnology, Govt. of India
National Woman Bioscientist Award for the year 2007 (Department of Biotechnology, Govt. of India) given by the President, Smt Pratibha Patil   
Best Poster Award in the 36th National Seminar in Crystallography, 2007 
Women Scientist of the Year 2006 (Biotech Research Society of India)
S V Talekar Medal for the best postgraduate of Department of Biophysics (AIIMS) for year 1998
Recent Significant Publications

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sharma, S., Kaushik, S., Sinha, M., Singh, A., Sikarwar, J., Chaudhary, A., Gupta, A., Kaur, P. & Singh, T.P. (2014). Structural and functional insights into Peptidyl-tRNA Hydrolase. Biochem. Biophys. Acta.1844 : 1279-1288
Rastogi, N., Singh, A., Pandey, S.N., Sinha, M., Bhushan, A., Kaur, P., Sharma, S. & Singh, T.P. (2014). Structure of the iron-free true C-terminal half of bovine lactoferrin produced by tryptic digestion and its functional significance in the gut. FEBS J. 281 : 2871-2882.  
Rastogi, R., Nagpal, N., Alam, N., Pandey, S., Gautam, L., Sinha, M., Shin, K., Manzoor, N., Virdi, J.S.,  Kaur, P., Sharma, S. & Singh, T.P.  (2014) Preparation and Antimicrobial Action of Three Tryptic Digested Functional Molecules of Bovine Lactoferrin. Plos One (2014)  9 : e90011.
Sharma, S., Sinha, M., Kaushik, S., Kaur, P. & Singh, T.P.  (2014). C-lobe of lactoferrin : The whole story of a half molecule. Biochem. Res. Int. (2013) Vol. 2013 : e271641.
Sharma, S., Singh, A.K., Kaushik, S., Sinha, M., Singh, R.P., Sharma, P., Sirohi, H.,  Kaur, P. & Singh, T.P. (2013) Lactoperoxidase : Stuctural Insights into Function, Ligand Binding and Inhibition. Int. J. Biochem. Mol. Biol. 4, 108-128.
Kaushik, S., Singh, N., Yamini, S., Singh, A., Sinha, M., Arora, A., Kaur, P., Sharma, S. & Singh, T.P. (2013). The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii. PLoS One. 8 : e67547.
Mir, R., Singh, N., Vikram, G., Kumar, R.P., Sinha, M., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S. & Singh, T.P. (2009)). Structural basis of the prevention  NSAID-induced d amage of the gastrointestinal tract by C-terminal half (C-lobe)  of bovine colostrums protein lactoferrin: Binding andstructural studies of the C-lobe complexes with indomethacin, diclofenac, aspirin and ibuprofen. Biophys. J. 97, 3178-3186
Mir, R., Singh, N., Vikram, G.,  Sinha, M., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S. & Singh, T.P. (2010).  Structural and binding studies of C-terminal half (C-lobe) of lactoferrin protein with COX-2-specific non-steroidal anti-inflammatory Drugs (NSAIDs). Arch. Biochem. Biophy. 500, 196-202
Sharma, S., Jasti, J., Kumar. J., Mohanty, A.K. & Singh, T.P. (2003). Crystal structure of a proteolytically generated functional monoferric C-lobe of bovine lactoferrin at 1.9Å resolution.  J. Mol.  Biol. 321, 1286-1296. 
 
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