Facilities

Dr Krishna Kishore Inampudi

2023-02-21T12:37:25+05:30

Dr Krishna Kishore Inampudi
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Current Designation & Contact Details	Additional Professor Room No. 3011, Third Floor, Teaching Block, Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India Email: krishna.inampudi@aiims.edu & kishorehcu@gmail.com Contact No: +91-11-26593834 (O)
Recent Employment Details (Past few years)	2019 – Present: Associate Professor, Department of Biophysics, AIIMS, New Delhi-INDIA 2015 – 2019: Assistant Professor, Department of Biophysics, AIIMS, New Delhi-INDIA Jan 2013 - Dec 2014: Postdoctoral Fellow, IECB, France & Yale University, USA Nov 2009 - Dec 2012: Postdoctoral Fellow, Yale University, USA Oct 2008 - Oct 2009: Global Infectious Diseases Postdoctoral Fellow, University of Washington, Seattle, USA
Brief Research Area	Lung Cancer (NSCLC) therapeutics Antibody-like inhibitors (Nanobodies) against of EGFR: Employing Protein Engineering, Computational Protein design and mRNA display Small molecule inhibitors (TKI) against drug-resistant EGFR kinases Aptamer inhibitors against the EGFR Multi-omics Approach of exosomes for Exploring the Molecular Mechanism and identification of early candidate biomarkers Non-small-cell lung carcinoma Oral Squamous Cell Carcinoma Coronary Artery Disease Designing/identifying potential inhibitors for viral non-structural proteins SARS-CoV2 Dengue virus Understanding the catalytic mechanism of the peptidyl-tRNA hydrolase from M. tuberculosis Protein-nucleic acid interactions (Computational)
Selected Publications/Patents (Last 5 years)	Google Scholar Link: https://scholar.google.com/citations?user=7G4HaXEAAAAJ&hl=en Rajkumar Kulandaisamy, Tushar Kushwaha, Anu Dalal, Vikas Kumar, Deepa Singh, Kamal Baswal, Pratibha Sharma, Kokkula Praneeth, Pankaj Jorwal, Srinivas Maddur, Tamanna Sharma, Manoj Kumar, Saroj Kumar, Aparoy Polamarasetty, Aekera Singh, Deepak Sehgal, Shivajirao L Gholap, Mohan B Appaiahgari, Madhumohan R Katika, Krishna K Inampudi. Repurposing of FDA approved drugs against SARS-CoV-2 Papain-Like protease by using computational, biochemical and in vitro studies, 2022. Frontiers in Microbiology 13, 877813, 1-23. Corresponding author (Impact factor: 6.06) Preeti Hooda, Mohd Ishtikhar, Shweta Saraswat, Pooja Bhatia, Deepali Mishra, Aditya Trivedi, Rajkumar Kulandaisamy, Soumya Aggarwal, Manoj Munde, Nemat Ali, Abdullah F. AlAsmari, Mohd A. Rauf, Krishna K. Inampudi, and Deepak Sehgal. Biochemical and Biophysical Characterisation of the Hepatitis E Virus Guanine-7-Methyltransferase, 2022, Molecules, 27, 1505 * Corresponding author. (Impact factor: 4.92) Anu Dalal, Tushar Kushwaha , Gourav Choudhir, Krishna K Inampudi, Tarak Karmakar, P Hariprasad, Shivajirao L Gholap. Computational investigations on the potential role of hygrophorones as quorum sensing inhibitors against LasR protein of Pseudomonas aeruginosa, 2022, J Biomol Struct Dyn 25;1-11 (Impact factor: 5.23) Ravi Bharadwaj, Tushar Kushwaha, Azhar Ahmad, Krishna K Inampudi, Tomoyoshi Nozaki and Somlata, An atypical EhGEF regulates phagocytosis in Entamoeba histolytica through EhRho1. 2021, PLOS Pathogens 17: 1-36 (Impact factor: 7.46) Rajkumar K, Tushar K, Vikas Kumar, Soumya De, Manoj Kumar, Saroj Kumar, Santosh K Upadhyay, Krishna K Inampudi, Characterization of Active/Binding Site Residues of peptidyl-tRNA Hydrolase Using Biophysical and Computational Studies. 2020, International Journal of Biological Macromolecules 159: 877-885 Corresponding author (Impact factor: 8.02) Sayantani Roy, Soumendu Boral, Snigdha Maiti, Tushar Kushwaha, Aditya J. Basak, Woonghee Lee, Amit Basak, Shivajirao L. Gholap, Krishna K. Inampudi and Soumya De, Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition. 2021, The FEBS Journal 1-18 (Impact factor: 5.62) Sulaiman A, McGarry S, El-Sahli S, Li L, Chambers J, Phan A, Al-Kadi E, Krishna K Inampudi, Gadde S, Wang L, Nanoparticles loaded with Wnt and YAP/mevalonate inhibitors in combination with paclitaxel stop the growth of TNBC patient-derived xenografts and diminish cancer stem cells and tumorigenesis. 2020, Advanced Therapeutics 3(11), 1-14 A. Carolin Seefeldt, Fabian Nguyen, Stéphanie Antunes, Natacha Pérébaskine, Michael Graf, Stefan Arenz, Krishna K Inampudi, Céline Douat, Gilles Guichard, Daniel N. Wilson & C. Axel Innis, 2015. The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the post-initiation complex. Nature Structural & Molecular Biology 22: 470-475. (Impact factor: 18.36) Stanley Howell, Krishna K. Inampudi, Doyle P Bean and Corey J. Wilson, 2014. Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases. Structure 22: 218-29. (Impact factor: 5.87) * equally contributed to this work Paul A. Beales, Nienke Geerts, Krishna K. Inampudi, Corey J. Wilson and T. Kyle Vanderlick, 2013. Reversible assembly of stacked membrane nano-platforms with reduced dimensionality and variable periodicity. Journal of American Chemical Society 135: 3335-8. (Impact factor: 16.38) Sarai Meyer, Roee Ramot, Krishna K. Inampudi, Beibei Luo, Chenyu Lin, Swathi Amere and Corey J. Wilson, 2013. Engineering alternate cooperative-communications in the lactose repressor protein scaffold. Protein Engineering Design and Selection 6: 433-443. equally contributed to this work (Impact factor: 1.95) Roee Ramot, Krishna K. Inampudi and Corey J. Wilson, 2012. The Lactose Repressor Experimental Folding Landscape: Fundamental Functional Unit and Tetramer Folding Mechanisms; Biochemistry 51: 7569–79. (Impact factor: 3.16) Kayode K. Ojo, Eric T. Larson, Katelyn R. Keyloun, Lisa J. Castaneda, Amy E. DeRocher, Krishna K. Inampudi, Jessica E. Kim, Tracy L. Arakaki, Ryan Murphy, Li Zhang, Alberto J. Napuli, Dustin J. Maly, Christophe L. M. J. Verlinde, Frederick S. Buckner, Marilyn Parsons, Wim G. J. Hol, Ethan A. Merritt and Wesley C. VanVoorhis, 2010. A Unique Variation of the ATP binding site makes Toxoplasma gondii Calcium-Dependent Protein Kinase 1 a drug target for selective kinase inhibitors; Nature Structural & Molecular Biology 17: 602-07. (Impact factor: 18.36)

Dr. Uddipan Das

2023-02-21T12:31:38+05:30

Dr. Uddipan Das
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Current Designation & Contact Details	Scientist-I Department of Biophysics, Near Lecture Theater-2, PC Block, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029 Phone (office): +91-11-26594259, Ext: 4259 Email: uddipan.das@aiims.edu
Recent Employment Details (Past few years)	2016 - present: Scientist-I (Department of Biophysics, All India Institute of Medical Sciences, New Delhi) 2014-2016: Senior Resident/Demonstrator (Department of Biophysics, All India Institute of Medical Sciences, New Delhi)
Brief Research Area	Structural biology: We are interested in understanding the intricate structure and function of Membrane proteins and Macromolecular complexes. To accomplish this, we are harnessing the power of Cryo-Electron microscopy and X-ray crystallography along with other biophysical and biochemical methods in order to understand the structure function relationships.
Awards & Honours	Visiting scientist at the University of Stanford, Cryo-EM center, California 2022-2023. SERB international research experience award (Government of India) 2022. Visiting scholar at European Molecular biology Laboratory, Hamburg, Germany, 2013. European Molecular Biology Organization (EMBO) Fellowship 2013. Indian Council of Medical Research Junior research fellowship 2009. Department of Biotechnology Junior research fellowship 2009. Graduate Aptitude Rest in Engineering (Life Sciences), 2009 Centre of Scientific and Industrial Research NET 2009.
Selected Publications/Patents (Last 5 years)	Google Scholar Link: https://scholar.google.com/citations?user=_YQkkBcAAAAJ&hl=en Singh M, Haque MA, Tikhomirov A, Shchekotikhin, A, Das U, Kaur, P (2022). Computational and biophysical characterization of heterocyclic derivatives of anthraquinone against Human Aurora Kinase A. ACS Omega (accepted) Sharma P, Kumar M, Tripathi MK, Gupta D, Vishwakarma P, Das U & Kaur P (2022) Genomic and structural mechanistic insight to reveal the differential infectivity of omicron and other variants of concern. Comput Biol Med 150, 106129. Sharma D, Singh M, Kaur P & Das U* (2022) Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis , provides insights into its trehalose specificity. Acta Crystallogr Sect D Struct Biol 78, 835–845. Gupta D, Kumar M, Singh M, Salman M, Das U & Kaur P (2022) Identification of polypharmacological anticancerous molecules against Aurora kinase family of proteins. J Cell Biochem 123, 719–735. Singh M, Malhotra L, Haque MA, Kumar M, Tikhomirov A, Litvinova V, Korolev AM, Ethayathulla AS, Das U, Shchekotikhin AE & Kaur P (2021) Heteroarene-fused anthraquinone derivatives as potential modulators for human aurora kinase B. Biochimie 182, 152–165. Sabharwal N, Varshney K, Rath PP, Gourinath S & Das U* (2020) Biochemical and biophysical characterization of nucleotide binding domain of Trehalose transporter from Mycobacterium tuberculosis. Int J Biol Macromol 152, 109–116. Das U*, Singh E, Dharavath S, Tiruttani Subhramanyam UK, Pal RK, Vijayan R, Menon S, Kumar S, Gourinath S & Srinivasan A (2019) Structural insights into the substrate binding mechanism of novel ArgA from Mycobacterium tuberculosis. Int J Biol Macromol 125, 970–978. Gupta AK, Pokhriyal R, Das U, Khan MI, Kumar DR, Gupta R, Chadda RK, Ramachandran R, Goyal V, Tripathi M & Hariprasad G (2019) Evaluation of α-synuclein and apolipoprotein e as potential biomarkers in cerebrospinal fluid to monitor pharmacotherapeutic efficacy in dopamine dictated disease states of parkinson’s diseaseand schizophrenia. Neuropsychiatr Dis Treat 15, 2073–2085. Das U, Pogenberg V, Subhramanyam UKT, Wilmanns M, Gourinath S & Srinivasan A (2014) Crystal structure of the VapBc-15 complex from mycobacterium tuberculosis reveals a two-metal ion dependent pin-domain ribonuclease and a variable mode of toxin-antitoxin assembly. J Struct Biol 188, 249–258. Das U, Kumar N, Gourinath S & Srinivasan A (2013) Preliminary crystallographic analysis of recombinant VapBC-15 toxin-antitoxin complex from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 69, 1242–1245.

Dr. Manoj Kumar

2023-02-21T12:05:39+05:30

Dr. Manoj Kumar
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Current Designation & Contact Details	Scientist II Room No. 1008, Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India Tel: +91-11-26594816 Email: mkrai@aiims.edu; manmath.manoj@gmail.com
Recent Employment Details (Past few years)	Scientist II, Department of Biophysics, AIIMS, New Delhi 2016 – till date Senior Demonstrator, Department of Biophysics, AIIMS, New Delhi 2012-2015
Brief Research Area	I am working in the area of drug discovery for tuberculosis using rational drug design approach. My goal is to design lead molecules for treatment of drug-resistant tuberculosis. I am also working on design of lead molecules for development of drugs to shorten the treatment duration.
Selected Publications/Patents (Last 5 years)	Google Scholar link: https://scholar.google.com/citations?user=wezA8UgAAAAJ&hl=en Naz F, Kumar M, Koley T, Sharma P, Haque MA, Kapil A, Kumar M, Kaur P, Ethayathulla AS. Screening of plant-based natural compounds as an inhibitor of FtsZ from Salmonella Typhi using the computational, biochemical and in vitro cell-based studies. Int J Biol Macromol. 2022 Aug 3; 219: 428-437 doi: 10.1016/j.ijbiomac.2022.07.241 Gupta V, Somarajan BI, Gupta S, Mahalingam K, Kumar M, Singh A. Association of EFEMP1 with juvenile-onset open angle glaucoma in a patient with concomitant COL11A1-related Stickler syndrome. Ophthalmic Genet. 2022 Aug 10:1-5. doi: 10.1080/13816810.2022.2109682. Koley T, Goswami A, Kumar M, Upadhyay N, Hariprasad G. Comparative Structural Analysis of Human ACE2 Receptor with Spike Protein of SARS-CoV-2 Variants: Implications to Understand Infectivity of the Virus. Adv Appl Bioinform Chem. 2022 Jun 16;15: 21-27. doi: 10.2147/AABC.S360787. Kulandaisamy R, Kushwaha T, Dalal A, Kumar V, Singh D, Baswal K, Sharma P, Praneeth K, Jorwal P, Kayampeta SR, Sharma T, Maddur S, Kumar M, Kumar S, Polamarasetty A, Singh A, Sehgal D, Gholap SL, Appaiahgari MB, Katika MR, Inampudi KK. Repurposing of FDA Approved Drugs Against SARS-CoV-2 Papain-Like Protease: Computational, Biochemical, and in vitro Studies. Front Microbiol. 2022 May 10; 13: 877813. doi: 10.3389/fmicb.2022.877813. Koley T, Chowdhury SR, Kushwaha T, Kumar M, Inampudi KK, Kaur P, Singh TP, Viadiu H, Ethayathulla AS. Deciphering the mechanism of p73 recognition of p53 response elements using the crystal structure of p73-DNA complexes and computational studies. Int J BiolMacromol. 2022 May 1; 206:40-50.doi: 10.1016/j.ijbiomac.2022.02.108. Anand V, Aggarwa B, Jauhari P, Kumar M, Gupta N, Kumar A, Gulati S, Kabra M. STAMBP gene mutation causing microcephaly-capillary malformation syndrome: a recognizable developmental and epileptic encephalopathy. Epileptic Disord. 2022 Jun 1;24(3):602-605. English. doi: 10.1684/epd.2021.1411. Koley T, Kumar M, Goswami A, Ethayathulla AS, Hariprasad G. Structural modeling of Omicron spike protein and its complex with human ACE-2 receptor: Molecular basis for high transmissibility of the virus. Biochem Biophys Res Commun. 2022 Feb 12; 592: 51-53. doi: 10.1016/j.bbrc.2021.12.082. Kumar A, Sharma R, Faruq M, Kumar M, Sharma S, Werner R, Hiort O, Vandana J. Clinical, Biochemical, and Molecular Characterization of Indian Children with Clinically Suspected Androgen Insensitivity Syndrome. Sex Dev. 2021 Oct 22:1-12. doi: 10.1159/000519047. Mishra P, Tandon G, Kumar M, Paital B, Swain SS, Kumar S, Samanta L. Promoter sequence interaction and structure based multi-targeted (redox regulatory genes) molecular docking analysis of vitamin E and curcumin in T4 induced oxidative stress model using H9C2 cardiac cell line. J BiomolStructDyn. 2021 Aug 31:1-20. doi: 10.1080/07391102.2021.1970624. Sharma S, Kumar R, Jain A, Kumar M, Gauttam R, Banerjee R, Mukhopadhyay J, Tyagi JS. Functional insights into Mycobacterium tuberculosis DevR-dependent transcriptional machinery utilizing Escherichia coli. Biochem J. 2021 Aug 27;478(16):3079-3098. doi: 10.1042/BCJ20210268. Garg S, Khan SI, Malhotra RK, Sharma MK, Kumar M, Kaur P, Nag TC, Ray R, Bhatia J, Arya DS. Cardioprotective effects of azilsartan compared with that of telmisartan on an in vivo model of myocardial ischemia-reperfusion injury. J BiochemMolToxicol. 2021 Jul;35(7):e22785. doi: 10.1002/jbt.22785. Koley T, Madaan S, Chowdhury SR, Kumar M, Kaur P, Singh TP, Ethayathulla AS. Structural analysis of COVID-19 spike protein in recognizing the ACE2 receptor of different mammalian species and its susceptibility to viral infection. 3Biotech. 2021 Feb;11(2):109. doi: 10.1007/s13205-020-02599-2. Malhotra L, Goyal HKV, Jhuria S, Dev K, Kumar S, Kumar M, Kaur P, Ethayathulla AS. Curcumin rescue p53Y220C in BxPC-3 pancreatic adenocarcinomas cell line: Evidence-based on computational, biophysical, and in vivo studies. BiochimBiophysActa Gen Subj. 2021 Feb;1865(2):129807. doi: 10.1016/j.bbagen.2020.129807. Kumar S, Tyagi YK, Kumar M, Kumar S. Synthesis of novel 4-methylthiocoumarin and comparison with conventional coumarin derivative as a multi-target-directed ligand in Alzheimer's disease. 3 Biotech. 2020 Dec;10(12):509. doi: 10.1007/s13205-020-02481-1. Tripathi A, Kumar B, Kumar M, Kaur P, Sagi SSK. Quercetin Prophylaxis: A Novel Approach to Prevent Hypoxia-Mediated Increase in Oxidative Stress, Pde-5 Activity and Transvascular Leakage in the Lungs of Rats. HSOA J Pulmo Med Respir Res. 2020 6: 041 doi:10.24966/PMRR-0177/100041 Garg S, Khan SI, Malhotra RK, Sharma MK, Kumar M, Kaur P, Nag TC, RumaRay, Bhatia J, Arya DS. The molecular mechanism involved in cardioprotection by the dietary flavonoid fisetin as an agonist of PPAR-γ in a murine model of myocardial infarction. Arch BiochemBiophys. 2020 Nov 15; 694:108572. doi: 10.1016/j.abb.2020.108572. Sharma P, Kumar M, Dahiya S, Sood S, Das BK, Kaur P, Kapil A. Structure based drug discovery and in vitro activity testing for DNA gyrase inhibitors of Salmonella entericaserovarTyphi. Bioorg Chem. 2020 Nov;104: 104244. doi: 10.1016/j.bioorg.2020.104244. Kumar S, Kumar M, Tyagi YK, Kumar S. Inhibition of Amyloid Fibrillation of HEWL by 4-Methylcoumarin and 4-Methylthiocoumarin Derivatives. Curr Pharm Biotechnol. 2021;22 (2):232-244. doi: 10.2174/1389201021666200915112849. Kumar A, Sharma R, Faruq M, Suroliya V, Kumar M, Sharma S, Werner R, Hiort O, Jain V. Spectrum of Pathogenic Variants in SRD5A2 in Indian Children with 46,XY Disorders of Sex Development and Clinically Suspected Steroid 5α-Reductase 2 Deficiency. Sex Dev. 2019;13 (5-6):228-239. doi: 10.1159/000509812. Naz F, Mashkoor M, Sharma P, Haque MA, Kapil A, Kumar M, Kaur P, Abdul Samath E. Drug repurposing approach to target FtsZ cell division protein from Salmonella Typhi. Int J BiolMacromol. 2020 Sep 15; 159:1073-1083. doi: 10.1016/j.ijbiomac.2020.05.063. Kulandaisamy R, Kushwaha T, Kumar V, De S, Kumar S, Upadhyay SK, Kumar M, Inampudi KK. Characterization of active/binding site residues of peptidyl-tRNA hydrolase using biophysical and computational studies. Int J BiolMacromol. 2020 Sep 15;159: 877-885. doi: 10.1016/j.ijbiomac.2020.05.133. Perveen S, Gupta N, Kumar M, Kaur P, Chowdhury MR, Kabra M. Spectrum of amyloglucosidase mutations in Asian Indian patients with Glycogen storage disease type III. Am J Med Genet A. 2020 May;182(5):1190-1200. doi: 10.1002/ajmg.a.61547. Tripathi A, Kumar M, Kaur P, Kumar B, Sagi SSK. Efficacy of Quercetin as a potent sensitizer of β2-AR in combating the impairment of fluid clearance in lungs of rats under hypoxia. RespirPhysiolNeurobiol. 2020 Feb;273: 103334. doi: 10.1016/j.resp.2019.103334. Pandey G, Bakhshi S, Kumar M, Thakur B, Jain P, Kaur P, Chauhan SS. Prognostic and therapeutic relevance of cathepsin B in pediatric acute myeloid leukemia. Am J Cancer Res. 2019 Dec 1; 9 (12): 2634-2649. Kumar A, Jain V, Chowdhury MR, Kumar M, Kaur P, Kabra M. Pathogenic/likely pathogenic variants in the SHOX, GHR and IGFALS genes among Indian children with idiopathic short stature. J PediatrEndocrinolMetab. 2020 Jan 28;33(1):79-88. doi: 10.1515/jpem-2019-0234. Sudarshan S, Kumar M, Kaur P, Kumar A, G S, Sapra S, Gulati S, Gupta N, Kabra M, Roy Chowdhury M. Decoding of novel missense TSC2 gene variants using in-silico methods. BMC Med Genet. 2019 Oct 26;20(1):164. doi: 10.1186/s12881-019-0891-y. Yadav P, Kumar M, Bansal R, Kaur P, Ethayathulla AS. Structure model of ferrochelatase from Salmonella Typhi elucidating metalation mechanism. Int J BiolMacromol. 2019 Apr 15;127: 585-593. doi: 10.1016/j.ijbiomac.2019.01.066. Gupta N, Tewari VV, Kumar M, Langeh N, Gupta A, Mishra P, Kaur P, Ramprasad V, Murugan S, Kumar R, Jana M, Kabra M. Asparagine Synthetase deficiency-report of a novel mutation and review of literature. Metab Brain Dis. 2017 Dec;3 2(6):1889-1900. doi: 10.1007/s11011-017-0073-6. Yenamandra VK, Vellarikkal SK, Kumar M, Chowdhury MR, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Ray SB, Dinda AK, Kabra M, Kaur P, Sharma VK, Sethuraman G. Application of whole exome sequencing in elucidating the phenotype and genotype spectrum of junctional epidermolysis bullosa: A preliminary experience of a tertiary care centre in India. J Dermatol Sci. 2017 Apr; 86(1):30-36. doi: 10.1016/j.jdermsci.2016.12.020.

Dr. Krishna Kumar Inampudi

2022-10-07T15:46:28+05:30

Dr. Krishna Kumar Inampudi

Dr. Jyotirmoy Banerjee

2021-10-16T11:13:32+05:30

Dr Jyotirmoy Banerjee

Current Designation & Contact Details:

Additional Professor

Room No. 11, 5^th Floor,

Porta Cabin, Teaching Block

Department of Biophysics,

All India Institute of Medical Sciences (AIIMS), New Delhi, India

Tel: 91-11-26549324

e-mail: jyotirmoybanerjee1@gmail.com

jyotirmoy@aiims.edu

Recent Employment Details:

July 2023-Till Date

Additional Professor, Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, India.

July 2020-June 2023

Associate Professor, Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, India.

May 2017-June 2020

Assistant Professor, Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, India.

Brief Area of Research:

Cellular electrophysiological studies to understand function of ion channels of central nervous system and investigating regulation of synaptic transmission in drug-resistant epilepsy pathologies at cellular and molecular level.

Awards and Honors:

AIIMS Excellence Research Award in Basic Sciences for the year 2024.
AIIMS Oncology Research Award in Basic Sciences for the year 2023.
AIIMS Oncology Research Award in Basic Sciences for the year 2022.
AIIMS Excellence Research Award in Basic Sciences for the year 2021.
AIIMS Excellence Research Award in Basic Sciences for the year 2020.

Recent Selected Publications (*As Corresponding Author):

Google scholar link: https://scholar.google.com/citations?user=81uRX7kAAAAJ&hl=en

1. Dubey V, Roy A, Dixit AB, Tripathi M, Pandey S, Jian S, Chandra PS, Banerjee J*. Dendritic reorganization in the hippocampus, anterior temporal lobe, and frontal neocortex of lithium-pilocarpine induced Status Epilepticus (SE). 2023, Journal of Chemical Neuroanatomy, 133: 102319. doi: 10.1016/j.jchemneu.2023.102329.

2. Kumar K, Dubey V, Zaidi SS, Tripathi M, Siraj F, Sharma MC, Chandra PS, Doddamani R, Dixit AB, Banerjee J*. RNA Sequencing of Intraoperative Peritumoral Tissues Reveals Potential Pathways Involved in Glioma-Related Seizures. 2023, Journal of Molecular Neuroscience, 73:437-447. doi: 10.1007/s12031-023-02125-y.

3. Dubey V, Dixit AB, Banerjee J*. Tempol Suppresses Generalized seizures in animal model of epilepsy. 2023, Neurology India, 71:412-413. doi: 10.4103/0028-3886.375411.

4. Sharma D, Tripathi M, Doddamani R, Sharma MC, Lalwani S, Chandra PS, Dixit AB, Banerjee J*. Correlation of Age at Seizure Onset with GABA_A receptor subunit and Chloride Co-transporter configuration in Focal Cortical Dysplasia (FCD). 2023, Neuroscience Letters, 796: 137065. doi: 10.1016/j.neulet.2023.137065. (IF-3.1).

5. Chakraborty A, Dey S, Kumar K, Dixit AB, Tripathi M, Sharma MC, Chandra PS, Banerjee J*. Novel variants in GABA_A receptor subunits: A possible association with benzodiazepine resistance in patients with drug-resistant epilepsy. 2023, Epilepsy Research, 189:107056. doi: 10.1016/j.eplepsyres.2022.107056.

6. Kumar K, Banerjee Dixit A, Tripathi M, Dubey V, Siraj F, Sharma MC, Lalwani S, Chandra PS, Banerjee J*. Transcriptomic profiling of nonneoplastic cortical tissues reveals epileptogenic mechanisms in dysembryoplastic neuroepithelial tumors. 2022, Functional & Integrative Genomics; 22:905-917. doi: 10.1007/s10142-022-00869-1.

7. Bera A, Srivastava A, Dubey V, Dixit AB, Tripathi M, Sharma MC, Lalwani S, Chandra PS, Banerjee J*. Altered hippocampal expression and function of cytosolic phospholipase A2 (cPLA2) in temporal lobe epilepsy (TLE). 2022, Neurological Research; 44: 748-753.doi: 10.1080/01616412.2022.2051131.

8. Dubey V, Dey S, Dixit AB, Tripathi M, Chandra PS, Banerjee J*. Differential glutamate receptor expression and function in the hippocampus, anterior temporal lobe and neocortex in a pilocarpine model of temporal lobe epilepsy. 2022, Experimental Neurology;347:113916. doi: 10.1016/j.expneurol.2021.113916.

9. Dey S, Banerjee Dixit A, Tripathi M, Doddamani RS, Sharma MC, Lalwani S, Chandra PS, Banerjee J*. Altered hippocampal kynurenine pathway metabolism contribute to hyperexcitability in human mesial temporal lobe epilepsy-hippocampal sclerosis. 2021, British Journal of Pharmacology; 178:3959-3976.doi: 10.1111/bph.15534.

10. Kumar S, Shanker OR, Kumari N, Tripathi M, Chandra PS, Dixit AB, Banerjee J*. Neuromodulatory effects of SARS-CoV2 infection: Possible therapeutic targets. 2021, Expert Opinion on Therapeutic Targets; 25:509-519.doi: 10.1080/14728222.2021.1953475.

11. Banerjee J, Srivastava A, Sharma D, Dey S, Tripathi M, Sharma MC, et al. Differential regulation of glutamatergic activity in the hippocampus and anterior temporal lobe by cyclin dependent kinase 5 (Cdk5) in mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS). 2021, Neuroscience Letters; 761: 136096. doi: 10.1016/j.neulet.2021.136096.

12. Dey S, Doddamani R, Dixit AB, Tripathi M, Sharma MC, Chandra PS, Banerjee J*. Altered spontaneous glutamatergic and GABAergic activity in the peritumoral cortex of low-grade gliomas presenting with history of seizures. 2021, Frontiers in Neuroscience; 15:689769. doi:10.3389/fnins.2021.689769

13. Sharma D, Dixit AB, Dey S, Tripathi M, Doddamani R, Sharma MC, Lalwani S, Gurjar HK, Chandra PS, Banerjee J*. Increased levels of α4-containing GABA_A receptors in focal cortical dysplasia: A possible cause of benzodiazepine resistance. 2021, Neurochemistry International; 148:105084.doi: 10.1016/j.neuint.2021.105084

14.Banerjee J*, Dey S, Dixit AB, Doddamani R, Sharma MC, Garg A, et al. GABA_A Receptor-Mediated Epileptogenicity in Focal Cortical Dysplasia (FCD) Depends on Age at Epilepsy Onset. 2020, Front Cell Neurosci; 14:562811.doi: 10.3389/fncel.2020.562811.

15. Banerjee J*, Dey S, Dixit AB, Tripathi M, Doddamani R, Sharma MC, et al. α7 nicotinic receptors contributes to glutamatergic activity in the hippocampus of patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS). 2020, J Neural Transmission; 127:1441-1446.doi: 10.1007/s00702-020-02239-2.

16. Banerjee J, Tripathi M, Chandra PS, Dixit AB. Do SARS-CoV2 viral proteins have neuromodulatory properties? 2020, Neurol India; 68:274-275.doi: 10.4103/0028-3886.283760.

17. Srivastava A, Dixit AB, Paul D, Tripathi M, Sarkar C, Chandra PS, Banerjee J* (2017). Comparative analysis of cytokine/chemokine regulatory networks in patients with hippocampal sclerosis (HS) and focal cortical dysplasia (FCD). Scientific Reports, 7:15904.doi: 10.1038/s41598-017-16041-w.

18. Banerjee J*, Dixit AB, Srivastava A, Ramanujam B, Kakkar A, Sarkar C, Tripathi M & Chandra PS (2017). Altered glutamatergic tone reveals two distinct resting state networks at the cellular level in hippocampal sclerosis. Scientific Reports, 7:319.doi: 10.1038/s41598-017-00358-7.

Dr. Ethayathulla Abdul Samath

2020-07-21T14:52:07+05:30

Dr. Ethayathulla Abdul Samath
Additional Professor R.No.3006, 3rd Floor Teaching Block All India Institute of Medical Sciences Ansari Nagar, New Delhi Email Id: ethayathulla@aiims.edu Phone (O) +91- 11 26594816 / 26593351
Recent employment details	Additional Professor,since July 2020-Till date Associate Professor, since July 2017-June 2020 Assistant Professor,since June 2014-June 2017
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
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	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. 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. 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. 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. 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. 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. Amin A, Ethayathulla AS, Guan L. Suppression of conformation-compromised mutants of Salmonella entericaserovar Typhimurium MelB. J Bacteriol. 2014;196(17):3134-9. 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. 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. 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. 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. 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. 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. 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

2020-03-23T13:21:37+05:30

Dr. Pradeep Sharma
Photograph
Current Designation & Contact Details	Assistant Professor Room No. 9, Department of Biophysics, AIIMS, New Delhi Email: pradeepbdk@gmail.com & pradeep@aiims.edu Phone: +91-11-26594608
Brief Research Area	Antimicrobial therapeutics, Protein Structure based drug design, Nanomedicine.
Awards & Honours	INSA Young Scientist Award (2013) DST-INSPIRE Faculty Award (2012) Ludo Frevel Crystallography Award, ICDD, USA (2011) Summer Training Award at ESRF, Grenoble, France (European Commission, 2009) Chaired, Society of Young Scientists, AIIMS, New Delhi (2009-10) IUCr Travel award to attend IUCr meeting at Osaka, Japan (2008) Awarded CSIR-Junior Research Fellowship (03.2006 – 03.2008) Awarded CSIR Senior Research Fellowship (04.2008- 03.2011) Gold Medalist from Maharshi Dayanand University, Rohtak-2005
Selected Publications/Patents (Last 5 years)	Google Scholar Link: https://scholar.google.com/citations?hl=en&user=h-T3UPYAAAAJ Ahmad N, Singh A, Gupta A, Pant P, Singh TP, Sharma S, Sharma P. Discovery of the Lead Molecules Targeting the First Step of the Histidine Biosynthesis Pathway of Acinetobacter baumannii. J Chem Inf Model. (2022) 62 :1744-1759. Sikarwar J, Singh J, Singh TP, Sharma P, Sharma S. The mechanism of action of Lactoferrin - Nucleoside Diphosphate Kinase complex in combating biofilm formation. Protein Pept Lett. (2022) Aug 16. doi: 10.2174/0929866529666220816160517. Singh PK, Ahmad N, Yamini S, Singh RP, Singh AK, Sharma P, Smith ML, Sharma S, Singh TP. Structural evidence of the oxidation of iodide ion into hyper-reactive hypoiodite ion by mammalian heme lactoperoxidase. Protein Sci. (2022) 31:384-395. Singh J, Maurya A, Singh PK, Viswanathan V, Ahmad MI, Sharma P, Sharma S, Singh TP. A Peptide Bond from the Inter-lobe Segment in the Bilobal Lactoferrin Acts as a Preferred Site for Cleavage for Serine Proteases to Generate the Perfect C-lobe: Structure of the Pepsin Hydrolyzed Lactoferrin C-lobe at 2.28 Å Resolution. Protein J. (2021) 40 :857-866. Gupta A, Vijayan V, Pant P, Kaur P, Singh TP, Sharma P, Sharma S. Structure prediction and discovery of inhibitors against phosphopantothenoyl cysteine synthetase of Acinetobacter baumannii. J Biomol Struct Dyn. (2021) Aug 4:1-13 Singh A, Ahmad N, Varadarajan A, Vikram N, Singh TP, Sharma S, Sharma P. Lactoferrin, a potential iron-chelator as an adjunct treatment for mucormycosis - A comprehensive review. Int J Biol Macromol. (2021) Sep 30;187:988-998. Singh J, Vijayan V, Ahmedi S, Pant P, Manzoor N, Singh TP, Sharma P, Sharma S. Lactosmart: A Novel Therapeutic Molecule for Antimicrobial Defense. Front Microbiol. (2021) 12:672589. Gupta A, Sharma P, Singh TP & Sharma S. Phosphopantetheine Adenylyltransferase: A promising drug target to combat antibiotic resistance. Biochim Biophys Acta Proteins Proteom (2021) 1869:140566. Viswanathan V, Rani C, Ahmad N, Singh PK, Sharma P, Kaur P, Sharma S & Singh TP Structure of Yak Lactoperoxidase at 1.55 Å Resolution. Protein J. (2021) 40:8-18. Singh PK, Pandey S, Rani C, Ahmad N, Viswanathan V, Sharma P, Kaur P, Sharma S & Singh TP. Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 Å resolution. J Biol Inorg Chem (2021) 26: 149-159 Sharma P, Singla A, Gupta A, Khan NI, Rani C, Singh TP & Sharma S. Biophysical characterization of Type III Pantothenate kinase (PanK) from Acinetobacter baumannii. Protein Pept Lett (2021) 28(4), 450-458. Sharma P, Vijayan V, Pant P, Sharma M, Vikram N, Kaur P, Singh TP, Sharma S. Identification of potential drug candidates to combat COVID-19: a structural study using the main protease (mpro) of SARS-CoV-2. J Biomol Struct Dyn. 2020; 3:1-11 Gupta A, Singh PK, Iqbal N, Sharma P, Baraigya HR, Kaur P, Umar MS, Ahmad F, Sharma A, Owais M, Sharma S, Singh TP. Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii. Biochim Biophys Acta Proteins Proteom. (2019) 1867:537-547. Pandey SN, Iqbal N, Singh PK, Rastogi N, Kaur P, Sharma S & Singh TP. Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with uracil and uridine. Proteins. (2019) 87:99-109. Chaudhary A, Kumar V, Singh PK, Sharma P, Bairagya HR, Kaur P, Sharma S & Singh TP. A glycoprotein from mammary gland secreted during involution promotes apoptosis: Structural and biological studies. Arch Biochem Biophys. (2018) 644:72-80 Kaushik S, Iqbal N, Singh N, Sikarwar JS, Singh PK, Kaur P, Sharma S & Singh TP. Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies. Biochem J. (2018) 475:547-560. Singh PK, Iqbal N, Sirohi HV, Bairagya HR, Kaur P, Sharma S & Singh TP. Structural basis of activation of mammalian heme peroxidases. Prog Biophys Mol Biol. (2018)133:49-55. Singh PK, Sirohi HV, Iqbal N, Tiwari P, Kaur P, Sharma S, Singh TP. Structure of bovine lactoperoxidase with a partially linked heme moiety at 1.98Å resolution. Biochim Biophys Acta. (2017) 1865:329-335. Iqbal N, Kumar M, Sharma P, Yadav SP, Kaur P, Sharma S, Singh TP. Binding studies and structure determination of the recombinantly produced type-II 3-dehydroquinate dehydratase from Acinetobacter baumannii. Int J Biol Macromol. (2017) 94:459-465. Sirohi HV, Singh PK, Iqbal N, Sharma P, Singh AK, Kaur P, Sharma S, Singh TP. Design of anti-thyroid drugs: Binding studies and structure determination of the complex of lactoperoxidase with 2-mercaptoimidazole at 2.30 Å resolution. Proteins. (2017) 85:1882-1890. Singh RP, Singh A, Sirohi HV, Singh AK, Kaur P, Sharma S, Singh TP. Dual binding mode of antithyroid drug methimazole to mammalian heme peroxidases - structural determination of the lactoperoxidase-methimazole complex at 1.97 Å resolution. FEBS Open Bio. (2016) 6:640-50. Rastogi N, Singh A, Singh PK, Tyagi TK, Pandey S, Shin K, Kaur P, Sharma S, Singh TP. Structure of iron saturated C-lobe of bovine lactoferrin at pH 6.8 indicates a weakening of iron coordination. Proteins. (2016) 84:591-9.

M.Sc. Biophysics Syllabus

2019-11-27T14:56:57+05:30

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

PAPER II

PAPER III

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

M.D Biophysics Syllabus

2019-11-27T14:52:24+05:30

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

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

Prof. Sujata Sharma

2017-09-27T16:45:32+05:30

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.