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Structural Biology and BioInformatics

Dr. Nakul C. Maiti

Senior Scientist

Ph.D. Chemistry, TIFR, Mumbai (Bombay)                  

Research Associate/lecturer California State University, Los Angeles, USA
Senior Research Associate, Biochemistry, Case, Cleveland, Ohio, USA
JSPS visiting scientist (postdoctoral), Institute for Molecular Science, Japan

Contact: ncmaiti@iicb.res.in

Current Research Interest

Key research areas: 

Research in my laboratory orients into three main areas

  1. Intrinsically disordered proteins (IDPs) and their link to cell signaling, cancer and neurological disorder
  2. Role of H-bond in the stability and function of IDPs and related other receptor and enzyme molecules
  3. Probing protein folding and disorderness inside living cell, and tissue-condition in disease state (cancer and Parkinson’s) by biological Raman method .
  4. Designing biological nano-conjugates with particular focus on IDPs

We use combination of advanced molecular biology techniques and spectroscopic methods such as solution state NMR, micro Raman/FT IR and advance fluorescence analysis. In addition, we utilize computational modeling, molecular docking, DFT analysis and a high level of bioinformatics approaches to address the above events.


Classical notion is that well defined 3D protein structure is pre-requisite for its function and this has been challenged. It may be a very simplistic view and true for action of proteins on small molecules. Recent studies indicates that a large number of proteins or regions of proteins are intrinsically disordered (ID). About 50% of human proteins contain at least one long (> 30 residues) disorder regions and higher eukaryotes has higher proportionate number of IDPs and this observation indicates evolutionary importance of the disordered proteins. The IDPs lack any well-defined three dimensional folded structures in solution physiological conditions. The lack of a rigid and folded stable structure may provide large plasticity and structurally they remain as an ensemble of interconverting conformations under to IDPs to interact efficiently with different targets, as compared to a globular protein with limited conformational flexibility. These characteristics aid good efficacy to IDPs in cell cycle regulation, membrane transport, different molecular recognition processes.

One of the research objectives of our group is to provide a description and behaviour of intrinsically disordered proteins (IDPs) in different solution conditions and in living cell. Further we attempt to define the role of this class of proteins in cell signalling and their implication in neurological disorder including amyloid diseases. Our target proteins are alpha synuclein, amyloid beta peptide, presen I and II, insulin, tau and their fragments. Special attention is on amyloid beta peptide (a-beta) and alpha-synuclein to know the mechanisum of cytotoxc effect. The structural description of the peptide/protein in different states of the aggregation is very crucial for several purposes and we are addressing the structural evolution during the formation of such assmbly structure. We aim to provide more insight about mechanism of neurotoxicity invoving protein disorder. We also started investigation of functional amyloids and importance of protein oligomers in neuro-transmittance. In addition we initiated study on cancer steam cell marker proteins, particularly role of disordered regions and their function to develop a suitable drug candidates.


 We started biological Raman and FT IR laboratory to probe biological molecules and events in crystal, semi-solid, and inside living cell. Using a Raman microscope, it is possible to obtain protein Raman spectroscopic data of decent quality. We plan to probe events ranging from small cooperative conformational changes to massive and unexpected secondary structural changes in the protein in different assembly structure.

One particular focus is to   derive the structural transformations of disordered proteins and peptide when they form aggregates and associated with diseases states and compare the disease affected brain tissues with healthy brain. Here our aim is to achieve and develop methodologies  to detect the early state pathological marker of  amyloid  disorder.  

Further, we want to see in real time how the protein and other macromolecules interact with each other and form membrane less organelles. This structure has significant role in cell signaling and neuro-transmittance and we, by biological Raman analysis, aim to derive detail structural information of these species


  1. EMPOWER (Encouraging and Motivating Pursuit of World Class Exploratory Research) grant, 2010-2012, CSIR, New Delhi
  2. DBT-grant, α-Synuclein and Tau Interaction: Implication on Neurodegenerative Diseases, 2012-, Department of Biotechnology, New Delhi

Positions Available

Positions are available for individuals with CSIR/UGC and other fellowships to conduct research. Contact Dr. Maiti : ncmaiti@iicb.res.in

Names of the group members including regular staff with designation and research fellows:
Staff: Fellow/RA
  1. Uttam Pal, DST Inspire Fellow, EMail : UttamPal@live.com
  2. Swagata Das, DST Inspire Fellow, EMail : swagata87@gmail.com
  3. Mritunjoy Maity, JRF (CSIR), EMail : mritunjoymt3@gmail.com
  4. Anupam Roy, SRF (UGC), EMail anupamkrroy89@gmail.com
  5. Supriya Das, SRF (UGC), EMail : das_supriya_cgr@yahoo.com
  6. Sudeshna Sen , JRF (CSIR), EMail ju.sudeshna@gmail.com
  7. Kaushik Bera, DST Inspire Fellow, EMail kaushik.chem.scc@gmail.com
  8. Sandip Dolui, SPR (network), EMail sandipdolui.w.b@gmail.com
  9. Animesh Mondal, JRF (CSIR), EMail animeshpresiz@gmail.com


List of important Publications:

  1. Banerji, B.; Chatterjee, M.; Paul, U. and Maiti, N. C. Molecular Details of Acetate Binding to a New Diamine Receptor by NMR and FT-IR Analyses, J. Phy. Chem. A. 2016 (accepted)
  2. Pal, U, Maity, M.; Khot, N.; Das, S.; Das, S.; Dolui, S. and Maiti, N. C. Statistical insight of binding regions in disordered human proteome, J. Proteins and Proteomics 2016, 7 47-60
  3. Maity, M.; Dolui S. and Maiti, N. C. Hydrogen bonding plays a significant role in the binding of coomassie brilliant blue-R to hemoglobin: FT-IR, fluorescence and molecular dynamics studies, Phys.Chem.Chem.Phys. 2015, 17, 31216
  4. Pal, U.; Pramanik, S, Bhattacharya, B; Banerji, B and Maiti, N. C. Binding interaction of a novel fluorophore with serum albumins: steady state fluorescence perturbation and molecular modeling analysis. SpringerPlus 2015, 4:548
  5. Chakraborty, B.; Dutta, D.; Mukherjee, S.; Das, S.; Maiti, N.C.; Das, P. and Chowdhury, C. , Synthesis and biological evaluation of a novel betulinic acid derivative as an inducer of apoptosis in human colon carcinoma cells (HT-29). Eur. J. Med. Chem. 2015, 102, 93–105
  6. Maiti N. C.; Mondal P. and Das, S. Role of Cyclophilin on Amyloid Formation and Protein Disaggregation, The FASEB Journal, 2015 29 Supplement 881.7
  7. Mal, K.; Das, S.; Maiti, N. C.; Natarajan R., and Das I., ZnI2-Catalyzed Diastereoselective [4 + 2] Cycloadditions of β,γ-Unsaturated α-Ketothioesters with Olefins, J. Org. Chem., 2015, 80, 2972−2988
  8. Maity, M.; Das, S. and Maiti, N. C. Stability and Binding Interaction of Bilirubin on Gold Nano-surface: Steady State Fluorescence and FT-IR Investigation. Phys. Chem. Chem. Phys. 2014, 16, 20013-22
  9. Preet , R.; Chakraborty, B.; Siddharth, S.; Mohapatra, P1, Das, D.; Satapathy, S. R.; Das, S. Maiti, N. C.; Maulik , P. Rr.; Kundu, C. N. and Chowdhury, C. Synthesis and biological evaluations of andrographolide analogues as anti-cancer agents. Eur. J. Med. Chem. 2014, 85, 95-106
  10. Banerji, B,; Pramanik, S. K,; Pal, U.; Maiti, N. C.; Binding of haemoglobin to ultrafine carbon nanoparticles: a spectroscopic insight into a major health hazard. RSC Adv. 2014, 4, 22536-22541
  11. Pal, U.; Sen, S.; Maiti, N. C. (2014) Cα-H Carries Information of Hydrogen Bond Involving Geminal Hydroxyl Group: A Case Study With Hydrogen Bonded Complex of HFIP and Tertiary Amines. J. Phy. Chem. A. 2014, 118(6), 1024-1030
  12. Das, S.; Pal, U.; Das, S.; Bagga, K.; Roy, A.; Mrigwani, A.; Maiti, N. C. (2014) Sequence Complexity of Amyloidogenic Regions in Intrinsically Disordered Human Proteins. PLOS ONE, 2014
  13. Sen, S.; Pal, U.; Maiti, N. C., pKa Determination of D-Ribose by Raman Spectroscopy, J. Phys. Chem. B. 2014, 118(4), 909-914
  14. Das, S.; Pal, U.; Das, S.; Maiti, N. C.., Chaperone action of cyclophilin on lysozyme and its aggregate. Journal of Proteins and Proteomics 2013, 4 (2), 129.
  15. Maity, M; Pramanik, SK; Pal, U; Banerji, B; and Maiti, N. C., Copper(I) oxide nanoparticle and tryptophan as its biological conjugate: a modulation of cytotoxic effects, Journal of Nanoparticle Research, 2013, 16:2179
  16. Chattopadhyay, P; Bhattacherjee, D; Ghorai, A; Pal, U; Maiti, N. C., Stereoselective Domino Azidation and (3+2) Cycloaddition: A Facile Route To Chiral Heterocyclic Scaffolds From Carbohydrate Derived Synthons; RSC Advances, 2013 (accepted)
  17. Mukherjee, D ; Patra, H ; Laskar, A ; Dasgupta, A ; Maiti, N. C. and Datta, AK Cyclophilin-mediated reactivation pathway of inactive adenosine kinase aggregates, Archives of Biochemistry and Biophysics, 2013, 537, 82-90 (sep1)
  18. Bhowmik, A.; Das, N.; Pal, U.; Mandal, M.; Bhattacharya, S.; Sarkar, M.; Jaisankar, P.; Maiti, N. C.; Ghosh, M. K. 7. 2,29-Diphenyl-3,39-Diindolylmethane: A Potent Compound Induces Apoptosis in Breast Cancer Cells by Inhibiting EGFR Pathway, PLOS ONE, 2013, 8, e59798
  19. Banerji, B,; Pramanik, S. K,; Pal, U.; Maiti, N. C.; Potent Anticancer Activity of Cystinebased Dipeptides and Their Interaction with Serum Albumins, Chemistry Central Journal, 2013, 7:91
  20. Rudra, D. S.; Pal, U.; Maiti, N. C.; Jeiter, R. J.; Swarnakar, S. (2013) Melatonin inhibits matrix metalloproteinase-9 activity by binding to its active site J. Pineal Res.; 54:398–405
  21. Banerji, B,; Pramanik, S. K,; Pal, U.; Maiti, N. C.; and Chaudhuri, K.; (2013) Dipeptide derived from benzylcystine forms unbranched nanotubes in aqueous solution Journal Of Nanostructure in Chemistry, 3:12.
  22. Maity, M.; Maiti, N. C. (2012) Sequence composition of binding sites in nativelyUnfolded human proteins, J. Proteins and Proteomics,3(2): 117-125
  23. Banerji, B,; Pramanik, S. K,; Mandal, S.;  Maiti, N. C.; and Chaudhuri, K.; Synthesis, characterization and cytotoxicity study of magnetic (Fe3O4) nanoparticles and their drug conjugate RSC Adv., 2012, 2, 2493-2497
  24. Alam, A., Pal, C., Goyal, M., Kundu, M.K., Kumar, R., Iqbal, M.S., Dey, S., Bindu, S., Sarkar, S., Pal, U., Maiti, N.C., Adhikari, S., and Bandyopadhyay, U. (2011), Synthesis and bio-evaluation of human macrophage migration inhibitory factor inhibitor to develop anti-inflammatory agent, Bioorganic & Medicinal Chemistry , 19, 7365-7373
  25. Maiti, N. C.;  Jiang, D.;  Wain, A.J.,  Dinh, KL,;  Patel, S.; Zhou, F. (2008) Mechanistic Studies of Cu(II) Binding to Amyloid-b Peptides and the Fluorescence and Redox Behaviors of the Resulting Complexes, J. Phys. Chem.  B, 2008, 112, 8406–8411
  26. Maiti, N. C.; Zhu, Y.; Carmichael, I.; Serianni, AS.; Anderson, Vernon E.  (2006) 1JCH Correlates with Alcohol H-bond Strength, J.  Org. Chem. 71, 2878-2880.
  27. Kun,  H.;  Maiti,  N. C.;  Phillips, N. B.; Carey, P. R.Weiss, M. A. (2006) Structure‑Specific Effects of Protein Topology on Cross-β Assembly: Studies of Insulin Fibrillation,  Biochemistry  45,  10278-10293.
  28. Apetri, M. M.; Maiti, N. C.;  Zagorski, M.G.; Carey, P.R.; Anderson, V.E. (2006) Secondary Structure of α-Synuclein Oligomers: Characterization by Raman and Atomic Force Microscopy, J.  Mol.  Biol. 355, 63-71.
  29. Jarmelo, S.; Maiti, N. C; Anderson, V.E.; Carey, P. R.; Fausto, R. (2005)  Cα-H Bond-Stretching Frequency in Alcohols as a  Probe of Hydrogen-Bonding Strength: A Combined Vibrational Spectroscopic and Theoretical Study of a-[1-D] Propanol,  J. Phys. Chem. A  109, 2069-2077.
  30. Overman, S. A.; Bondre, P.; Maiti, N. C.; Thomas, G. J., Jr.  (2005) Structural Characterization of the Filamentous Bacteriophage PH75 from Thermus thermophilus by Raman and UV-Resonance Raman Spectroscopy, Biochemistry, 44, 3091-3100.
  31. Maiti, N.C.; Apetri, M.M.; Zagorski, M.G.; Carey, P.R.; Anderson, V.E.  (2004) Raman  Spectroscopic Characterization of Secondary Structure in Natively Unfolded Proteins: α-Synuclein,   J. Am. Chem. Soci.126, 2399-2408.
  32. Minkler, P.E.; Anderson, V.E.; Maiti, N. C.; Kerner, J.; Hoppel, C.L. (2004) Isolation and Identification of Two Isomeric Forms of Malonyl-coenzyme A in commercial malonyl-coenzyme-A, Anal. Biochem. 328, 203-209. 
  33. Maiti, N. C.; Carey, P.R.; Anderson, V.E. (2003) Correlation of an Alcohol's αC-D Stretch with Hydrogen Bond Strength in Complexes with Amines, J.  Phys.  Chem. A   107, 9910-9917.
  34. Maiti, N. C.; Tomita, T.; Kitagawa, T. Okamoto, K.; Nishino, T. (2003) Resonance Raman studies on xanthine oxidase: observation of Mo (VI)-ligand vibrations, J. Biol.Inor. Chem.  8, 327-333.
  35. Maity, H.; Maiti, N. C.; Jarori, G.K. (2000) Time-resolved fluorescence of tryptophans in yeast hexokinase-PI: effect of subunit dimerization and ligand binding, J. Photochem. Photobio. B: Biology. 55 (1), 20-26.
  36. Prasad, S.; Maiti, N. C.; Mazumdar, S.; Mitra, S. (2002)  Reaction of hydrogen peroxide and peroxidase activity in carboxymethylated cytochrome c: spectroscopic and kinetic studies, Biochimica et Biophysica Acta  (2002), 1596 (1), 63-75.
  37. Aziz, A.; Narasimhan, K. L.; Periasamy, N.; Maiti, N. C. (1999)  Electrical and optical properties of porphyrin monomer and its J-aggregate.    Philosophical Magazine B: Physics of Condensed Matter: Statistical Mechanics, Electronic, Optical and Magnetic Properties  79 (7),  993-1004.
  38. Maiti, N. C.; Mazumdar, S.;  Periasamy, N. (1998) J- and H-aggregates of porphyrins with surfactants: fluorescence, stopped flow and electron microscopy studies, Journal of Porphyrins and Phthalocyanines  2 (4-5), 369-376.
  39. Maiti, N. C.; Mazumdar, S.;  Periasamy, N. (1998)  J- and H-Aggregates of Porphyrin-Surfactant Complexes: Time-Resolved Fluorescence and Other Spectroscopic Studies, Journal of Physical Chemistry B  102 (9), 1528-1538.
  40. Maiti, N. C.; Krishna, M. M. G.; Britto, P. J.; Periasamy, N. (1997),  Fluorescence Dynamics of Dye Probes in Micelles, Journal of Physical Chemistry B  101 (51), 11051-11060.  
  41. Maiti, N. C.; Ravikanth, M. (1996), Fluorescence study of some deformed zinc (II) porphyrins, Journal of Photochemistry and Photobiology, A: Chemistry  101 (1), 7-10.
  42. Maiti, N. C.; Mazumdar, S.;  Periasamy, N.  (1996), Controlled J-aggregation of porphyrins by cationic surfactants.    Current Science 70 (11), 997-999.  
  43. Maiti, N. C.; Ravikanth, M. (1996), Effects of non-planarity and β-substitution on the singlet-excited-state properties of basket-handle porphyrins, Journal of the Chemical Society, Faraday Transactions  92 (7), 1095-100.
  44. Maiti, N. C.; Ravikanth, M. (1995), Photophysical properties of structurally deformed basket-handle porphyrins, Journal of the Chemical Society, Faraday Transactions 91 (24), 4369-73.
  45. Maiti, N. C.; Ravikanth, M. (1995),  Photophysical properties of structurally deformed basket-handle porphyrins, Journal of the Chemical Society, Faraday Transactions 91 (24), 4369-73.  
  46. Maiti, N. C.; Ravikanth, M.; Mazumdar, S; Periasamy, N. (1995), Fluorescence Dynamics of Noncovalently Linked Porphyrin Dimers, and Aggregates, Journal of Physical Chemistry 99 (47), 17192-97.
  47. Maiti, Nakul C.; Mazumdar, S; Periasamy, N.  Dynamics of Porphyrin Molecules in Micelles. Picosecond Time-Resolved Fluorescence Anisotropy Studies, Journal of Physical Chemistry (1995),  99(27),  10708-15


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