Industrial Research And Consultancy Centre

Diffractometer : 

  • Maximum rated output : 1.2 kW
  • Rated tube voltage-current : 40kV; 30mA
  • Target : Cu
  • Radiation enclosure : Full safety shielding with plastic shield
  • Scanning mode : 0 - 180o ω scan: 0-180 θ scan
  • Optics : Multilayer confocal type
  • Detector : Rigaku R Axis IV ++
  • Beam size at the sample : 100 µm
  • X-Ray diffraction
  • Automated crystallization set up facility
  • Automate crystal visualization camera

 

In the present world of science, X-ray crystallography is the most widely used technique for determination of structures of biological macromolecules. This technique allows us to determine macromolecule structures that provides a detailed understanding of the interactions occurring at the molecular levels. Structure based drug design, study of protein-ligand interactions and structure-function relationships are the major fields where X-ray crystallography acts as a major tool. X-Ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by crystals as they have a wavelength (in Å ~10-10 m) corresponding to the size of an atom

Principle of X-ray diffraction

Each crystal has its unit cell parameters (a,b,c and α, β, γ) and in a crystal lattice infinite sets of plane can be drawn from the lattice points. These planes can be considered as source of diffraction and designated by set of miller indices. According to Braggs laws, when a wavelength (λ nm) with an angle θ passes through a crystal (which has a set of equivalent planes with hkl) a diffracted beam with the same angle is produced from which we can calculate the d spacing of the planes.

Bragg's law

                nλ = 2dsinθ

                Where    n : Order of diffracted beam
                              d : Spacing between two adjacent planes of atoms
                              λ : Wavelength of incident X-ray
                              θ : Angle of incidence of X-ray

The sets of d and intensities from protein crystals come in a unique diffraction pattern. 

 
 

List of publications using data from the Protein Crystallography facility (2016-2022)

  • 2022:
  1. Singh, J.; Sahil, M.; Ray, S.; Dcosta, C.; Panjikar, S.; Krishnamoorthy, G.; Mondal, J.; Anand, R. Phenol Sensing in Nature Is Modulated via a Conformational Switch Governed by Dynamic Allostery. Journal of Biological Chemistry 2022, 298 (10), 102399. https://doi.org/10.1016/j.jbc.2022.102399.
  2. Sharma, N.; Singh, S.; Tanwar, A. S.; Mondal, J.; Anand, R. Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase. ACS Catalysis 2022, 12 (3), 1930–1944. https://doi.org/10.1021/acscatal.1c05521.
  3. Kesari, P.; Deshmukh, A.; Pahelkar, N.; Suryawanshi, A. B.; Rathore, I.; Mishra, V.; Dupuis, J. H.; Xiao, H.; Gustchina, A.; Abendroth, J.; Labaied, M.; Yada, R. Y.; Wlodawer, A.; Edwards, T. E.; Lorimer, D. D.; Bhaumik, P. Structures of Plasmepsin X from Plasmodium Falciparum Reveal a Novel Inactivation Mechanism of the Zymogen and Molecular Basis for Binding of Inhibitors in Mature Enzyme. Protein Science 2022, 31 (4), 882–899. https://doi.org/10.1002/pro.4279.
  4. Sakunthala, A.; Datta, D.; Navalkar, A.; Gadhe, L.; Kadu, P.; Patel, K.; Mehra, S.; Kumar, R.; Chatterjee, D.; Devi, J.; Sengupta, K.; Padinhateeri, R.; Maji, S. K. Direct Demonstration of Seed Size-Dependent α-Synuclein Amyloid Amplification. The Journal of Physical Chemistry Letters 2022, 13 (28), 6427–6438. https://doi.org/10.1021/acs.jpclett.2c01650.
  5. Kadu, P.; Gadhe, L.; Navalkar, A.; Patel, K.; Kumar, R.; Sastry, M.; Maji, S. K. Charge and Hydrophobicity of Amyloidogenic Protein/Peptide Templates Regulate the Growth and Morphology of Gold Nanoparticles. Nanoscale 2022, 14 (40), 15021–15033. https://doi.org/10.1039/d2nr01942f.
  6. Mehra, S.; Ahlawat, S.; Kumar, H.; Datta, D.; Navalkar, A.; Singh, N.; Patel, K.; Gadhe, L.; Kadu, P.; Kumar, R.; Jha, N. N.; Sakunthala, A.; Sawner, A. S.; Padinhateeri, R.; Udgaonkar, J. B.; Agarwal, V.; Maji, S. K. α-Synuclein Aggregation Intermediates Form Fibril Polymorphs with Distinct Prion-like Properties. Journal of Molecular Biology 2022, 434 (19), 167761. https://doi.org/10.1016/j.jmb.2022.167761.
  7. Chatterjee, D.; Jacob, R. S.; Ray, S.; Navalkar, A.; Singh, N.; Sengupta, S.; Gadhe, L.; Kadu, P.; Datta, D.; Paul, A.; Arunima, S.; Mehra, S.; Pindi, C.; Kumar, S.; Singru, P.; Senapati, S.; Maji, S. K. Co-Aggregation and Secondary Nucleation in the Life Cycle of Human Prolactin/Galanin Functional Amyloids. eLife 2022, 11. https://doi.org/10.7554/elife.73835.

 

  • 2021:
  1. Godsora, B. K. J.; Prakash, P.; Punekar, N. S.; Bhaumik, P. Molecular Insights into the Inhibition of Glutamate Dehydrogenase by the Dicarboxylic Acid Metabolites. Proteins: Structure, Function, and Bioinformatics 2021, 90 (3), 810–823. https://doi.org/10.1002/prot.26276.

 

  • 2020:
  1. Sharma, N.; Ahalawat, N.; Sandhu, P.; Strauss, E.; Mondal, J.; Anand, R. Role of Allosteric Switches and Adaptor Domains in Long-Distance Cross-Talk and Transient Tunnel Formation. Science Advances 2020, 6 (14). https://doi.org/10.1126/sciadv.aay7919.
  2. Rathore, I.; Mishra, V.; Patel, C.; Xiao, H.; Gustchina, A.; Wlodawer, A.; Yada, R. Y.; Bhaumik, P. Activation Mechanism of Plasmepsins, Pepsin‐like Aspartic Proteases from Plasmodium, Follows a Unique Trans‐Activation Pathway. The FEBS Journal 2020, 288 (2), 678–698. https://doi.org/10.1111/febs.15363.
  3. Badgujar, D. C.; Anil, A.; Green, A. E.; Surve, M. V.; Madhavan, S.; Beckett, A.; Prior, I. A.; Godsora, B. K.; Patil, S. B.; More, P. K.; Sarkar, S. G.; Mitchell, A.; Banerjee, R.; Phale, P. S.; Mitchell, T. J.; Neill, D. R.; Bhaumik, P.; Banerjee, A. Structural Insights into Loss of Function of a Pore Forming Toxin and Its Role in Pneumococcal Adaptation to an Intracellular Lifestyle. PLOS Pathogens 2020, 16 (11), e1009016. https://doi.org/10.1371/journal.ppat.1009016.
  4. Kadu, P.; Pandey, S.; Neekhra, S.; Kumar, R.; Gadhe, L.; Srivastava, R.; Sastry, M.; Maji, S. K. Machine-Free Polymerase Chain Reaction with Triangular Gold and Silver Nanoparticles. The Journal of Physical Chemistry Letters 2020, 11 (24), 10489–10496. https://doi.org/10.1021/acs.jpclett.0c02708.

 

  • 2019:
  1. Yarramala, D. S.; Prakash, P.; Ranade, D. S.; Doshi, S.; Kulkarni, P. P.; Bhaumik, P.; Rao, C. P. Cytotoxicity of Apo Bovine α-Lactalbumin Complexed with La 3+ on Cancer Cells Supported by Its High Resolution Crystal Structure. Scientific Reports 2019, 9 (1), 1780. https://doi.org/10.1038/s41598-018-38024-1.

 

  • 2018:
  1. Pandey, S.; Phale, P. S.; Bhaumik, P. Structural Modulation of a Periplasmic Sugar-Binding Protein Probes into Its Evolutionary Ancestry. Journal of Structural Biology 2018, 204 (3), 498–506. https://doi.org/10.1016/j.jsb.2018.09.006.
  2. Mishra, V.; Rathore, I.; Arekar, A.; Sthanam, L. K.; Xiao, H.; Kiso, Y.; Sen, S.; Patankar, S.; Gustchina, A.; Hidaka, K.; Wlodawer, A.; Yada, R. Y.; Bhaumik, P. Deciphering the Mechanism of Potent Peptidomimetic Inhibitors Targeting Plasmepsins – Biochemical and Structural Insights. The FEBS Journal 2018, 285 (16), 3077–3096. https://doi.org/10.1111/febs.14598.
  3. Wangchuk, J.; Prakash, P.; Bhaumik, P.; Kondabagil, K. Bacteriophage N4 Large Terminase: Expression, Purification and X-Ray Crystallographic Analysis. Acta Crystallographica Section F Structural Biology Communications 2018, 74 (4), 198–204. https://doi.org/10.1107/s2053230x18003084.
  4. Prakash, P.; Punekar, N.; Bhaumik, P. Structural Basis for the Catalytic Mechanism and α-Ketoglutarate Cooperativity of Glutamate Dehydrogenase. Journal of Biological Chemistry 2018, 293(17), 6241-6258. https://doi.org/10.1074/jbc.RA117.000149.
  5. Kirti, S.; Patel, K.; Das, S.; Shrimali, P.; Samanta, S.; Kumar, R.; Chatterjee, D.; Ghosh, D.; Kumar, A.; Tayalia, P.; Maji, S. K. Amyloid Fibrils with Positive Charge Enhance Retroviral Transduction in Mammalian Cells. ACS Biomaterials Science & Engineering 2018, 5 (1), 126–138. https://doi.org/10.1021/acsbiomaterials.8b00248.
  6. Mehra, S.; Ghosh, D.; Kumar, R.; Mondal, M.; Gadhe, L. G.; Das, S.; Anoop, A.; Jha, N. N.; Jacob, R. S.; Chatterjee, D.; Ray, S.; Singh, N.; Kumar, A.; Maji, S. K. Glycosaminoglycans Have Variable Effects on α-Synuclein Aggregation and Differentially Affect the Activities of the Resulting Amyloid Fibrils. Journal of Biological Chemistry 2018, 293 (34), 12975–12991. https://doi.org/10.1074/jbc.ra118.004267.
  7. Sharma, H.; John, K.; Gaddam, A.; Navalkar, A.; Maji, S. K.; Agrawal, A. A Magnet-Actuated Biomimetic Device for Isolating Biological Entities in Microwells. Scientific Reports 2018, 8 (1). https://doi.org/10.1038/s41598-018-31274-z.

 

  • 2017:
  1. Gaded, V.; Anand, R. Selective Deamination of Mutagens by a Mycobacterial Enzyme. Journal of the American Chemical Society 2017, 139 (31), 10762–10768. https://doi.org/10.1021/jacs.7b04967.
  2. Ray, S.; Maitra, A.; Biswas, A.; Panjikar, S.; Mondal, J.; Anand R. Functional Insights into the Mode of DNA and Ligand Binding of the Tetr Family Regulator Tylp from Streptomyces fradiae.  Journal of Biological Chemistry 2017, 292 (37), 15301-15311. https://doi.org/10.1074/jbc.M117.788000.
  3. Ghosh, S.; Salot, S.; Sengupta, S.; Navalkar, A.; Ghosh, D.; Jacob, R.; Das, S.; Kumar, R.; Jha, N. N.; Sahay, S.; Mehra, S.; Mohite, G. M.; Ghosh, S. K.; Kombrabail, M.; Krishnamoorthy, G.; Chaudhari, P.; Maji, S. K. P53 Amyloid Formation Leading to Its Loss of Function: Implications in Cancer Pathogenesis. Cell Death & Differentiation 2017, 24 (10), 1784–1798. https://doi.org/10.1038/cdd.2017.105.

 

  • 2016:
  1. Pandey, S.; Modak, A.; Phale, P. S.; Bhaumik, P. High Resolution Structures of Periplasmic Glucose-Binding Protein of Pseudomonas Putida CSV86 Reveal Structural Basis of Its Substrate Specificity. Journal of Biological Chemistry 2016, 291 (15), 7844–7857. https://doi.org/10.1074/jbc.m115.697268.
  2. Jacob, R. S.; Das, S.; Ghosh, S.; Anoop, A.; Jha, N. N.; Khan, T.; Singru, P.; Kumar, A.; Maji, S. K. Amyloid Formation of Growth Hormone in Presence of Zinc: Relevance to Its Storage in Secretory Granules. Scientific Reports 2016, 6 (1). https://doi.org/10.1038/srep23370.
  3. Jacob, R. S.; George, E.; Singh, P. K.; Salot, S.; Anoop, A.; Jha, N. N.; Sen, S.; Maji, S. K. Cell Adhesion on Amyloid Fibrils Lacking Integrin Recognition Motif. Journal of Biological Chemistry 2016, 291 (10), 5278–5298. https://doi.org/10.1074/jbc.M115.678177.
  • Well isolated protein crystals obtained via sitting/hanging drop method.
  • Crystals flash frozen in liquid nitrogen using appropriate cryo-protectant and maintained in a Dewar can also be provided.
  • The user has to come with prepared Cryo-protectant solutions.
  • Coverslips, bridges for soaking and loops appropriate for your proteins will be provided only on request.
  • At the time of X-ray diffraction of crystal, the user should be present.
  • Images of diffraction will be given in CD format. Please bring your own CD. USB drives are strictly not allowed due to virus threat.
  • Samples and Measurement data should be collected as soon as the diffraction gets completed with a maximum duration of one week.

Only online registration through the IRCC webpage will be accepted. The users will be informed about their date and time of slot by email. If the appointment is given but the user cannot come, a mail should be immediately sent to protxrd@iitb.ac.in to cancel his/her slot.