Saumen Datta , Ph.D.

Chief Scientist
Structural Biology & Bioinformatics
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Research Interest

Structural and functional investigations of important biological protein and protein complexes primarily using X-ray crystallography, SPR, CD, Cryo-electron microscopy, mass-spectrometry.

Current Research topic : Type III Secretion Systems

Many gram negative pathogenic bacteria use type three secretion systems (TTSS) to inject virulent proteins into the host cells through a specialized device called injectisome. After getting injected, these proteins disrupt cell’s cytoskeletal assembly and impair immune system; take control of the cell machinery for bacterial survival, replication and dissemination; and at the last promote cell death. These bacterial infestations are manifested by several diseases in animals and plants starting from mild gastroenteritis, dysentery, diarrhea to the acute and life-threatening typhoid fever, bubonic plague, and pneumonia. TTSS includes a complex macromolecular machinery (injectisomes), translocator and effector proteins, chaperone and other accessory proteins. Nearly 20 proteins, highly conserved among various bacterial species, constitute the injectisome. Structurally, the TTSS injectisome consists of two parts: a basal part which spans the inner and outer membrane of bacteria, and an extracellular needle that protrudes out of the bacterial surface. A central pore through the injectisome helps in the secretion of toxic effectors. Among secreted proteins, the effectors are highly variable but mostly act in similar ways, while translocators that form the tip of the needle complex are highly conserved. Chaperones have been classified into three categories depending on the nature of their substrates. Class I chaperone are related to effectors, Class II chaperones are used for translocators while the Class III chaperones act on needle proteins. TTSS chaperones are indispensable for their crucial roles in the assembly and functioning of injectisome and aids in translocation of various translocators and effector molecules through this injectisome.The virulent proteins do not have any identified secretory signal and the translocation of them directly facilitated by few dedicated chaperones. Biochemical, biophysical and structural investigations are being carried out to characterize all the virulent and other TTSS proteins but with limited success. Most of them are appeared to be bi-functional and manipulate eukaryotic cellular functions by structural mimicry of their host counterparts. Few three dimensional structures available to date substantially corroborate this view. The structural characterization of these proteins are therefore utmost important to clearly understand their hostile activity in side the host cell.

Credentials

  • Senior Research Fellow, University of Limerick, 2008
  • Quick Hire Fellow, Central Leather Research Institute, 2004-2006 
  • Assistant Research Scientist, John Hopkins University, Maryland, USA., 2002-2004
  • Postdoctoral associate, Washington University in St. Louis, Missouri, USA., 1999-2002 
  • Postdoctoral associate, University of Connecticut, Connecticut, USA., 1998-1999
  • PhD, Indian Institute of Science, Bangalore, India.

Patents & Publications

  • Choudhury A, Khanppnavar B, Datta S. Crystallographic and biophysical analyses of Pseudomonas aeruginosa ketopantoate reductase: Implications of ligand induced conformational changes in cofactor recognition. Biochimie. 2022 Feb;193:103-114. doi: 10.1016/j.biochi.2021.10.015. Epub 2021 Oct 30. PMID: 34757166

The rate-limiting step in the pantothenate biosynthesis pathway is catalysed by ketopantoate reductases. NAD+ was shown to be very dynamic in the catalytic pocket of KPR in our structure. The potential significance of ordered substrate binding kinetics in cofactor selection has been discussed.

  • Ekka M, Mondal A, Singh R, Sen H, Datta S, Raychaudhuri S. Arginine 37 of Glycine Linker Dictates Regulatory Function of HapR. Front Microbiol. 2020 Aug 21;11:1949. doi: 10.3389/fmicb.2020.01949. PMID: 32973706; PMCID: PMC7472637.

        

HapR is a Vibrio cholerae high cell density quorum sensing master regulatory protein. The importance of the glycine-rich linker connecting helices 1 and 2 was discovered. Key arginine inside the linker at position 37 contributes to HapR–DNA binding activity.

  • Khanppnavar B, Roy A, Chandra K, Uversky VN, Maiti NC, Datta S. Deciphering the structural intricacy in virulence effectors for proton-motive force mediated unfolding in type-III protein secretion. Int J Biol Macromol. 2020 Sep 15;159:18-33. doi: 10.1016/j.ijbiomac.2020.04.266. Epub 2020 May 11. PMID: 32437799.

The mechanism by which pathogenic bacteria unfold and emit hundreds of harmful proteins via the type-III secretion system (T3SS) is still completely unclear. A comprehensive effort combining experimental and computational   techniques was used to gain mechanistic insights into the unfolding of effectors in T3SS secretion. The decreased energetic cost associated with ExoY's global unfolding was mostly owing to its inherent stereo-chemical difficulties. Many     of the T3SS effectors belong to the category of intrinsically disordered proteins (IDPs) and have comparable conserved structural motifs to exoY to promote early-stage unfolding.

  • Roy C, Kumar R, Datta S. Comparative studies on ion-pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya. Proteins. 2020 Jul;88(7):865-873. doi: 10.1002/prot.25878. Epub 2020 Feb 7. PMID: 31999377.

Salt-bridges have a unique role in protein structure and functional stability. It is currently unclear how these salt-bridges contribute to the overall thermodynamic stability of protein structure and function throughout diverse domains of         life. The stability of archaeal proteins (∆∆Gnet = -5.06 3.8) is significantly higher than that of eubacteria (∆∆Gnet = -3.7 2.9) and eukarya (∆∆Gnet = -3.54 3.1). Overall, we anticipate that our comparative analysis will be valuable for         protein engineering and bioinformatics research since it sheds light on the importance of unique electrostatic interactions in proteins from diverse domains of life.

  • Khanppnavar B, Chatterjee R, Choudhury GB, Datta S. Genome-wide survey and crystallographic analysis suggests a role for both horizontal gene transfer and duplication in pantothenate biosynthesis pathways. Biochim Biophys Acta  Gen Subj. 2019 Oct;1863(10):1547-1559. doi: 10.1016/j.bbagen.2019.05.017. Epub 2019 May 25. PMID: 31136784.                                                                                                                                                                        Pantothenate is the metabolic precursor of Coenzyme A, which is required for many key cellular activities. A comparison of the apo and NADP+ bound crystal structures of P. aeruginosa KPR with orthologs revealed that the residues involved in the interaction with the specific phosphate moiety of NADP+ are relatively less conserved, implying dynamic evolutionary trajectories for redox cofactor selection in KPRs. Our structural and biochemical findings further reveal that the unique conformational changes induced by NADPH binding enable ketopantoate cooperative binding. It appears that the binding of ketopantoate is allosterically controlled to confer redox cofactor selectivity, based on the considerably lower catalytic activity for NADH catalysed the process with significantly greater KM of ketopantoate            
  • Halder PK, Roy C, Datta S. Structural and functional characterization of type three secretion system ATPase PscN and its regulator PscL from Pseudomonas aeruginosa. Proteins. 2018 Dec 18. doi: 10.1002/prot.25648. [Epub ahead of print] PubMed PMID: 30561072.
  • Roy C, Datta S. ASBAAC: Automated Salt-Bridge and Aromatic-Aromatic Calculator. Bioinformation. 2018 Apr 30;14(4):164-166. doi:10.6026/97320630014164. eCollection 2018. PubMed PMID: 29983486; PubMed Central PMCID: PMC6016756.
  • Khanppnavar B, Datta S. Crystal structure and substrate specificity of ExoY, a unique T3SS mediated secreted nucleotidyl cyclase toxin from Pseudomonas aeruginosa. Biochim Biophys Acta Gen Subj. 2018 Sep;1862(9):2090-2103. doi:10.1016/j.bbagen.2018.05.021. Epub 2018 May 30. PubMed PMID: 29859257.
  • Mondal A, Chatterjee R, Datta S. Umbrella Sampling and X-ray Crystallographic Analysis Unveil an Arg-Asp Gate Facilitating Inhibitor Binding Inside Phosphopantetheine Adenylyltransferase Allosteric Cleft. J Phys Chem B.2018 Feb 8;122(5):1551-1559. doi: 10.1021/acs.jpcb.7b09543. Epub 2018 Jan 30. PubMed PMID: 29345931
  • Mondal A, Datta S. Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins. Proteins. 2017 Jun;85(6):1046-1055. doi: 10.1002/prot.25271. Epub 2017 Mar 17. PubMed PMID: 28241377
  • Chatterjee R, Mondal A, Basu A, Datta S. Transition of phosphopantetheineadenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa. BiochimBiophysActa. 2016 Jul;1864(7):773-86. doi: 10.1016/j.bbapap.2016.03.018. Epub 2016 Apr 13. PubMed PMID: 27041211
  • Basu A, Das A, Mondal A, Datta S. Structural analysis of inter-genus complexes of V-antigen and its regulator and their stabilization by divalent metal ions. EurBiophys J. 2016 Mar;45(2):113-28. doi: 10.1007/s00249-015-1081-2. Epub 2015 Oct 13. PubMed PMID: 26463823.
  • Banerjee A, Dey S, Chakraborty A, Datta A, Basu A, Chakrabarti S, Datta S.Binding mode analysis of a major T3SS translocator protein PopB with its chaperone PcrH from Pseudomonas aeruginosa. Proteins. Dec;82(12):3273-85. doi: 10.1002/prot.24666Epub 2014 Oct 21. PubMed PMID: 25116453.
  • Basu A, Das U, Dey S, Datta S. PcrG protects the two long helical oligomerization domains of PcrV, by an interaction mediated by the intramolecular coiled-coil region of PcrG. BMC Struct Biol. 2014 Jan 24;14(1):5. doi:10.1186/1472-6807-14-5.
  • Dey S, Datta S. Interfacial residues of SpcS chaperone affects binding of effector toxin ExoT in Pseudomonas aeruginosa: novel insights from structural and computational studies. FEBS J. 2014 Jan 4. doi: 10.1111/febs.12704. [Epub ahead of print]
  • Chatterjee R, Halder PK, Datta S. Identification and molecular characterization of YsaL (Ye3555): a novel negative regulator of YsaN ATPase in type three secretion system of enteropathogenic bacteria Yersinia enterocolitica. PLoS One. 2013 Oct 4;8(10):e75028
  • Basu A, Chatterjee R, Datta S. YspC: A unique translocator exhibits structural alteration in the complex form with chaperone SycB. Protein J. 2012 Aug;31(6):487-98.
  • Dey S, Basu A, Datta S. Characterization of molten globule PopB in absence and presence of its chaperone PcrH. Protein J. 2012 Jun;31(5):401-16.
  • Basu A, Chatterjee R, Datta S. Expression, Purification, Structural and Functional Analysis of SycB: A Type Three Secretion Chaperone From Yersinia enterocolitica. Protein J. 2012 Jan;31(1):93-107.
  • Chen ZW, Datta S, Dubois JL, Klinman JP, Mathews FS. Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity. Biochemistry. 2010 Aug 31;49(34):7393-402.
  • Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF. Inter- and intramolecular determinants of the specificity of single-stranded  DNA binding and cleavage by the F factor relaxase. Structure. 2005 Oct;13(10):1533-44.
  • Aravinda S, Datta S, Shamala N, Balaram P. Hydrogen-bond lengths in polypeptide helices: no evidence for short hydrogen bonds. Angew Chem Int Ed Engl. 2004 Dec 10;43(48):6728-31.
  • Datta S, Rathore RN, Vijayalakshmi S, Vasudev PG, Rao RB, Balaram P, Shamala N. Peptide helices with pendant cycloalkane rings. Characterization of conformations of 1-aminocyclooctane-1-carboxylic acid (Ac8c) residues in peptides. J Pept Sci. 2004 Mar;10(3):160-72.
  • Datta S, Larkin C, Schildbach JF. Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Structure. 2003 Nov;11(11):1369-79.
  • Datta S, Ikeda T, Kano K, Mathews FS. Structure of the phenylhydrazine adduct  of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution. Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1551-6.
  • Larkin C, Datta S, Nezami A, Dohm JA, Schildbach JF. Crystallization and preliminary X-ray characterization of the relaxase domain of F factor TraI. Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1514-6.
  • Datta S, Mori Y, Takagi K, Kawaguchi K, Chen ZW, Okajima T, Kuroda S, Ikeda T, Kano K, Tanizawa K, Mathews FS. Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.  Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14268-73.
  • Datta S, Uma MV, Shamala N, Balaram P. Stereochemistry of Schellman Motifs in Peptides. Crystal Structure of a Hexapeptide with a C-terminus 6®1 Hydrogen Bond.   Biopolymers 1999 50; 13-22.
  • Datta S, Shamala N, Banerjee A, Balaram P. Hydrogen bonding in peptide helices. Analysis of two independent helices in the crystal structure of a peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe. J Pept Res. 1997 Jun;49(6):604-11.
  • Datta S, Shamala N, Banerjee A, Balaram P. Conformational Variability of Gly-Gly Segments in Peptides. A Comparison of the Crystal Structures of an Acyclic Pentapeptide and an Octapeptide. Bioplolymers 1997: 41; 331-336.
  • Datta S, Kaul R, Rao RB, Shamala N, Balaram P. Stereochemistry of Linking Segments in the Design of Helix-Helix Motifs in Peptides: Crystallographic Comparison of a Glycyl-Dipropyl-Glycyl Segment in a Tripeptide and in a 14 residue peptide.  J. Chem. Soc., Perkin Trans. 1997: 2; 1659-1664.
  • Datta S, Shamala N, Banerjee A, Pramanik A, Bhattacharya S, Balaram P. Characterization of Helix Terminating Schellman Motifs in Peptides. Crystal Structure and Nuclear Overhausser Effect Analysis of a Synthetic Heptapeptide Helix.  J. Am. Chem. Soc. 1997, 119; 9246-9251.
  • Banerjee A, Datta S, Pramanik A, Shamala N, Balaram P. Heterogeneity and Stability of Helical Conformation in Peptides: Crystallographic and NMR studies of a Model Heptapeptide.  J. Am. Chem. Soc. 1996, 118; 9477-9483.
  • Datta S, Shamala N, Gurunath R, Balaram P. Observation of a mixed antiparallel and parallel beta-sheet motif in the crystal structure of Boc-Ala-Ile-Aib-OMe. Int J Pept Protein Res. 1996 Sep;48(3):209-14.
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