Presentation is loading. Please wait.

Presentation is loading. Please wait.

INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (ICGEB), NEW DELHI, INDIA Structural and Computational Biology Group.

Similar presentations


Presentation on theme: "INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (ICGEB), NEW DELHI, INDIA Structural and Computational Biology Group."— Presentation transcript:

1 INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (ICGEB), NEW DELHI, INDIA Structural and Computational Biology Group

2 Organ  Tissue  Cell  Molecule  Atoms Structural Biology Medicine and Biology at Atomic Scale

3 High Resolution Structural Biology Atomic structure - communication

4 Anti-tumor Activity Duocarmycin SA Evolution: Machine and Control Atomic interactions

5 Biological linguistics Molecule Structural Genomics Pathway Structural Proteomics Activity Systems Biology RPA NER BER RR

6 Techniques propel discoveries NMR Spectroscopy X-ray Crystallography Computation Atomic maps

7 Experimental Buffet RPA-B RPA-AB RPA-A Fluorescence Intensity Ratio of T-ag/RPA

8 3D Molecular Structures X-ray X-rays Diffraction Pattern  Direct detection of atom positions  Crystals NMR  Indirect detection of H-H distances  In solution

9 Flavours… n X-ray- highest resolution, automation n NMR- enables solution variations; n direct tap on motions and on weak interactions n Computation- fundamentals of structure, dynamics

10 Structures breathe Need to incorporate motion

11 Challenges… 3D structures are static Biological process (recognition, interaction, chemistry) are dynamic New methods for molecular motions

12 Malaria ~40/400 are vectors Anopheles gambiae Plasmodium falciparum Plasmodium vivax Plasmodium ovale Plasmodium malaria

13 Biology of model organisms - relevance to the malaria parasite? Baldauf, Science 300, 1703 (June 2003) “…from yeast to man” Plasmodium Trypanosoma

14 Example 1

15 Duffy-binding-like domains from the erythrocytic stage Invasion of erythrocytes by malaria parasites

16 Electron micrograph from Aikawa et al (1978) J. Cell Biol. 77:72 apical orientation microneme secretion junction formation receptor/ligand interactions rhoptry discharge RBC invasion

17 The Duffy-Binding-Like (DBL) Superfamily SSTMIIII - VVICYTII (DBL) F1F2 P. vivax / P. knowlesi P. falciparum DBL1  DBL2  DBL3  DBL4  CIDR1  Exon 2TM Erythrocyte invasion: mediated by Erythrocyte binding protein family Cytoadherence: mediated by PfEMP-1 family P. falciparum DBL

18 Erythrocyte P. vivax RBC invasion P. falciparum RBC invasion Duffy antigen Sialic acid/GA Sialic acid/GC unknown

19 Overall domain architecture of PkDBL 

20 DARC-PkDBL  engagement Polar Sulfation of tyrosine 41 on DARC increases binding affinity ~1000X Apolar Polar

21 Invasion and evasion Sialic acid binding site CCR5 binding site DARC binding site Antigenic shift/drift by Conformational masking, Just-in-time release? sequence variation glycan shield, mutants Haemagglutinin gp120 PkDBL 

22 P. vivax versus P. falciparum

23 Structural and functional conservation - mechanistic divergence F1 : F2 = 1.9Å (185 C  ) F1 : Pk  -DBL = 1.6Å (195 C  ) F2 : Pk  -DBL = 1.8Å (156 C  ) Pk DBL Pf F1+F2 DBLs

24 Structural and functional conservation - mechanistic divergence Insertions

25 Structural and functional conservation - mechanistic divergence P. vivax/P. knowlesi P. falciparum Module duplication Insertions Monomeric assembly Dimeric assembly

26 RBC Polymorphic sites DARC binding site Subdomain 3 loop P. vivax Invasion P. falciparum

27 Example 2

28 Proteins that play crucial roles for the parasite UIS3 from the pre-erythrocytic stage

29 Entry and Development – Liver Stages

30 Structural congruence, functional divergence

31 Genetics and structure driving insights into function

32

33

34 Example 3

35 SH3 PFG27 Novel fold Unique 3D structure RNA binding SH3 binding PxxP motifs Signaling intermediate Gametocytogenesis in P. falciparum

36 Review of binding sites of interest on Pfg27 Two RNA-binding sites per dimer Four SH3-binding sites per dimer A dimer interface RNA-binding site Deep cavity SH3-binding site Dimer interface Pfg27 monomer

37 Docking pattern on Pfg27 Visual analysis of top 200 dockings Deep cavity RNA-binding site Dimer interface SH3-binding site Other sites FlexX GOLD (values in percent)

38 RNA-binding site surface deeper Docking at RNA-binding site fragmentligand

39 Dockings at RNA-binding site RNA-binding site surfacedeeper fragmentligand

40 Ligand profiles at RNA-binding site 2D structural similarity: ~35% for top 20 Notable base fragment (present in 6 ligands) Functional group: SO 3 (present in 11 ligands) H-bonding interactions: Ser72,Arg75, Tyr76, Lys79 hydrophobic interactions/close contacts: Leu52, Phe87, Leu52, Asn82 Molecular weight: Drug likeness: 20% (WDI)

41 Development of Databases for Screenings NCI 1990 diverse Open collection 240,000 Pubchem 250,000 Chembridge 50,000 diverse Maybridge 60,000 diverse All libraries converted into relational database format Pubchem - 46,000 diverse library generated Filtered based on lipinski’s rule of 5 Redundancy checks performed Specs 10,000 diverse Final database: 149,865 compounds with < 90% structural similarity

42 Example 4

43 Structural and functional dissection of the two nucleosome assembly proteins from Plasmodium falciparum Amit Sharma ICGEB, New Delhi

44 Nucleosome assembly in P. falciparum Importance

45 NC NC PfNAPS PfNAPL Nucleosome assembly in P. falciparum 1. Expressed in all stages of the parasite 2. Localized both to the cytoplasm and the nucleus 3. Differential localization in asexual/sexual stages 4. Differential phosphorylation of the two NAPz 5. Similar histone binding specificities Workplan

46 Nucleosome assembly in P. falciparum

47 Nucleosome assembly protein from P. falciparum

48

49 Nucleosome assembly in P. falciparum

50 Example 5

51 Use Iodides for Phasing Protein Structures using home Xray source

52

53 Example 6

54

55

56

57

58

59 Funding agencies Wellcome Trust European Union DBT, Govt. of India ICGEB Manickam Yogavel Rachna Hora Ashwani Sharma Anuj Kumar Jasmita Gill Prakash Mishra Shoshanna Tharu Tarun Bhatt Manvi Gupta Anupama Yadav J. Sebastian Raja


Download ppt "INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (ICGEB), NEW DELHI, INDIA Structural and Computational Biology Group."

Similar presentations


Ads by Google