1.  A cell is an organization of millions of molecules  Proper communication between these molecules is essential to the normal functioning of the cell  To understand communication between molecules:  To understand communication between molecules: *determine the arrangement of the atoms* Organ  Tissue  Cell  Molecule  Atoms Structural Biology Medicine and Biology at the Atomic Scale

2. High Resolution Structural Biology Using atomic structure to understand how biomolecules communicate

3. Anti-tumor Activity Duocarmycin SA The Reward: Understanding  Control Shape Atomic interactions

4. Hierarchy of Structural Biology Molecule Structural Genomics Pathway Structural Proteomics Activity Systems Biology RPA NER BER RR

5. High Resolution Structural Biology Three Complementary Techniques NMR Spectroscopy X-ray Crystallography Computation Determine experimentally or model 3D structures of biomolecules

6. What Tools Do We Use? NMRComputation RPA-B RPA-AB RPA-A Fluorescence Intensity Ratio of T-ag/RPA Biophysical Analysis Expression/Mutations Crystallography

7. Experimental Determination of 3D Structures X-ray X-rays Diffraction Pattern  Direct detection of atom positions  Crystals NMR RF Signals H0H0  Indirect detection of H-H distances  In solution

8. Representations of Structure Conformational Ensemble PRECISION RMSD of the ensemble Neither crystal nor solution structures are properly represented by a single conformation  Intrinsic motions  Imperfect data

9. Computational Determination of 3D Structures Specify the forces that act on each atom Simulate these forces on a molecule of known atomic composition Start with experimental data or approximate experimental structure or just sequence Many algorithms in use, all treatments for bio-macromolecules are empirical

10. Unique Contributions of Each Structural Biology Technique X-ray- highest resolution, automation coming NMR- enables wide variation of solution conditions; direct characterization of motions and of weakly interacting systems Computation- fundamental understanding of structure, dynamics and interactions; models without experiment; fast

11. Challenges For Understanding The Meaning of Structure Structures determined by NMR, computation, and X-ray crystallography are static snapshots of highly dynamic molecular systems Biological process (recognition, interaction, chemistry) require molecular motions (from femto-seconds to minutes) New methods are needed to comprehend and facilitate thinking about the dynamic structure of molecules: visualization

12. Visualization of Structures Intestinal Ca 2+ -binding protein!  Need to incorporate 3D and motion

13. Calcium-Dependent Protein Kinase A Target for Anti-Malarial Drug Design

14. Ca 2+ Target (kinase) Calcium Signal Transduction EF-Hand Ca 2+ Sensors

15. Regulation of Protein Kinase Activity by Ca 2+ -Calmodulin Ca 2+ signal Kinase Activation

16. Protozoa Have A Unique Kinase The Ca 2+ -Dependent Protein Kinase (CDPK) Kinase  CDPK has its own regulatory apparatus!!  How does it work? Standard auto- inhibitory segment Calmodulin-like domain (CaM-LD)

17. Structure of CDPK Reveals Intra-molecular Kinase Activation

18. Anti-Malarial Drug Design Must Inhibit CaM-LD But Not Calmodulin Calmodulin CaM-LD

19. Center for Structural Biology A Trans-Institutional Initiative Increase molecular/physical thinking in medical and biological research Foster multi-disciplinary approaches Focal point bridging medicine and biology to physics and chemistry

20. Structural Biology Resource But Not A Core!! Education/project origination Enabling expertise: 3 Ph.D. Staff Scientists Enabling hardware: technologies to visualize and determine structures Open-access focal point in BIOSCI/MRBIII