 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

Structure of CDPK Reveals Intra-molecular Kinase Activation

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

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

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