-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

*determine the arrangement of the atoms*

*Atomic Resolution Structural Biology**Atomic Resolution Structural Biology*

Organ Organ Tissue Tissue Cell Cell Molecule Molecule Atoms Atoms

Medicine and Biology at the Atomic ScaleMedicine and Biology at the Atomic Scale

High Resolution Structural BiologyHigh Resolution Structural BiologyUsing atomic structure to understand how Using atomic structure to understand how

biomolecules communicatebiomolecules communicate

Anticancer DrugDuocarmycin SA

Biological Specificity from StructureBiological Specificity from Structure

Shape

Atomic interactions

Putting Structures in ContextPutting Structures in Context

MoleculeStructural Genomics

PathwayStructural Proteomics

ActivitySystems Biology

RPARPA

NER

BER

RR

Strategy and ApproachesStrategy and Approaches

NMR Spectroscopy X-ray Crystallography

Computation

It’s not about the structure or the technique,it’s about the Biology!!!!

Determination of 3D StructuresDetermination of 3D Structures

X-ray NMR

X-rayDiffraction

Pattern RF

RFResonance

H0

Direct detection ofatom positions

Crystals

Indirect detection ofH-H distances

In solution

Static Structure/Dynamic BiologyStatic Structure/Dynamic Biology

• 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

Challenges for Converting Challenges for Converting Structure to FunctionStructure to Function

• Neither crystal nor solution structures are properly represented by a single low energy conformer

• To be called a structure (not a model), there must be a complete representation of what parts are well known and what parts are not well known

Conformational EnsembleConformational Ensemble: : Representing Representing aa Structure Structure

C

N

Uncertainty/Precision: RMSD of the ensemble

Unique ContributionsUnique Contributions

• X-ray crystallography- highest resolution structures; fast

• NMR- enables widely varying solution conditions; characterization of motions and dynamic, weakly interacting systems

• Computation- fundamental understanding of structure, dynamics and interactions; models without experiment

Center for Structural BiologyCenter for Structural Biology

• Increase molecular thinking

• Foster multi-disciplinary research

• Focal point bridging medicine and biology to math, physics, chemistry

• >12 research groups (8 new!!)

• Promote collaborations involving structural Promote collaborations involving structural biology researchbiology research

How Does NMR Work?How Does NMR Work?

Ho

parallel

anti-parallel

Alignment Energy

E = h Ho

Efficiency factor-nucleus

Constants Strength ofmagnet

Resonance: Perturb EquilibriumResonance: Perturb Equilibrium

ap

hE

p

ap

p

equilibrium

non-equilibrium

If energy is input at exactly the right frequency (), it gets absorbed

E

Resonance: Read Out SignalsResonance: Read Out Signals

+

-

Ho =

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

1. force non-alignment 2. release

p

ap

p

ap

p

ap

NMR of MoleculesNMR of Molecules

CH3-CH2-OH

Resonance assignment: which signal for which H atoms?

OH CH2 CH310 0

Challenges of NMR on ProteinsChallenges of NMR on Proteins

• Proteins have hundreds/thousands of signals

• Resonance assignment is a huge challenge

• Need to use computer programs to convert from NMR data to structures

Uses of Solution NMR to Uses of Solution NMR to Elucidate Protein FunctionElucidate Protein Function

• Analytical and Physical Characterization

– Is the protein folded?

– Sequence, post-translational modifications

– Important: measure binding constants

• Assess structural homology/effect of mutations

• Three-dimensional structure determination

• UniqueUnique: Measure flexibility/dynamics: Measure flexibility/dynamics

*To address “static structure/dynamic biology”**To address “static structure/dynamic biology”*