Structural Biology

Medicine and Biology at the Atomic Scale

Organ → Tissue → Cell → Molecule → Atoms

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*
High Resolution Structural Biology
Using atomic structure to understand how
biomolecules communicate
The Reward: Understanding→Control
Anti-tumor Activity
Duocarmycin SA

Atomic interactions

Shape
 Hierarchy of Structural Biology

NER
RPA
BER
RR

Molecule Pathway Activity

Structural Genomics Structural Proteomics Systems Biology
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?
Expression/Mutations Biophysical Analysis Crystallography

Fluorescence Intensity
RPA-A

RPA-B

RPA-AB

Ratio of T-ag/RPA

NMR Computation
 Experimental Determination
of 3D Structures
X-ray NMR

RF
Diffraction
X-rays RF Signals
Pattern

H0

Direct detection of Indirect detection of

atom positions H-H distances
Crystals In solution
Representations of Structure
Conformational Ensemble

Neither crystal nor

solution structures
are properly
represented by a
single conformation
 Intrinsic motions
 Imperfect data

PRECISION
RMSD of the ensemble
 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 Ca2+ -binding protein!

 Need to incorporate 3D and motion

Calcium-Dependent Protein Kinase
A Target for Anti-Malarial Drug Design
Calcium Signal Transduction
EF-Hand Ca2+ Sensors

Ca2+

Target
(kinase)
Regulation of Protein Kinase
Activity by Ca -Calmodulin
2+

Ca2+ signal

Kinase Activation
 Protozoa Have A Unique Kinase
The Ca2+ -Dependent Protein Kinase (CDPK)
Standard auto-
inhibitory segment
Calmodulin-like
domain (CaM-LD)

Kinase

 CDPK has its own regulatory apparatus!!

How does it work?
 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