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*
*Atomic Resolution Structural Biology*
High Resolution Structural Biology
Using atomic structure to understand how
biomolecules communicate
Biological Specificity from Structure
Anticancer Drug
Duocarmycin SA
Atomic interactions
Shape
Putting Structures in Context
NER
RPA
BER
RR
Molecule
Pathway
Activity
Structural Genomics
Structural Proteomics
Systems Biology
Strategy 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 Structures
X-ray
X-ray
Diffraction
Pattern
NMR
RF
Resonance
RF
H0
Direct detection of
atom positions
Crystals
Indirect detection of
H-H distances
In solution
Static 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
Structure 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 Ensemble:
Representing a Structure
C
N
Uncertainty/Precision: RMSD of the ensemble
Unique 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 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
biology research
How Does NMR Work?
Ho
Alignment
Energy
Efficiency factornucleus
anti-parallel
DE = h g Ho
parallel
Constants
Strength of
magnet
Resonance: Perturb Equilibrium
non-equilibrium
ap
p
hn = DE
If energy is input at
exactly the right
frequency (n), it gets
absorbed
ap
DE
p
equilibrium
Resonance: Read Out Signals
p
ap
ap
ap
+
-
+
-
-
+
-
=
+
-
Ho
1. force non-alignment
+
-
+
-
+
+
-
+
-
+
+
-
+
-
+
-
2. release
+
-
+
-
p
+
-
p
NMR of Molecules
CH3-CH2-OH
10
OH
CH2 CH3
0
Resonance assignment: which signal for which H atoms?
Challenges 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
Elucidate 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
• Unique: Measure flexibility/dynamics
*To address “static structure/dynamic biology”*