Download Coarse-Graining of Macromolecules

Lecture 1
(Block et al.)
(Wuite et al.)
Rob Phillips
California Institute of Technology
Gibbs and the Calculus of
Equilibrium
ATP and ADP
The Statistical Mechanics of
DNA/Protein Interactions
Schrodinger’s Great Question
Our mission: build up simple
quantitative models at the
biology/physics/chemistry
interface.
“A physics that has no place for life is as impoverished as would be a biology
not informed by chemistry.” F. Harold
X-Ray Crystallography of Proteins
PDB Structures and PDB Files
NMR of Macromolecules: A Step
Towards Dynamics
Case Studies in Molecular Biology:
Polymerase Chain Reaction
Case Studies in Molecular Biology:
Cloning
Genomic libraries constructed
by chopping up DNA of interest
with restriction enzymes and
then gluing these fragments into
the phage genome and then
infecting cells with the modified
phage.
The phage DNA circularizes
within E. coli and is then
propagated from one
generation of E. coli to the next
and carries with it copies of the
original genome.
Visit the Stratagene website.
www.stratagene.com
The Tools of Single Molecule
Science
Optical Tweezers
AFM
FRET
Optical Microscopy and Fluorescent
Dyes: The Cytoskeleton
Huge advances have taken place in microscopy which allow for
the real time examination of biological structures and their
temporal evolution – the cell is teeming with activity.
This slide: staining of the cytoskeleton.
Actin filaments
Microtubules
Intermediate Filaments
Laser Tweezers: The Manipulation
of Single Molecules
Concept: Attach optical
beads (micron size) to
molecules of interest. Use
laser light to apply force
through radiation pressure.
Molecular velcro –
biotin/streptavidin complex.
(Bennink et al.)
(Prost group)
The setup: optical microscope with
a laser port and a digital camera.
Optical Tweezers in Action:
Transcription by RNA Polymerase
(Wang et al.)
(Gelles et al.)
ATPase: Observations of a Rotary
Motor in Action
ATPase: Rotary molecular factory which exploits proton gradient
to produce ATP.
Rotary Assay: Actin filament attached to ATP rotary head and
then the rotation of the stained actin filament is observed.
Single Molecule Experiments with
the AFM
(Fernandez et al.)
Concrete example of dynamical
force spectroscopy in the case
of the giant muscle protein titin.
Key modeling challenge: the
precise details of the
force/extension curve.
Note that by performing
mutations on the titin molecule,
the force/extension signature
can be altered.
Biological Structure: Spatial
Hierarchy
Structure exists at many length scales → structural
hierarchies
Bond lengths: ~1-3Å
Amino Acids: ~1nm
Proteins: 2-5nm
Macromolecular assemblies: 5-50nm
Organelles: 50-1000nm
Cells: microns and beyond
Tissues
Biological Structure: Spatial
Hierarchy
Structure exists at many length scales →
structural hierarchies.
Each of these scales in the hierarchy is
amendable to modeling.
Not surprisingly, all of the usual multiscale
challenges are presence with a vengeance
because often different levels in the hierarchy
cannot be isolated.
Amino Acids and Proteins
Amino Acids are the building blocks of Proteins
Biological Structure: Protein
Structure
Structural Levels
Primary (amino acid sequence)
Secondary (α-helices, β-strands)
Tertiary (domains)
Quaternary (active sites)
Case Studies in Protein Structure:
Protein Diversity
Proteins come in a variety of shapes and
sizes. Enzymes are usually huge in
comparison with the molecules for which
they catalyze reactions (i.e. their
substrates).
Question: Is there a simple scaling of
protein size with the number of amino
acid residues?
Close packing leads to:
Random walk description of polymer
leads to:
Somes: The Biologists Ons
Macromolecular Assemblies
Physicists characterize collective
excitations as ONS (phonons,
magnons, excitons, etc…)
Biologists also consider collective
phenomena in the form of
interacting macromolecular
complexes.
Proteosome
Replisome
Ribosome
Collections of Molecules Organelles
Structure of Viruses
Viruses and Their Hosts
Procaryotic Cells - Bacteria
Eucaryotic Cells
Yeast cells
Collections of Cells - Tissues
C Elegans – a worm with 959 cells
Biological Processes: Temporal
Hierarchy
Processes exists at many time scales → hierarchies of
processes.
Not surprisingly, all of the usual multiscale challenges are
presence with a vengeance because often different levels in
the hierarchy cannot be isolated.
(Chan and Dill)