Introduction
This is an early working draft for the syllabus of two prospective courses that still requires much discussion and editing. It is the product of the first of several meetings (12/07/09). Present: Dave Peyton (PSU), Drake Mitchell (PSU), Jeffrey Karpen (OHSU), Chris Kroenke (OHSU), Jim Whittaker (OHSU), Ujwal Shinde (OHSU), Dave Farrens (OHSU) & Michael Chapman (OHSU).
The first course would be a Winter or Spring introductory course for 1st year graduate and advanced undergraduate students, with essentially no prerequisites. The second course would be more advanced, targeted for the Fall of 2nd year graduate students and advanced undergraduates. The goal is for the first course to be offered early in 2011.
Topics might still be shuffled. Hours planned are preliminary. 30-40 will constitute the total for each course. In the first course, several of the topics will likely be expanded a bit as time budgets are tighter than they might need to be.
1 Introduction to Molecular Biophysics
1.1 Introduction to Macromolecular Structure; Inter-atomic Forces & Force Fields (4.5 hr)
1.1.1 Primary Through Quaternary Structure
1.1.2 Covalent Bonding
1.1.3 Non-bonded Interactions (hydrophobic effect covered later)
1.1.4 Forces/Fields Used to Model Interactions Computationally
1.2 Thermodynamics & Kinetics (7.5 hr)
Illustrated with applications to Membrane Transport.
1.2.1 Energy, Entropy, Free Energy
1.2.1.1 Hydrophobic effect
1.2.2 Statistical mechanics & determinism
1.2.3 Equilibria
1.2.3.1 Reactions
1.2.3.2 Binding
1.2.3.3 Calorimetry
1.2.3.4 Conformation
1.2.4 Transport & Diffusion
1.2.4.1 Membranes / Proteins
1.2.4.2 Ion channels & pumps
1.2.4.3 Action potentials / measurement / synapses
1.3 Theory of Crystallography (6 hr)
1.3.1 Diffraction theory
1.3.2 Phasing methods
1.3.3 Maps, Models & Refinement
1.3.4 Quality assessment
1.4 Spectroscopy - Visible & UV (6 hr)
1.4.1 Absorption
1.4.2 Polarization spectroscopy
1.4.3 Fluorescence
1.4.3.1 Fluorescence anisotropy
1.4.3.2 FRET
1.5 Introduction to Magnetic Resonance (7.5 hr)
1.5.1 Spin Physics & 2-state models
1.5.2 Magentic Resonance Imaging
1.5.3 Biomolecular Structure determination (Introduction)
2 Advanced Molecular Biophysics
2.1 Avanced Magnetic Resonance (7.5 hr):
2.1.1 Methods of Biomolecular Structure Determination
2.1.2 Probing the dynamics of macromolecules
2.1.3 Special topics: Paramagnetic NMR & ESR, spin labeling & Solid-state NMR
2.2 Visible & Electron Microscopy (4 hr)
2.2.1 Theory of Light Microscopy (1 hr)
2.2.2 Fluorescence, Confocal & Correlative Microscopy (0.5 hr)
2.2.3 Transmission EM – theory
2.2.2 Biological samples
2.2.3 3D reconstruction
2.3 Practical Crystallography (8 hr)
2.3.1 Crystallization (+ lab)
2.3.2 Data collection (+ lab?)
2.3.3 Phasing by molecular replacement (+ computer exercise?)
2.3.4 Model-building & Refinement (+ computer exercise)
2.4 Interpretation of Structure (5.5 hr)
2.4.1 Databases & their use
2.4.2 Homology modeling
2.4.3 Docking
2.4.4 Electrostatics – Potentials & pKs
2.5 Molecular Dynamics (2.5 hr)
2.5.1 Simulated annealing
2.5.2 Normal modes
2.5.3 Accelerated methods / enhanced sampling
2.6 Mass spectrometry in biomolecular structure / interactions (2 hr)
2.6.1 Footprinting
2.6.2 Dynamics
2.7 Single Molecule Methods (time available, or reading)
2.7.1 Fluorescence
2.7.2 AFM
2.9 Case Studies to be woven in:
(a) Molecular Motors
(b) Protein Mis-folding & Disease
2.10 Topics to be covered in reading (only)
(a) Surface Plasmon Resonance
3 Sources
UPenn Biochemistry and Molecular Biology Graduate Program
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