Tentative syllabus for BICM 77000, Spring 2009
1/27: PROTEIN STRUCTURE (TL)
a) Introduction
b) Conformations of Peptides and Proteins
c) Factors Affecting Conformations
d) Predictions of Protein Conformation
e) Chou-Fasman Approach
2/3: THERMODYNAMICS (TL)
1st and 2nd laws, Maxwell Eqs, Mixtures, ideal and ideal dilute
solutions, osmotic effect, chemical reaction equilibria
2/10: no class, Thursday schedule
2/17: STATISTICAL THERMODYNAMICS AND COMPUTATIONAL METHODS (TL)
Statistical Thermodynamics: ensembles, ideal gases, liquids
Molecular interpretation of thermodynamic quantities
Interactions, Energy functions, Solvation
Methods:energy minimization, molecular dynamics, Monte Carlo,
free energy simulations, normal modes, Brownian dynamics,
continuum electrostatics
2/24: TRANSPORT PHENOMENA (TL)
Nonequilibrium thermodynamics
Diffusion (passive,active), Sedimentation, Electrophoresis
3/3: PROTEIN FOLDING AND CONFORMATIONAL TRANSITIONS (TL)
Theoretical framework, Energy landscape. Scanning Calorimetry
Interactions responsible for stability. Hydrophobic effect
Experimental work: equilibrium, kinetics
Theoretical work: Helix-coil transition theory, Simulations
Bioinformatics of protein structure prediction:
sequence alignments, homology modeling, threading
3/10: BINDING (TL)
Theoretical framework: translational/rotational entropy
Contributions to binding affinity, specificity
Isothermal titration calorimetry
Multiple ligand binding, cooperativity, and linkage
Proton binding and pH titration
Structure based drug design
3/17: MEMBRANES (TL)
Structures, phases, thermodynamics, dynamics
Forces between bilayers. Membrane fusion
3/24: Final Exam (TL part)
3/31: Protein Structure, De Novo Design, and Membrane Proteins
-Conformations of proteins and peptides
-De novo protein design: structure and function
-Amphiphilic helices and membrane proteins
-Biophysics of membrane proteins: GPCRs, rhodopsin, ion channels
-Nucleo-cytoplasmic transport
4/7: Absorption, Fluorescence and Circular Dichroism Spectroscopies
-Absorption spectroscopy
Electronic transitions of the peptide bond
Electronic transitions of amino acid side chains
-Fluorescence Spectroscopy
Nature of emission processes-fluorescence,phosphorescence
Jablonski Diagram; Definition of terms -quantum yield-lifetimes
Fluorescent Groups in Biopolymers
Applications: FRET, anitrosopy, binding, environments
-Circular Dichroism Spectroscopy
Optical activity of proteins and peptides; protien conformations and secondary structure; nucleic acids
4/8-4/17: Spring break
4/21: Vibrational Spectroscopy-IR and Raman (Desamero-York College)
-Molecular motions
-Hookebs Law
-Comparison of IR and Raman spectroscopy: energy diagrams,selection
rules, limitations
-Vibrational Techniques: IR/Raman difference spectroscopy,drop coat
deposition Raman (DCDR) spectroscopy,surface enhanced Raman
Spectroscopy (SERS)
-Applications: pKa determination,dihedral angles,enzyme mechanism
4/28: Mass Spectrometry
-Parts of a mass spectrometer
-Ionization: MALDI and ESI
-Mass Analysis: time-of-flight; quadrupole; ion traps
-Tandem MS and Hybrid Instruments
-Applications: structure determination; H/D exchange; LC/MS; protein ID and proteomics
5/5: Nuclear Magnetic Resonance Spectroscopy (Ghose - Brooklyn College)
-A brief introduction to the basics of NMR.
-FT-NMR to multidimensional NMR
-Resonance assignments in proteins
-Structural constraints and structure calculations
-Other biomolecular NMR applications
-NMR and dynamics
5/12: Macromolecular crystallography: (de Carlo - CCNY)
-Two-Dimensional Patterns, Bravais Lattices and crystal symmetries
-X-ray scattering, Bragg Law of Diffraction
-Protein crystals, generation of diffraction data
-Fourier Transform and the Phase problem
-Solving a structure - obtaining an electron density map
-Structure quality and refinement methods
-Crystallography without crystals: SAXS and Cryo-EM
5/19: Final exam (Second half)