Tentative syllabus for BICM 77000, Spring 2012

 

1/31: Protein Structure, De Novo Design, and Membrane Proteins  (EC)
	-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

2/7: Absorption, Fluorescence and Circular Dichroism Spectroscopies (EC)
  	-Absorption spectroscopy 
      	Electronic transitions of the peptide bond 
      	Electronic transitions of amino acid side chains
	-Circular Dichroism Spectroscopy
	Optical activity of proteins and peptides; protein conformations and secondary structure; nucleic acids
	-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

2/14: Vibrational Spectroscopy-IR and Raman (Desamero-York College)
	-Molecular motions
	-Hooke's 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

2/21: No class/Monday schedule

2/28:  Mass Spectrometry  (EC)
	-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

3/6:  Nuclear Magnetic Resonance Spectroscopy (Ghose - City 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

3/13: Macromolecular crystallography: (Poget - CSI)
	-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

3/20: Exam first half

3/27: PROTEIN STRUCTURE (TL)
      a) Introduction
      b) Conformations of Peptides and Proteins
      c) Factors Affecting Conformations
      d) Predictions of Protein Conformation
      e) Chou-Fasman Approach

4/3:  THERMODYNAMICS (TL)
      1st and 2nd laws, Maxwell Eqs, Mixtures, ideal and ideal dilute
      solutions, osmotic effect, chemical reaction equilibria

4/10: Spring break

4/17: 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

4/24: TRANSPORT PHENOMENA (TL)
      Nonequilibrium thermodynamics
      Diffusion (passive,active), Sedimentation, Electrophoresis

5/1:  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

5/8: 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

5/15: MEMBRANES  (TL)  
      Structures, phases, thermodynamics, dynamics
      Forces between bilayers.   Membrane fusion

5/22: Final Exam (TL part)