Syllabus for BICM 77000, Spring 2011
Instructors : Dr. Fred Naider – College of Staten Island
Dr. Themis Lazaridis – City College
Guest Lectures
Mass Spectometry: Dr.Emmanuel Chang- York College
Raman Spectroscopy-Dr. Laura Juszczak –Brooklyn College
2/1: PROTEIN STRUCTURE (FN)
a) Introduction
b) Conformations of Peptides and Proteins
c) Factors Affecting Conformations
d) Predictions of Protein Conformation
e) Chou-Fasman Approach
f) Intrinsically Disordered Proteins
2/08: : Membrane Proteins, De Novo Design, IR, UV SPECTROSCOPY (FN)
a) Amphiphilic Helices and Membrane Proteins
b) De Novo Design of 4-Helix bundle, β -hairpins
c) Use of Spectroscopy for Conformational Analysis of Peptides
d) IR of Peptides - use in analysis of 2° structure and H-bonding
e) Absorption spectroscopy
e) Electronic transitions of the peptide bond
f) Hypochromism of helices and exciton splitting
g) Absorption spectroscopy of nucleic acids
2/15: CIRCULAR DICHROISM (FN)
a) Optical activity of peptides and proteins
b) Study of helix coil transitions using polarimetry
c) ORD and CD of the peptide chromophore
d) CD of Polypeptides
e) Estimation of Protein 2° structure with CD
f)
CD of membrane proteins
g) Applications of CD
a. Designing HIV-1 Fusion inhibitors
h) Limitations of CD approach
i)
Structure of Nucleic acids
j)
CD of nucleic acids
2/22: FLUORESCENCE SPECTROSCOPY (FN)
a) Fluorescence Spectroscopy
b) Nature of emission processes -fluorescence; phosphorescence
c) Jablonski Diagram
d) Definition of terms -quantum yield-lifetimes
e) Experimental issues
f) Fluorescent Groups in Biopolymers
g) Solvent Effects-determination of environments
h) Measurement of binding constants
i) Fluorescence Anisotropy
j) FRET - Experiments
3/01: NUCLEAR MAGNETIC RESONANCE (FN)
a) Introduction to NMR-Rotating Frame Pulse Sequences
b) NMR of Amino Acids
c) Use of coupling constants for Dihedral Angle Analysis
d) NMR of Homologous Oligopeptides
e) NMR of Cyclic Peptides - NOE effects, difference spectroscopy
g) 2D NMR Techniques - COSY, Relays
3/08: NUCLEAR MAGNETIC RESONANCE (FN)
a) Nuclear Overhauser enhancement approaches
b) NOESY spectroscopy
c) 3D and 4D heteronuclear Experiments
d) Conformational Analysis of Biologically Active Peptides
e) Extension to Small Proteins
f) NMR Analysis of Protein - Substrate Interactions
1) Use of Deuteration
2) Transferred NOE Spectroscopy
g) NMR analysis of membrane proteins
1) NMR in detergents
2) Selective labeling
3) Use of spin labels.
h) In vivo NMR - Studies on Yeast Cells
1) Studies on Algae - Determination of a metabolic pathway
2) Extension to Mammalian Cells
3/15 Guest Lecturers
Mass Spectrometry – Professor Emmanuel Chang
1) Mass Spectrometry
a. Parts of a mass spectrometer
2) Ionization: MALDI and ESI
a. Mass Analysis: time-of-flight
b. quadrupole; ion trap
3) Tandem MS and Hybrid Instruments
4) Applications
a.
structure determination
b.
H/D exchange
c.
LC/MS
d. protein ID and proteomics
Raman Spectroscopy-Professor Laura Juszczak
1) Brief Review of Photophysical Concepts
2) Selection Rules for Infrared versus Raman Spectroscopy
3) Comparative Advantages of Infrared versus Raman Spectroscopy
4) Resonance Raman: A Raman Refinement and the Advantages Conferred
5) Biological Applications of UV Resonance Raman
a. Studies of the Amino Acid residue, Tryptophan, with respect to Protein
Environment and correlations with steady state fluorescence emission
b. Conformation and Reactivity of the Copper II-binding Octapeptide Tandem
Repeat from the Prion Protein
c.
Time-Resolved Conformational Switching in Encapsulated Human Hemoglobin A
3/22 Midterm Exam Fred Naider Part (Questions from lectures 1-7)
3/29: THERMODYNAMICS (TL)
1st and 2nd laws, Maxwell Eqs, Mixtures, ideal and ideal dilute
solutions, osmotic effect, chemical reaction equilibria
4/5: 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
4/12: TRANSPORT PHENOMENA (TL)
Nonequilibrium thermodynamics
Diffusion (passive,active), Sedimentation, Electrophoresis
4/17-4/26 Spring Recess
5/3: 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
5/10: 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
5/17: MEMBRANES (TL)
Structures, phases, thermodynamics, dynamics
Forces between bilayers. Membrane fusion
5/24 Final exam on Themis Lazaridis part