| Week |
Lecture Topic |
Lab |
Reading |
2 (1/25) |
Introduction to Structural Biology: Protein Motifs
|
Protein Fold
Visualization |
- Class Handout : Summary and Introduction
- Branden and Tooze : Ch 1-5.
|
3 (2/1) |
Protein Structural Analysis Tools
|
Protein
Fold
Visualization
|
- The
Protein Data Bank, Bourne, et.al., Nucleic Acids Res. 28, 235-42 (2000).
- Who
checks the Checkers? Four Validation Tools applied to Eight Atomic
Resolution Structures, EU 3D Validation Network, J
Mol Biol 276, 417-36 (1998).
- Where Freedom is given, liberties are taken, Kleywegt,
G.J., Jones, T.A., Struct. 3, 535-40 (1995), (Class Handout)
- A
systematic comparison of protein structure classifications: SCOP, CATH
and FSSP, Hadley,C., Jones. D.T., Struct.
7, 1099-1112 (1999).
- About
the use of protein models, Peitsch, M.C., Bionf., 18, 934-8 (2002).
- Class Notes 01/31
- New: Class notes_1_2_05
|
4 (2/8)
|
Protein Folding
Thermodynamics
|
Cambridge Structural Database
Course: 5%
Due : Tuesday 2/15 |
- Protein
Structure and the Energetics of Protein Stability, Robertson, A.D.,
Murphy, K.P., Chem.
Rev. 97, 1251-68 (1997)
- Stability of the Folded Conformation, Creighton, T. E. Proteins.
(Class Handout)
- A
view of the hydrophobic effect, Southhall, N.T., Dill K.A., Haymet,
A.D.J., J
Phys Chem B 106, 521-33 (2002).
- HOMEWORK and Notes 02/08.
- New: Lecture Notes 3_6_05
Optional
- Water structure changes
induced by hydrophobic and polar solutes revealed by simulations and
infrared spectroscopy, Sharp, K.A., et.al. J Chem. Phys. 114,
1791-96 (2001).
|
5 (2/15)
|
Molecular Mechanics:
Force Field and Solvation
|
Maestro
and Macromodel
Course: 5%
Due:
Tuesday 2/22
Homework
Modeling:
Due: Friday, 3/4
|
- Development
and Testing of the OPLS All-Atom Force Field on Conformational
Energetics and Properties of Organic Liquids, Jorgensen, W.L., Maxwell.
D.S. , Tirado-Rives, J.,JACS
118 : 11225 (1996).
- Class Notes Force
Fields ppt or pdf
Class Notes
Molecular Dynamics
(ppt) or pdf
Optional
- A
Second Generation Force Field for the Simulation of
Proteins, Nucleic Acids, and Organic Molecules, Kollman, P.A., et. al.
JACS
117, 5179 (1995).
- All-Atom
Empirical Potential for Molecular Modeling and Dynamics Studies of
Proteins, Karplus, M, et. al., J
Phys Chem B 102, 3586 (1998).
- Parametrization
of Aliphatic CHn United
Atoms of GROMOS96 Force Field, van Gunsteren, F. et. al., J
Comp Chem 19 : 535 (1998).
|
6 (2/22)
|
Molecular Dynamics
and Samplings |
Molecular
Dynamics of BPTI
Course : 5%
Due:
Tuesday 3/11 |
- Novel
methods of sampling phase space in the simulation of biological
systems, Berne, B. , Straub. J.E., Curr
Opin Struct Biol 7, 181-9 (1997)
- Molecular
dynamics simulations of biomolecules, Karplus, M., McCammon, Nat
Struct Biol 9, 646-52 (2002).
Class Notes Solvent Models
(ppt) or pdf
New: Polarizable
Force Field Notes ppt
Optional
- Generalized-Ensemble
Algorithms for MolecularSimulations
of Biopolymers, Okamoto, Y. et. al.. Biopolymers
60, 96-123 (2001).
- GROMACS
3.0: a package for molecular simulation and trajectory analysis,
Lindahl, E., Hess, B., van der Spoel, D. , J
Mol Model 7, 306-17 (2001).
|
7 (3/1) |
Protein Folding Kinetics
|
Molecular
Dynamics of BPTI
Course : 5%
Due:
Tuesday 3/8
|
- Methods
for exploring early events in protein folding, Roder, H.,Shastry, R.,Curr
Open Struct Biol 9, 620-6 (1999).
- Dependence
on Solution Conditions of Aggregation and Amyloid Formation by an SH3
domain, Dobson. C.M. et. al.,
J.Mol.Biol. 311, 325-40 (2001)
New: Class notes on Protein Folding
Optional
- The fast protein folding
problem, Gruebele,M., Annu
Rev Phys Chem 50, 485-516 (1999).
- GROMACS
3.0: a package for molecular simulation and trajectory analysis,
Lindahl, E., Hess, B., van der Spoel, D. , J
Mol Model 7, 306-17 (2001).
|
8 (3/8) |
Sequence Homology
and
Structural Similarity |
Homology in Gene Sequences
Course: 5%
Due: TBA
|
- Branden and Tooze : Ch 1-5.
- Gapped
BLAST and PSI-BLAST: a new generation of database search programs.
Lipman. D.J., et.al. Nucleic
Acids Res. 25, 3389-402 (1997).
- PDBsum:
summaries and analyses of PDB structures, Laskowski, R.A.,
Nucleic
Acids Res. 29, 221-2 (2001).
- Reliability
of Assessment of Protein Structure Prediction, Rost, B., Sali A.,
et.al. MethodsStruct.
10, 435-40 (2002).
- Local
Alignment Statistics, Gusfield, D. and Stelling, P., Methods Enzymol.
266, 460-80 (1996).
- Protein
Modelling for all, TIBS
24, 364-7 (1999)
- BLAST
course
- Identification of common molecular subsequences, Smith,
T.F., Waterman, M.S., J. Mol. Biol. 147, 195-7 (1981)
- New: Class
Notes Correlation_function
- New: Class Notes
Sequence_Align_Scores.pdf
|
9
(3/14) |
******* * * * SPRING BREAK * * * *****
|
10
(3/22)
|
MIDTERM
TUESDAY IN CLASS
(Review Session:
Wednesday, March) 16th
4-5 pm in 320 Havemayer
New: Review session: Rfree
and E value (BLAST)
Old Midterms as pdf: #1 #2
|
3/25
|
Introduction on NMR
Method
|
|
1. NMR O handout in Class
2. NMR 1 handout in Class |
3/29 |
NMR -
Chemical shifts and proteins |
|
|
4/5
|
NMR - Bloch equation
|
Mathematica
simulation of NMR spectra
Course : 5%
Due: 4/19
|
- Protein
Folding Intermediates and Pathways Studied by Hydrogen Exchange,
Englander S.W., Annu
Rev Biophys Biomol Struct 29, 213-38 (2000).
|
4/12
|
NMR- Relaxation and the NOE |
Homework Question1
Due:
Homework Question2
Due:
|
NMR
notes (not necessarly complete), handouts are more relevant: NMR.ppt
|
TBA |
HIV
Protease
|
Special Projects
(select one from the following projects, prepare a webpage and a brief
presentation)
|
- Structural
and biochemical studies of retroviral proteases, Wlodawer A.,
Gustschina, A., Biochim
Biophys Acta 1477, 16-34 (2000).
- Rapid structural
fluctuations of the free HIV protease
flaps in solution: Relationship to crystal structures and
comparison with predictions of dynamics calculations, D. Torchia et.al.
Protein Science (2002), 11:221–232.
- Role of
Conformational Fluctuations in the Enzymatic
Reaction of HIV-1 Protease, Parrinello et. al. J. Mol. Biol. (2002)
319, 567–583.
- Protein dynamics
from NMR, D. Torchia et. al., Nature
Struct. Biol, 7 (2000) 740-744.
- Flexibility and Function
in HIV Protease: Dynamics of the
HIV-1 Protease Bound to the Asymmetric Inhibitor Kynostatin 272
(KNI-272), D. Torchia et. al., J. Am. Chem. Soc. 1998, 120, 7916-7923.
Notes (ppt): HIV protease
|
TBA |
HIV
Protease |
- Branden and Tooze : Ch 11.
|
TBA |
Potassium Channels
|
- The Structure of the Potassium Channel:
Molecular Basis of K1 Conduction and Selectivity, McKinnon, R., et.
al.. Science 280, 69-77 (1998).
- Branden and Tooze : Ch 12.
|
3/05
|
Special Projects
|
Presentations in Havemeyer 711
|
5/10
|
FINAL EXAM
May 10th 2005
209 Havemeyer, 4:10 to
7pm
(Review Session: Saturday, May 7th)
2-4 pm in 711 Havemayer !!!
Old Final as pdf: Final2003
|
