BMB961 - FS07

Dynamics and Interactions of Proteins and Nucleic Acids

InstructorsMichael Feig (
Leslie Kuhn (
Maria Zavodszky (
Lecture:3:00 p.m. - 3:50 p.m. Tuesday in BCH 502A
Computer Lab:3:00 p.m. - 5:00 p.m. Thursday in BCH 202
Lecture 8/28 Proteins and nucleic acids Feig
Lab 8/30 Setup, UNIX intro, pyMol tutorial Feig
Assigned Reading A Conversation with James D. Watson: Scientific American, April 2003, online

Lecture 9/4 Intro to Docking and Scoring Kuhn
Lab 9/6 Intro to Docking and Scoring Kuhn
Assigned Reading D. Kitchen, H. Decornez, J. Furr, J. Bajorath: Docking and Scoring in Virtual Screening for Drug Discovery: Methods and Applications, Nature Reviews (2004), 3, 935-949 PDF
I. Kuntz: Structure-Based Strategies for Drug Design and Discovery, Science (1992), 257, 1078-1082 PDF

Lecture 9/11 Protein-protein Docking Zavodszky
Lab 9/13 Protein-protein Docking Zavodszky
Assigned Reading Zhou HX, Qin S. Interaction-Site Prediction for Protein Complexes: a Critical Assessment.Bioinformatics. 2007 Jun 22; [Epub ahead of print] PDF
Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol. 2002 Feb;12(1):28-35 PDF

Lecture 9/18 Flexibility Modeling Zavodszky
Lab 9/20 Flexibility Modeling Zavodszky
Assigned Reading Carlson HA. Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol. 2002 Aug;6(4):447-52 PDF
Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol. 2006 Apr;16(2):194-200 PDF

Lecture 9/25 Small Molecule Docking Kuhn
Lab 9/27 Small Molecule Docking Kuhn
Assigned Reading Slide Quick Guide 3.0a PDF
M. Zavodszky, P. C. Sanschagrin, R. S. Korde, L. A. Kuhn: Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J. Comp. Aid. Mol. Des. (2002) 16, 883-902 PDF

Lecture 10/2 Ligand Screening Kuhn
Lab 10/4 Ligand Screening Kuhn
Assigned Reading

Lecture 10/9 Molecular dynamics simulations Feig
Lab 10/11 First molecular dynamics simulations
MD projects are assigned Feig
Assigned Reading A. D. MacKerell jr.: Empirical Force Fields for Biological Macromolecules: Overview and Issues, J. Comp. Chem. (2004) 25, 1584-1604 PDF
W. F. van Gunsteren, A. E. Mark: Validation of molecular dyanmics simulation, J. Chem. Phys. (1998) 108, 6109-6116 PDF

Lecture 10/16 Simulating biological environments Feig
Lab 10/18 Explicit vs. implicit solvent simulations Feig
Assigned Reading V. Makarov, B. M. Pettitt, M. Feig: Solvation and Hydration of Proteins and Nucleic Acids: A Theoretical View of Simulation and Experiment, Accounts of Chemical Research (2002) 35, 376-384 PDF
B. Roux, T. Simonson: Implicit solvent models, Biophysical Chemistry (1999) 78, 1-20 PDF

Lecture 10/23 Trajectory analysis Feig
Lab 10/25 Trajectory analysis Feig
Assigned Reading P. Auffinger, L. Bielecki, E. Westhof: The Mg2+ Binding Sites of the 5S rRNA Loop E Motif as Investigated by Molecular Dynamics Simulations, Chemistry & Biology (2003) 10, 551-561 PDF
A. Grossfield, S. Feller, M. Pitman: Convergence of molecular dynamics simulations of membrane proteins. Proteins (2007) 67, 31-40 PDF

Lecture 10/30 Enhanced sampling Feig
Lab 11/1 Biased sampling/replica exchange Feig
Assigned Reading S.Izrailev,S.Stepaniants,B.Isralewitz,D.Kosztin,H.Lu, F.Molnar,W.Wriggers,and K.Schulten: Steered Molecular Dynamics PDF
A. Mitsutake, Y. Sugita, and Y. Okamoto: Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers (Peptide Science) (2001) 60, 96-123 PDF

Lecture 11/6 Free energy calculations Feig
Lab 11/8 MMPB/SA analysis Feig
Assigned Reading P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417 PDF

Lecture 11/13 Dynamic mode analysis Feig
Lab 11/15 Mode analysis Feig
Assigned Reading A. W. van Wynsberghe, Q. Cui: Comparison of Mode Analyses at Different Resolutions Applied to Nucleic Acid Systems. Biophysical Journal (2005) 89, 2939-2949 PDF
AJ Rader. Chakra Chennubhotla, Lee-Wei Yang, and Ivet Bahar: The Gaussian Network Model: Theory and "Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems" Eds Qiang Cui and I Bahar, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006. PDF

Lecture 11/20 MD project discussions Feig
Lab 11/22 Thanksgiving: NO LAB

Lecture 11/27 Student presentations (30 min. each):
Linxia Zhang & Ming Wu
Lecture 11/29 Student presentations (30 min. each):
Chao Li & Yujie Chen

Lecture 12/4 Student presentations (30 min. each):
Rahman Saleem & Sean Law
Lecture 12/6 Student presentations (30 min. each):
Maryam Sayadi & Cun Liu & Kin Lee

Finals 12/14 Project write-up is due
Suggested Texts Andrew R. Leach: Molecular Modelling: Principles and Applications, 2001, Pearson Education
on reserve at MSU Math library
Tamar Schlick: Molecular Modeling and Simulation: An Interdisciplinary Guide, 2002, Springer
on reserve at BPS library
Kensal van Holde, Curtis Johnson, Shing Ho: Principles of Physical Biochemistry, 2006, Pearson Education
Nelson, Cox: Lehninger Principles of Biochemistry, 2005, Freeman & Co.
on reserve at BPS library
GradesBased on homework during first part of course (40%), project presentation (30%) and write-up (30%).

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