BIOQUANT > Research Groups > Genome Organization & Function > Teaching > Interactions of Proteins and Nucleic Acids I (1-8)
Physico-Chemical Methods in Systems Biology - Submodule for Major on Systems Biology - Lectures & Excercises by Karsten Rippe
Program Major Systems Biology
Biophysics books
- K. E. van Holde, W. C. Johnson, & S. P. Ho, Principles of Physical Biochemistry 2nd edition, Prentice-Hall, 2006
- C. Cantor und P. Schimmel, Biophysical Chemistry, Vol I, II und III, Freeman Press, 1980
- M. Daune, Molecular Biophysics, Oxford University Press, 1999
- P. Nelson, Biological Physics, Freeman, 2004.
- I. N. Serdyuk, N. R. Zaccai & J. Zaccai, Methods in Molecular Biophysics: Structure, Dynamics, Function, Cambridge University Press, 2007
Seminar papers
- Slattery et al. (2014). Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 39, 381–399
- Dill et al. (2011). Physical limits of cells and proteomes. Proc Natl Acad Sci USA 108, 17876–17882
- Poorey et al. (2013). Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science 342, 369–372
- Baum et al. (2014). Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells. Nat Commun 5, 4494
- Redding et al. (2015). Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System. Cell 163, 854–865
- Erdel & Greene (2016). Generalized nucleation and looping model for epigenetic memory of histone modifications. Proc Natl Acad Sci USA.
01 Interactions between macromolecules, July 6, 2016
- Lecture slides Interactions between macromolecules
- Bionumbers database: http://bionumbers.hms.harvard.edu
- R. Milo & R. Philipps, Cell Biology by the Numbers, 2015. Download pdf draft, web page http://book.bionumbers.org
- Timescales in cell biology
- Key numbers in cell biology
Additional reading "hydrophobic effect"
- Summary nonbonding interactions (van Holde) (14 MB)
- Key reference: The hydrophobic effect (Tanford 1962)
- Hydrogen bonds make a major contribution to protein stability (Pace et al. 2004)
- Hydrogen bonds make a major contribution to protein stability, see Honig 1999, section "The free energy balance"
- Sharp, K.A. & Honig, B. (1990). Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19, 301-32.
- Protein denaturation by Urea (Nozaki & Tanford 1963)
Additional reading "Induced fit model" for site specific protein binding to DNA
- Key reference "Induced fit model" site specific protein binding to DNA (Spolar & Record, 1994)
- Comment Peter von Hippel on Spolar & Record paper
- Comment Stephen Burley on Spolar & Record paper
3D structure coordinates in pdb format
02 Enthalpy and Entropy of Protein-DNA interactions, July 7, 2016
Additional reading
- Introduction to ligand binding (Rippe, 1997)
- Key reference Entropy/Enthalpy in Protein-DNA complexes (Jen-Jacobson, 2000)
- Review of Lac repressor structures (Charalampos, 2004)
- Specific vs unspecific complex, NMR structure
- Comment Peter von Hippel on NMR structure
- Thermodynamic analysis of specific and unspecific LacI-DNA complexes
3D structure coordinates in pdb format
- Lac repressor complete dimer + SymL DNA, crystal structure
- Lac repressor head piece + SymL DNA, NMR
- Lac repressor head piece + O1 DNA, NMR
- Lac repressor head piece + unspecific DNA, NMR
- Lac repressor head piece + Operator DNA
- TATA box binding protein (TBP) + promoter DNA
- CAP (Catabolite Gene Activator Protein) + DNA
- Lambda C1 repressor + operator DNA
- GCN4 + AP-1 DNA
Links background
- phi and psi angles peptide backbone (Power Point file)
- Torsion/dihedral angle (Flash animation)
- Protein synthesis.pdf
- Movie protein synthesis, overview (8 Mb)
- Movie protein synthesis, detailed (32 Mb)
- RCSB Protein Data Bank (pdb)
- VMD molecular visualization program
- RCSB Protein Data Bank (pdb)
- VMD molecular visualization program
03 Ligand binding, July 7, 2016
Contact: E-Mail
