BIOQUANT > Research Groups > Genome Organization & Function > Teaching > Interactions of Proteins and Nucleic Acids I (1-8)
Interactions of Proteins and Nucleic Acids - Biophysical Concepts and Theoretical Descriptions
01 Introduction on DNA, RNA, proteins and protein-DNA complexes, Oct 14, 2014
02 The energy, length and time coordinate system, Oct 21, 2014
Problem set 1, due Tuesday, Oct 28
Additional reading
- 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)
03 Thermodynamics of protein-DNA interactions, Oct 28, 2014
04 Diffusion, Oct 30
Problem set 2, due Wednesday, Nov 6
Additional reading
- Hydrodynamics Review by Bloomfield
- Key reference: Berg & von Hippel, Diffusion controlled reactions
- Berg & von Hippel, review on protein target location
- Halford & Marko, review on protein target location
- Halford, measurements on target location by restriction enyzmes
- Widom, review on protein target location
- Shimamoto, review on 1D diffusion
05 Kinetics of DNA/RNA/Protein interactions, Nov 6
Problem set 3, due Wednesday, Nov 13
Additional reading
- Michaelis-Menten Equation
- Copasi simulation program
- Copasi manual
- Publication describing Copasi
- Copasi parameter file remodeler nucleosome translocation mechanism (text files with extension ".cps")
- Copasi parameter file Michaelis-Menten Kinetics (text file with extension ".cps")
- Copasi parameter file transcription factor NF-kappaB Oscillation (text file with extension ".cps")
- Overview kinetic modeler programs
06 Essentials of protein-DNA/RNA interactions, Nov 13
Additional reading
- The DNA double helix (Watson, J.D., andF.H. Crick. 1953. A structure for deoxyribose nucleic acid. Nature 171:737-738)
- B-DNA 12mer Crystal structure (Drew, H.R., R.M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, andR.E. Dickerson. 1981. Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci U S A 78:2179-2183)
- Kneale, G., Brown, T., Kennard, O. & Rabinovich, D. (1985). G . T base-pairs in a DNA helix: the crystal structure of d(G-G-G-G-T-C-C-C). J. Mol. Biol 186, 805-14.
- The DNA double helix (Watson, J.D., andF.H. Crick. 1953. A structure for deoxyribose nucleic acid. Nature 171:737-738)
- Review on Z-DNA (Rich, A., andS. Zhang. 2003. Timeline: Z-DNA: the long road to biological function. Nat Rev Genet 4, 566-572)
- The B-Z-DNA junction (Ha, S.C., K. Lowenhaupt, A. Rich, Y.G. Kim, and K.K. Kim. 2005. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437:1183-1186
- Paper by Schalch et al on Tetranucleosome structure
Problem set 4, due Wednesday, Nov 20
3D structure coordinates for problems set #4
- coordinates for "DNA_unusal.pdb"
- canonical B-DNA duplex "B-DNA_20mer.pdb"
- TATA box binding protein (TBP) with DNA
- TBP protein alone
- coordinates B-Z-DNA junction with Z-DNA binding peptide
other 3D structure coordinates in pdb format
- 3D coordinates of B-DNA 12mer with K+ counter ions from crystal structure
- DNA with unusual base pair
- Tripeptide
- coordinates nucleosome.pdb
Links
- phi and psi angles peptide backbone (Power Point file)
- Torsion/dihedral angle (Flash animation)
- RCSB Protein Data Bank (pdb)
- VMD molecular visualization program
- VMD tutorial
- Coordinates of ubiquitin for VMD tutorial
06 Enthalyp-Entropy distribution, November 20, 2013, starts at 10:30!
Additional reading
07 Ligand binding and local folding, November 27, 2013, starts at 10:30!
Problem set 5, due Wednesday, Dec 4
Additional reading
- Introduction to ligand binding (Rippe, 1997)
- 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
- Structure analysis of Lac repressor and its complexes with DNA
3D structure coordinates in pdb format
- Lac repressor pdb coordinates (protein only)
- Lac repressor + DNA pdb coordinates
- 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
08 Complex ligand binding, December 4, 2013
Additional reading
- Forces+hydrophobic_effect.pdf
- 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
09 Dynamic interactions in the cell nucleus, Dec 11, 2013
Problem set 6, due Wednesday, December 18
Additional reading
- Review mobility in the nucleus, Görisch et al. 2005
- Genome dynamics and stability, Wachmuth et al. 2008
10 Chromatin organization and intro to fluorescence microscopy, Dec 18, 2013
Problem set 7, due Wednesday, January 15
11 Fluorescence microscopy/spectroscopy and diffusion reaction kinetics, Jan 8, 2014
- Fluorescence fluorescence microscopy: Fluorescence bleaching and correlation methods (updated again)
Additional reading
- Protein mobility maps, Erdel et al. 2010
- FRAP bleach frame analysis: Pixel-wise Photobleaching Profile Evolution Analysis - 3PEA, Erdel & Rippe, 2012
12 Cross-correlation analysis for mapping protein interactions and the cellular environment, Jan 15+22, 2014
- Protein interaction analysis in living cells
- Mapping the cellulare environment from a protein's point of view
Problem set 8, due Wednesday, January 22
13 Protein-protein interactions mediated by DNA-looping, Feb 5, 2014
- Intro Protein contacts mediated by looping of DNA and RNA
- Experimental studies of interactions that involve DNA/RNA looping
Problem set 9, due Wednesday, January 29
Additional reading
- Simulation of one-dimensional diffusion
- Key reference: Rippe, Looping mediated contacts on nucleic acids
- Chromosome conformation capture assay
14 Mapping protein-DNA/RNA interactions by genome-wide sequencing, Feb 12, 2014
Contact: E-Mail
