Here are the references for the first few class meetings. The easiest way to find them is to use PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi The PubMed ID (PMID) is given for most papers. One theme of the course is the potential for substantial interaction between "omics" (e.g., genomics and proteomics) and physical chemistry (PChem). Thursday, 1 April 2004 Ridg Scott presenting ---------------------- ---------------------- We begin by looking at basic genomics. DNA microarrays have revolutionized the acquistion of gene expression data. We look at the structure of noise (non-specific hybridization) in DNA microarrays and proposals for dealing with it. Li, C., and Wong, W. H. Model-based analysis of oligonecleotide arrays: expression index computation and outlier detection. Proc.Natl.Acad.Sci.U.S.A. 98 (2001), 31-36. PMID: 11134512 Tobler, J. B., Molla, M. N., Nuwaysir, E. F., Green, R. D., and Shavlik, J. W. Evaluating machine learning approaches for aiding probe selection for gene-expression arrays. Bioinformatics 18 (2002), S164-S171. PMID: 12169544 Tuesday, 6 April 2004 Ridg Scott presenting ---------------------- ---------------------- People have suggested chosing oligos based on sequence composition. Li, F., and Stormo, G. D. Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 17, 11 (2001), 1067-76. PMID: 11724738 Owczarzy, R., Vallone, P. M., Gallo, F. J., Paner, T. M., Lane, M. J., and Benight, A. S. Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers 44, 3 (1997), 217-239. PMID: 9591477 Thursday, 8 April 2004 ---------------------- ---------------------- The following papers kick things off with proteomics. The first also provides a review of terminology about structural motifs. Daniel Chasman and R. Mark Adams Predicting the Functional Consequences of Non-Synonymous Single Nucleotide Polymorphisms: Structure-Based Assessment of Amino Acid Variation J Mol Biol. 2001 307 683-706 PMID: 11254390 Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol. 1996 Jul 26;260(4):604-20. PMID: 8759323 Tuesday, 13 April 2004 ---------------------- ---------------------- Hydrogen bonds are the most common bond holding proteins together. The first paper shows how a database can be used to understand better how they function. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol. 2003 Feb 28;326(4):1239-59. PMID: 12589766 Vila JA, Ripoll DR, Scheraga HA. Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13075-9. PMID: 11078529 Thursday, 15 April 2004 ---------------------- ---------------------- Water is the basis for life as we know it. The Hydrophobic Effect is critical to protein-protein binding as well as elsewhere in biology. These papers give us a start on this issue. Southall, N.T., K.A. Dill, and A.D.J. Haymet. A View of the Hydrophobic Effect. Journal of Physical Chemistry B 106: 521-533 (2002). PMID: ? Fernandez A, Scheraga HA. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):113-8. Epub 2002 Dec 23. PMID: 12518060 Tuesday, 20 April 2004 ---------------------- ---------------------- Everything is made of protein complexes. What determines how they bind? Why are we not just blobs of proteins? The hydrophobic effect appears to play a role, but it is much more specific than when it causes fat to avoid water. Here are a couple of suggestions. Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14116-21. Epub 2002 Oct 15. PMID: 12381794 Ariel Fernandez, L. Ridgway Scott and Harold A. Scheraga. Amino-acid residues at protein-protein interfaces: Why is propensity so different from relative abundance? J. Phys. Chem. B, 107, no. 36, 9929-9932 (2003). PMID: ? Thursday, 22 April 2004 ----------------------- ---------------------- We continue the discussion of protein complexes and what determines how they bind. Ma B, Elkayam T, Wolfson H, Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5772-7. Epub 2003 May 01. PMID: 12730379 Ariel Fernandez and L. Ridgway Scott. Dehydron: a structurally encoded signal for protein interaction. Biophysical Journal 85, 1914-1928 (2003). PMID: ? Tuesday, 27 April 2004 ---------------------- ---------------------- Now we back up and look at what determines how proteins fold. Baker, D. A surprising simplicity to protein folding. Nature. 2000 May 4;405(6782):39-42. PMID: 10811210 Kristina Rogale and Ariel Fernández Protein folding: a good structure protector is also a good structure seeker Physics Letters A Volume 321, Issue 4, Pages 263-266 PMID: ? Thursday, 29 April 2004 Ridg Scott presenting ---------------------- ---------------------- Since water is essential to life, we should know how well we can model it. Breaking with tradition, we look at more than two papers, but they are quite short! Well, at least the take-home messages are short. Michael W. Mahoney and William L. Jorgensen A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions The Journal of Chemical Physics -- May 22, 2000 -- Volume 112, Issue 20, pp. 8910-8922 PMID: ? Michael W. Mahoney and William L. Jorgensen Diffusion constant of the TIP5P model of liquid water The Journal of Chemical Physics, 2001--Volume 114, Issue 1, pp. 363-366 PMID: ? Martin Lísal, Jií Kolafa and Ivo Nezbeda An examination of the five-site potential (TIP5P) for water The Journal of Chemical Physics, 2002--Volume 117, Issue 19, pp. 8892-8897 PMID: ? Sotiris S. Xantheas Cooperativity and hydrogen bonding network in water clusters, Chemical Physics, 2000 v. 258, Pages 225-231 You will get a break for the days 4-6 May. The remainder of the course schedule will be discussed in mid April.