Guide for literature readings relating to "NMR Fingerprints of Proteins" lectureMain reading:Discovering high-affinity ligands for proteins: SAR by NMRSB Shuker, PJ Hajduk, RP Meadows, SW Fesik, Science 274, 1531 (1996).optional additional reading:A polar, solvent-exposed residue can be essential for native protein structureRB Hill and WF DeGrado, Structure 8, 471 (2000).On Tuesday, January 28 or Thursday, January 30, we will spend some time discussingthe Shuker article in class. Be prepared to discuss the questions below. The ppt notesshould be a helpful companion in understanding a bit about what a 2D HSQC spectrumis, since this is the first time you will have seen a multidimensional NMR spectrum inthis class. This paper is sort of a segue into our learning about multidimensional NMR,and for now you can think of a 2D HSQC as a fancier version of a 1D spectrum in whicheach peak represents the intersection of the chemical shifts of a group of two covalentlybonded nuclei, rather than just a single chemical shift arising from a single nucleus. Inessence, it's a "fingerprint" of a protein that is spread out in an extra dimension, making iteasier to "read".The Hill & DeGrado article is optional, and relates to one of the slides in the NMRFingerprints ppt lecture. Although Shuker et al and Hill & DeGrado are very differentstudies, the two articles have in common the use of changes in simple 1D and 2D NMRspectra to detect changes in proteins due to structural alterations or ligand binding events.Shuker article:The “SAR by NMR” method produces high affinity ligands for a target protein using twoseparate NMR screening steps. These two steps involve binding of two differentmolecules to two different target sites, in each case with micromolar to millimolaraffinity. The two molecules are then linked to each other to form a single ligand withnanomolar to picomolar affinity. To enable effective linkage using short connectors, thetwo binding sites must be nearby each other but essentially nonoverlappingWhy not just screen for a single molecule with nanomolar to picomolar affinity in the firstplace?How do they make sure the two sites aren’t overlapping?How do they make sure the two sites are nearby each other?Why are 15N-1H HSQCspectra such good tools for a method like this?If you get to the Hill article, think about the following:Hill & DeGrado article:Rather than try to understand this article in its entirety and in depth, I’d like you to focuson how simple NMR spectra are being used to interpret the structural effects of mutationsin a designed protein. I’d like you to pay particular attention to the meaning of Figures 5,6 and 9:How do the authors interpret the differences in 1D NMR spectra for the position 7mutants (Figure 5)?What are some alternative explanations for the differences in 1D NMR spectra, and howdo they rule out these alternatives?What is the difference between Figures 5 and 6? Why do they include Figure 6?What model for the structure of the E7V mutant is being implied by Figure
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