New version page

Homework

This preview shows page 1 out of 2 pages.

View Full Document
View Full Document

End of preview. Want to read all 2 pages?

Upload your study docs or become a GradeBuddy member to access this document.

View Full Document
Unformatted text preview:

HW5-1. Due on Feb 15.Notes that you need in the comp lab.1) Not every machine has TopSpin software, the following drawings are the layout of the computers in the two labs, T means the software is there. Please pick one of the machines labeled as T.Computer Lab1 Computer Lab2T T T NoNo No T NoT T T NoNo No T TT T T Door Door2) Pelase check if you have the data directory <MB3_Jan2007>Type in the terminal window:cd /opt/topspin/data/guest/nmr/lsYou should see MB3_Jan20073) Double click on TopSpin1.3 icon on the desktop-ignore the error and the warning messages-on the left navigation bar click on /opt/topspin/navigate intodata guestMB3_Jan2007 Now each folder there contains one experiment.4) Comparison of all the spectra recordedIn preparation of this section, read the paper handed out to you: “NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline” (2005) by Rebecca Page, Wolfgang Peti, Ian A. Wilson, Raymond C. Stevens, and Kurt Wuthrich, PNAS 102 (6), 1901–1905. You can access the paper here. The username : MB3 the password: 2007You and your colleagues recorded six samples labeled A, B, D, E, F, H in the experimental setup portion of the NMR tutorial. Below are the Sample IDs mapped to the Experiment IDsSample IDs Experiment IDsB 1-7F 10-15A 20-23D 30-33E 40-43H 50-53B 60, 61F 70, 71F 100-103B 110-113Your next job is to compare the six samples with each other, and also to compare zg, zgpr, selabs, hsqcfpgpf3gphwg experimental results in each case. Some questions to think about:a. What are the differences between samples, and for a given sample between different experiments for that sample, what are the similarities? b. Why can you obtain NH signals in some but not all cases?c. What do you think is the difference in sample preparations?d. How would judge the quality of the spectra, is it likely that one can determine the structure of any of the samples given to you or your colleagues?Some useful pieces of information / reminders to help you in the analysis:1.) Pulse sequence detailszg = records all 1H's in your samplezgpr = same as zg but with water suppressionselabs = the way we set it up, it records only NH regionhsqcfpgpf3gphwg = in short: hsqc = records all 1H's attached to 15N2.) Chemical shift ranges of resonances encountered4.7ppm =water H20NH region ~ 7-11 pmOH region ~ 4-5 ppmCH2/CH3 < 3ppmaromatic CH ~ 5-7 ppmHint: The samples have one or more of the following contents: water, protein, and detergent


Loading Unlocking...
Login

Join to view Homework and access 3M+ class-specific study document.

or
We will never post anything without your permission.
Don't have an account?
Sign Up

Join to view Homework and access 3M+ class-specific study document.

or

By creating an account you agree to our Privacy Policy and Terms Of Use

Already a member?