Presentations:

• NMR & Mass Spectroscopy and Biomolecular Structure

Readings and Resources:

• NMR Spectrometry
  • Rubinson, Kenneth A. and Rubinson, Judith F. ; "Nuclear Magnetic Resonance Spectroscopy;" Chapter 11: Contemporary Instrumental Analysis; Prentice Hall Press; 2000. [pdf]
  • Friebolin, Horst; "Basic One-and Two-Dimensional NMR Spectroscopy;" Wiley-VHC; 2005.
  • Wüthrich, Kurt; "NMR of Proteins and Nucleic Acids;" Wiley-Interscience; 1986.
  • Clark, Jim; "Chemguide: Understanding Chemistry, NMR Spectroscopy;" 2005 [html]
  • James Keeler's NMR Tutorial [html]
  • ¹H-NMR Proton Resonance Assignments for Amino Acids in Peptides. [pdf]
  • Overview of the the 2002 Nobel Prizes in Chemistry [pdf]
  • Kurt Wüthrich's 2002 Nobel Lecture [pdf] (Please read this one.)
  • The Biological Magnetic Resonance Data Bank [html]
• Mass Spectrometry
  • John Fenn's 2002 Nobel Lecture [pdf] (Please read this one.)
  • Exact masses for the amino acids [pdf]

Applications:

• Bruker Topspin 2.1.6
  • This is the application that you used to collect your spectra. You can also use it to process your data. It is used to be available on nearly all of the Windows PC's on campus until the Windows 7 upgrade(?) occured.
• iNMR
  • This application can also be used to process your data. It is located on the two Mac's in P468. You will need to Map to the deptdir drive to access your data (\\cass1\deptdir\chem\Instruments\NMR\chem453_F11)
  • Use iNMR to process spectra and create input files for Sparky
  • There are manuals and tutorials available at the inmr site (http://www.inmr.net/)
• ACD/NMR Processor
  • This application can be used to process your data. It is located on the PC's in P468 and elsewhere on campus. You will need to Map to the deptdir drive to access your data (\\students\deptdir\chem\Instruments\NMR\chem453_F12)
• Sparky
  • This is a free application that is used to make resonance ansignments using 2D-NMR spectra. Spectra processed with iNMR can be saved in a format that can be read by Sparky. If you want your own copy of Sparky you can download it from http://www.cgl.ucsf.edu/home/sparky/. An online manual for Sparky can be found at http://www.cgl.ucsf.edu/home/sparky/manual/index.html
• ChemDoodle
  • This a a structure application that you can use to draw structures of your amino acids and peptides [html]
  • If you save your structures as MDL Molfiles you can reload them into ChemDoodle by copying-and-pasting the contents of .mol file into the text box that comes up when you click on the Load icon.
  • You can also use ChemDoodle to create a 3D model of your amino acids and petides [html]
  • ChemDoodle is also able to simulate the NMR and Mass spectra of your amino acids and peptides [html]

Tasks:

• Week 1 (121115-121119)
  • Sit through overview of mass spectrometry and NMR spectrometry, with emphasis on the contributions of John Fenn and Kurt Wüthrich.
  • Mass spec analysis of dipeptide unknowns. Will work in groups of two.
  • Each group will be given a vial contain 10 to 15 mg of and unknown dipeptide.
    • Dissolve 1 mg of unknown dipeptide in 1 mL H₂O
      • Dilute 10 μL to 1.0 mL (1/100) with H₂O for UV/Vis analysis
      • Dilute 20 μL to 500 μL (1/25 dilution) with H₂O and plance in an HPLC vial for the LC/MS analysis
    • Perform LS/MS runs on your unknown dipeptides and predict its amino acid composition from its observed mass.
• Week 2 (121126-121129)
  • Sit through the presentation and demonstration on using Topspin to collect 1D and 2D spectra and iNMR for processing spectra.
    • Set temperature (edte)
    • Lock (lock)
    • Tune and match the probe (atma)
    • Shim the magnet (topshim)
    • Determine the offset and 90° pulse width (paropt on p1, look for 360° null)
    • Set receiver gain (rga)
    • Run (zg) 1D proton with WATERGATE solvent suppresion (P3913GP)
    • Run (zg) 2D TOCSY with WATERGATE solvent suppression (MLEVGPPH19SW)
  • Make up 10 mM samples of your unknown in 650 μL 90% H₂O/10% D₂O
    • Check to make certain that all material dissolve, if not the case, spin in microfuge for 5 min.
    • Transfer to clean, labeled NMR tube.
  • Run spectra
    • 1D proton with WATERGATE solvent suppression (P3913GP)
    • 2D TOCSY with WATERGATE solvent suppression (MLEVGPPH19SW)
    • 2D ¹³C-HSQC (HSQCEDETGP)
  • Make ¹H and ¹³C assignments and identify the dipeptide sequence
• Week 3 (121203-121206)
  • Use iNMR to process your dipeptide spectru and share your dipeptide results with the other members of the class. We are interested in discerning the different patterns that are characteristic for the different amino acids.
  • Evaluate the LC/MS run for the unknown oligopeptide and estimate the number of amino acid residues that it contains
  • Working in your groups of 2, begin using Sparky to analyze the NMR experiments for the unknown oligopeptide in DMSO. Your goal is to determine both the amino acid composition and sequence for this oligopeptide.
    • 1D-proton
    • 2D-COSY (Observe through bond couplings between ¹H's that are separated by 2-3 bonds)
    • 2D-TOCSY (Similar to the COSY spectrum, but shows all members of a spin system for each member of a spin system)
    • 2D-ROESY (Observer though space couplings between ¹H's that are separated by < 5Å)
    • 2D-¹³C-HSQC (Observe through bond couplings between ¹H's and ¹³C for those pairs that are directly bonded to one another)
    • 2D-¹³C-HMBC (Observe through bond couplings between ¹H's and ¹³C for those pairs that are 2 to 4 bonds apart, but not directly bonded to one another)
  • A packacge containing the NMR and mass spectral data for the oligopeptide can be downloaded here.
  • Using the TOCSY, COSY and HSQC spectra, identify the spin systems and likely amino acid candidates for these spin systems
    • iNMR is the recommended application for processing the spectra and Sparky is the recommended application for making assignments.
  • Using the ROESY and HMBC spectra to propose a sequence for the oligopeptides.
• Week 4 (121210-121213)
  • In groups of two, use Sparky to analyze the spectra collected on the unknown oligopeptide
  • Make proton and ¹³C assignments, identify the amino acids from their spin systems, and use interresidue couplings to sequence the oligopeptide.

Assignment:

• Download copies of the worksheet here [pdf] [docx]
• Worksheet are due by 4:00 pm on on the day that your Final Exam is scheduled (Tuesday, 18. December for Section 002 or Friday, 21. December for Section 001).