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Core C-2: NMR Center P.I. C. Allen Bush [[email protected] ] Director: Bruce Johnson [ [email protected] ] Newly Installed Instrumentation Four Bruker 3-channel Avance III consoles with cryoprobe 500, 600 MHz, 800 MHz and 950 MHz All have identical Topspin 3.2 software Data processing and analysis facility Data easily networked off-site Funds available for training and exploratory work

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Page 1: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

Core C-2: NMR CenterP.I. C. Allen Bush [[email protected]]

Director: Bruce Johnson [[email protected]]

Newly Installed InstrumentationFour Bruker 3-channel Avance III consoles with

cryoprobe500, 600 MHz, 800 MHz and 950 MHzAll have identical Topspin 3.2 software

Data processing and analysis facilityData easily networked off-site

Funds available for training and exploratory work

mailto:[email protected]
mailto:[email protected]
Page 2: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

NMR Spectrometer

An NMR instrument is composed of a magnet, a computer and a box of radios.

Page 3: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 4: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

Free induction decay

FID spectrum

Page 5: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 6: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 7: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 8: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 9: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

Diaxial protons in -anomer > large J coupling valueEquatorial protons (gauche) in -anomer > smallJ coupling value

Page 10: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 11: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 12: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 13: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

In the 2-d COSY spectrum the directly detected FID(blue) is recorded as the interval between the pulsesis incremented (the indirect dimension.)

Page 14: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 15: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 16: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

Tocsy spectrum- pneumococcal CPS type 10F

Page 17: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 18: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

Cosy spectrum- pneumococcal CPS type 10F

Page 19: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 20: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 21: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

1H-13C HSQC spectrum of CPS of S. pneumoniae type 39

Anomeric signals Central region of spectrum

Page 22: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 23: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

What can NMR do ?Structure, conformation, ligand binding

Oligosaccharide, glycopeptides, polysaccharide, glycolipid

Small protein (<30kD), peptide

Ligand binding to (large) protein

Cannot do

1. small sample (<100 g)

2. insoluble solids3. big protein (>50kD)

Page 24: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

Practical Aspects

Choice of Solvents – D2O for:Oligosaccharides, glycopeptides, polysaccharides

D2O exchange: Lyophilize from D2O

Other solvents (deuterated form): DMSO, CD3OD, CDCl3:

Page 25: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

What can you see ?

protons – 1H bonded to carbon

Amide protons in H2O (sometimes)

Hydroxyl protons exchange rapidly in D2O

Page 26: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

NMR Sample Requirements

1. Reasonably pure sample (~80%). Any impurity is readily obvious from the spectrum

2. High resolution NMR requires true solubility – cloudy solutions pose problems

3. Sample size: 1 micromole is good, 100 nM is OK. More sample provides more information, eg. 1H-13C heteronuclear data in natural abundance

4. Isotope enrichment often used. eg. 13C, 15N in peptides or proteins

Page 27: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

NMR Data Lab

Page 28: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 29: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 30: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

Martin-Pastor and Bush, Biochemistry, 39, 4674-4683 (2000)

Page 31: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 32: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 33: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation
Page 34: Core C-2: NMR Center P.I. C. Allen Bush [bush@umbc.edu]bush@umbc.edu Director: Bruce Johnson [johnsonb@umbc.edu]johnsonb@umbc.edu Newly Installed Instrumentation

[ PO46GalNAc13Rha14Glc16Galf16GalNAc13Gal1] n

[ PO46GalNAc13Rha14Glc16Galf16GalNAc13Gal1] n

Rha12

[ PO46GalNAc13Rha14Glc16Galf16Gal13GalNAc1] n

Rha12

1Gn (S. oralis 34)

2Gn (S. gordonii 38)

2G (S. mitis J22)

RPS Type (strain) Antigenic Region Receptor Region

Structural Types of Receptor Polysaccharides (RPSs)

3G (S. oralis ATCC 10557) [ PO46Gal13Rha14Glc13Galf16Gal13GalNAc1] n

2 6(OAc)0.33

(OAc)0.33

[ 1ribitol5 PO46Galf13Gal16Galf16GalNAc13Gal1] n 4Gn (S. oralis C104)

[ 3ribitol5 PO46Galf13Gal16Galf16GalNAc13Gal1] n 5Gn (S. oralis SK144)


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