Residue-specific structural kinetics of proteins through the union of isotope labeling, mid-IR pulse shaping, and coherent 2D IR spectroscopy.
We describe a methodology for studying protein kinetics using a rapid-scan technology for collecting 2D IR spectra. In conjunction with isotope labeling, 2D IR spectroscopy is able to probe the secondary structure and environment of individual residues in polypeptides and proteins. It is particularly useful for membrane and aggregate proteins. Our rapid-scan technology relies on a mid-IR pulse shaper that computer generates the pulse shapes, much like in an NMR spectrometer. With this device, data collection is faster, easier, and more accurate. We describe our 2D IR spectrometer, as well as protocols for (13)C(18)O isotope labeling, and then illustrate the technique with an application to the aggregation of the human islet amyloid polypeptide implicated in type 2 diabetes.
Middleton
Chris T
CT
Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1396, United States.
Woys
Ann Marie
AM
Mukherjee
Sudipta S
SS
Zanni
Martin T
MT
D000596:Amino Acids / Q000138:chemical synthesis; D000682:Amyloid / Q000737:chemistry; D002247:Carbon Isotopes; D006801:Humans; D007553:Isotope Labeling / Q000379:methods; D007700:Kinetics; D008565:Membrane Proteins / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular; D010103:Oxygen Isotopes; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013055:Spectrophotometry, Infrared / Q000295:instrumentation / Q000379:methods
D000596:Amino Acids; D000682:Amyloid; D002247:Carbon Isotopes; D008565:Membrane Proteins; D010103:Oxygen Isotopes; D011506:Proteins
J Am Chem Soc. 2008 May 28;130(21):6698-9
18459774
Opt Express. 2006 Dec 25;14(26):13120-30
19532209
Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7720-5
18499799
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2379-84
15699340
Phys Rev Lett. 1996 Aug 19;77(8):1648-1651
10063131
Proc Natl Acad Sci U S A. 2007 Sep 4;104(36):14237-42
17551015
Opt Express. 1998 Nov 9;3(10):366-75
19384383
Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17751-6
19815514
Org Lett. 2007 Nov 22;9(24):4935-7
17958432
J Mol Biol. 2000 Jul 21;300(4):677-85
10891262
Methods Enzymol. 1990;193:338-48
2074825
Langmuir. 2007 Nov 6;23(23):11677-83
17939695
J Am Chem Soc. 2009 Mar 11;131(9):3385-91
19256572
Proc Natl Acad Sci U S A. 2007 Sep 4;104(36):14197-202
17502604
Biochemistry. 2010 Feb 9;49(5):872-81
20028124
Annu Rev Phys Chem. 2009;60:21-38
18851709
Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5759-64
8650166
Acc Chem Res. 2006 Mar;39(3):169-75
16548505
Opt Express. 2003 May 5;11(9):1021-8
19465966
Org Lett. 2010 Jan 1;12(1):104-6
20035564
Chem Pharm Bull (Tokyo). 2001 Sep;49(9):1189-91
11558610
Biochemistry. 1992 Jul 14;31(27):6279-84
1320934
Nat Struct Biol. 1994 Aug;1(8):512-7
7664078
Opt Express. 2009 Aug 17;17(17):14526-33
19687931
Protein Sci. 2009 Jul;18(7):1343-58
19530249
J Phys Chem B. 2005 Oct 6;109(39):18652-63
16853400
Org Lett. 2005 Feb 17;7(4):693-6
15704927
J Phys Chem B. 2006 Dec 7;110(48):24740-9
17134238
Biochim Biophys Acta. 2007 Sep;1767(9):1073-101
17692815
Opt Lett. 2007 Oct 15;32(20):2966-8
17938668
Opt Lett. 1993 Nov 15;18(22):1943-5
19829455
J Am Chem Soc. 2009 Feb 18;131(6):2042-3
19199613
New J Phys. 2009 Oct 1;11:105046
20463848
Opt Lett. 2006 Mar 15;31(6):838-40
16544641
Annu Rev Phys Chem. 2008;59:291-317
17988202
Opt Lett. 2002 Mar 15;27(6):433-5
18007825
Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6614-9
19346479
Opt Lett. 2006 Oct 1;31(19):2918-20
16969422
Phys Chem Chem Phys. 2009 Feb 7;11(5):748-61
19290321
J Phys Chem B. 2009 Feb 26;113(8):2498-505
19182939
Proc Natl Acad Sci U S A. 1989 Nov;86(21):8387-91
2554314
Annu Rev Biophys Biomol Struct. 2000;29:327-59
10940252
Curr Opin Chem Biol. 2006 Oct;10(5):394-401
16935550
Opt Lett. 2002 Jan 15;27(2):131-3
18007735
J Phys Chem B. 2009 Jun 18;113(24):8231-51
19351162
J Am Chem Soc. 2010 Mar 3;132(8):2832-8
20136132
Acc Chem Res. 2009 Sep 15;42(9):1385-94
19462972
J Phys Chem B. 2009 Nov 26;113(47):15679-91
19883093