Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies.
The combination of chemical probing and high-resolution mass spectrometry constitutes a powerful alternative for the structural elucidation of biomolecules possessing unfavorable size, solubility, and flexibility. We have developed nested Arg-specific bifunctional crosslinkers to obtain complementary information to typical Cys- and Lys-specific reagents available on the market. The structures of 1,4-phenyl-diglyoxal (PDG) and 4,4'-biphenyl-diglyoxal (BDG) include two identical 1,2-dicarbonyl functions capable of reacting with the guanido group of Arg residues in proteins, as well as the base-pairing face of guanine in nucleic acids. The reactive functions are separated by modular spacers consisting of one or two benzene rings, which confer greater rigidity to the crosslinker structure than it is afforded by typical aliphatic spacers. Analysis by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry has shown that the probes provide both mono- and bifunctional products with model protein substrates, which are stabilized by the formation of diester derivatives in the presence of borate buffer. The identification of crosslinked sites was accomplished by employing complementary proteolytic procedures and peptide mapping by ESI-FTICR. The results showed excellent correlation with the solvent accessibility and structural context of susceptible residues, and highlighted the significance of possible dynamic effects in determining the outcome of crosslinking reactions. The application of nested reagents with different spacing has provided a new tool for experimentally recognizing flexible regions that may be involved in prominent dynamics in solution. The development of new bifunctional crosslinkers with diverse target specificity and different bridging spans is expected to facilitate the structure elucidation of progressively larger biomolecular assemblies by increasing the number and diversity of spatial constraints available for triangulating the position of crosslinked structures in the three dimensions.
Zhang
Qingrong
Q
University of Maryland Baltimore County, Baltimore, MD 21228, United States.
Crosland
Elizabeth
E
Fabris
Daniele
D
D000595:Amino Acid Sequence; D000818:Animals; D001120:Arginine / Q000378:metabolism*; D002417:Cattle; D002623:Chemistry Techniques, Analytical / Q000295:instrumentation*; D003432:Cross-Linking Reagents / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D010658:Phenylglyoxal / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D021241:Spectrometry, Mass, Electrospray Ionization; D013379:Substrate Specificity
D003432:Cross-Linking Reagents; D011506:Proteins; C018360:1,4-phenyldiglyoxal; D001120:Arginine; D010658:Phenylglyoxal
Rapid Commun Mass Spectrom. 2003;17(2):155-62
12512095
J Biol Chem. 2000 Jun 9;275(23):17571-7
10747904
Biochemistry. 1996 Oct 22;35(42):13519-30
8885831
Biopolymers. 1998;48(2-3):167-80
10333744
Proc Natl Acad Sci U S A. 1987 Feb;84(3):620-3
3468502
Science. 1987 Aug 28;237(4818):992-8
3303336
Biochemistry. 1997 Mar 25;36(12):3496-505
9131999
Protein Sci. 1997 Dec;6(12):2568-77
9416606
Nucleic Acids Res. 1978 Nov;5(11):4065-75
724507
Biochemistry. 1997 May 27;36(21):6270-82
9174342
Mol Vis. 2004 Nov 16;10:857-66
15570221
J Biol Chem. 1988 Mar 25;263(9):4293-301
3279034
Trends Biochem Sci. 2005 Oct;30(10):583-92
16126388
Biochemistry. 1998 Jul 14;37(28):9912-7
9665696
Nucleic Acids Res. 2004 Sep 21;32(16):e132
15383647
J Biol Chem. 1992 Aug 15;267(23):16467-71
1322903
J Mass Spectrom. 2003 Dec;38(12):1225-37
14696200
Biochemistry. 1969 Jan;8(1):238-45
5777326
Biochem Biophys Res Commun. 1997 Oct 9;239(1):217-22
9345298
J Biol Chem. 2000 Dec 29;275(52):41458-68
11006293
J Mol Biol. 2003 Aug 8;331(2):303-13
12888339
Anal Chem. 1988 Oct 15;60(20):2299-301
3239801
Anal Biochem. 2004 Nov 15;334(2):356-66
15494143
Methods. 2002 Feb;26(2):170-81
12054894
Acta Crystallogr D Biol Crystallogr. 2004 Apr;60(Pt 4):792-5
15039588
Methods Mol Biol. 2000;146:113-31
10948499
Anal Chem. 2002 May 1;74(9):1939-45
12033289
Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12248-53
18713870
J Am Soc Mass Spectrom. 2006 Nov;17(11):1570-1581
16875836
J Biol Chem. 1997 Jun 6;272(23):14547-55
9169412
Methods Enzymol. 1991;208:468-96
1779844
Anal Chem. 2004 May 1;76(9):2438-45
15117181
Nat Rev Mol Cell Biol. 2007 Aug;8(8):645-54
17593931
Mass Spectrom Rev. 2006 Jan-Feb;25(1):158-70
16208684
Methods Enzymol. 1988;164:310-8
3071671
Protein Sci. 1999 Dec;8(12):2806-12
10631998
J Am Soc Mass Spectrom. 2001 Feb;12(2):222-7
11212007
Biochim Biophys Acta. 1985 Dec 9;822(3-4):289-317
2865974
Biol Mass Spectrom. 1991 Dec;20(12):796-800
1812990
Anal Chem. 2005 Jan 15;77(2):495-503
15649045
Biochemistry. 1999 Sep 7;38(36):11734-40
10512629
Proc Natl Acad Sci U S A. 2000 May 23;97(11):5802-6
10811876
Mass Spectrom Rev. 2002 May-Jun;21(3):163-82
12476441
Protein Sci. 2001 Oct;10(10):1989-2001
11567090
J Biol Chem. 2004 Apr 9;279(15):15305-13
14749331
Annu Rev Phys Chem. 1999;50:517-36
10575730
J Mol Biol. 2005 Jan 7;345(1):69-80
15567411
Anal Biochem. 1996 Nov 1;242(1):55-63
8923964
Anal Chem. 2000 Jan 15;72(2):267-75
10658319
Nucleic Acids Res. 1996 Oct 1;24(19):3866-72
8871569
J Protein Chem. 1997 Jul;16(5):375-83
9246617
Biochemistry. 2005 Mar 1;44(8):2759-69
15723520
Protein Sci. 1993 Sep;2(9):1441-51
8401229
Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679-82
6159633
J Mass Spectrom. 2005 Oct;40(10):1372-81
16237662
Electrophoresis. 1997 Mar-Apr;18(3-4):403-8
9150918
EMBO J. 1995 Sep 15;14(18):4578-88
7556101
Eur J Mass Spectrom (Chichester). 2003;9(6):623-31
15100473
Methods Enzymol. 1988;164:287-309
3071669
Biochemistry. 2004 Apr 27;43(16):4703-15
15096039
Rapid Commun Mass Spectrom. 2002;16(3):149-59
11803535
Biochim Biophys Acta. 1977 Mar 28;491(1):305-16
14699
Nucleic Acids Res. 1998 Jan 15;26(2):645-9
9421528
Biochemistry. 2001 Jul 3;40(26):7903-13
11425319
J Mol Biol. 2003 Jul 4;330(2):211-23
12823962