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. 2001 Jul;10(7):1293-304.
doi: 10.1110/ps.51201.

Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers

N S Green  1 , E Reisler, K N Houk
Affiliations

Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers

N S Green et al. Protein Sci. 2001 Jul.

Abstract

Homobifunctional chemical cross-linking reagents are important tools for functional and structural characterization of proteins. Accurate measures of the lengths of these molecules currently are not available, despite their widespread use. Stochastic dynamics calculations now provide quantitative measures of the lengths, and length dispersions, of 32 widely used molecular rulers. Significant differences from published data have been found.

Supplemental material: See www.proteinscience.org

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Figures

Fig. 1.
Fig. 1.
N,N′-1,2-phenylenedimaleimide (oPDM). (A) Frequency vs. cross-linking span for oPDM; (B) cross-linking span vs. time for oPDM; (C) structure of oPDM; (D) reaction of oPDM and other bis-maleimide cross-linking reagents with sulfhydryl groups. l is the S-S distance and the cross-linking span of the reagent. (oPDM) N,N′-1,2-phenylenedimaleimide.
Fig. 2.
Fig. 2.
The bis-maleimide cross-linking reagents. (mPDM) N,N′1,3-phenylenedimaleimide; (oPDM) N,N′-1,2-phenylenedimaleimide; (pPDM) N,N′-1,4-phenylenedimaleimide; (BM) N,N′-(methylene-4-1-phenylene)bismaleimide; (NDM) naphthalene-1,5-dimaleimide; (BMOE) bismaleimidoethane; (BMB) 1,4-bismaleimidobutane; (BMDB) 1,4-bis-maleimidyl-2,3-dihydroxybutane; (DTME) dithio-bis-maleimdoethane; (BMH) 1,6-bismaleimidohexane; (BM[PEO]3) 1,8-bismaleimidotriethyleneglycol; (BM[PEO]4) 1,11-bis-maleimidotetraethyleneglycol.
Fig. 3.
Fig. 3.
Frequency plots showing overlap of mPDM, oPDM, and pPDM spans. (mPDM) N,N′1,3-phenylenedimaleimide; (oPDM) N,N′-1,2-phenylenedimaleimide; (pPDM) N,N′-1,4-phenylenedimaleimide.
Fig. 4.
Fig. 4.
Disulfide exchange cross-linking reagents. (A) Structures of the arene-disulfide exchange reagents. (B) Reaction of bis-disulfide cross-linking reagents with sulfhydryl groups. Å is the cross-linking span of the reagent.
Fig. 5.
Fig. 5.
Frequency plot for 1,4-bismaleimidobutane (BMB). The structures shown represent conformations of BMB with cross-linking spans corresponding to the two modes. Both conformations have two gauche NCCC dihedral angles.
Fig. 6.
Fig. 6.
C-6 and C-8 disulfides. (A) Frequency plot for C-8 arene disulfide; (B) frequency plot for C-6 arene disulfide; (C) two major conformations of the C-6 disulfide reagent and the corresponding S-S distances.
Fig. 7.
Fig. 7.
The bis-imidoester cross-linking reagents. (DMA) dimethyl adipimidate; (DMP) dimethyl pimelimidiate; (DMS) dimethyl suberimidate; (DTBP) dimethyl 3,3′-dithiobis-propionimidate.
Fig. 8.
Fig. 8.
The bis-N-hydroxysuccinimide ester cross-linking reagents. (DST) disuccimimidyl tartarate; (DSG) disuccinimidyl glutarate; (DSP) dithiobis(succinimidylpropionate); (DSS) disuccinimidyl suberate; (BSOCOES) bis(2-[succinimidooxycarbonyloxy]ethyl)sulfone; (EGS) ethyleneglycol bis-(succinimidylsuccinate).
Fig. 9.
Fig. 9.
The small rigid cross-linking reagents. (DFDNB) 1,5-difluro-2,4dinitrobenzene; (DFDNPS) 4,4′-difluoro3,3′-dinitrodiphenylsulfone; (bBBr) dibromobimane.
See this image and copyright information in PMC

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