Fig. 4: Mapping protein–DNA interactions in the transcription factor nuclear factor 1/C.
a Overview of the identified peptide–nucleotide cross-links. The possible cross-link locations are indicated by red letters in the peptide sequence. Cross-linked (XL)-nucleotide and XL-base information derived from specific MS1 and MS2 mass shifts are specified. b Location of the annotated DNA-binding domain of nuclear factor 1/C (NF1) and location of the detected cross-links (red stars). A represents the unspecific DNA-binding subdomain and B the sequence-specific DNA-binding subdomain according to Dekker et al.26. c Location of the cross-links (red stars) on the palindromic consensus DNA-binding sequence of NF1. Blue letters indicate nucleotides, which fit to the NF1 consensus sequence TTGGC(N)6CC32. d–g MS2 ion series and spectra of four NF1–DNA cross-links. In the MS2 spectra, nucleotides are annotated in red, amino acids in regular letters. N′ denotes the nucleobase, and N the deoxynucleotide monophosphate (with N being one of the four bases A/T/G/C). The following abbreviations describe neutral losses after MS2 fragmentation: Asterisk: neutral loss of H2SO3, −CO: neutral loss of carbon monoxide, −A: neutral loss of ammonia, −/+W: neutral loss or adduct of water, −HP: neutral loss of hydrogen peroxide, −p: neutral loss of HPO3, −P: neutral loss of H3PO4. In the MS2 ion series, cross-linked fragments are depicted with the cross-linked nucleotide (A/T/G or C) in superscript. MOx represents oxidated methionine and CTriox trioxidated cysteine (cysteic acid). The prefix IM before the respective amino acid indicates an immonium ion. The superscripted NL represents the neutral loss of sulfurous acid or hydrogen peroxide. All other symbols represent the same neutral losses as in the MS2 spectra.
