YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression.

The DNA guanine quadruplexes (G4) play important roles in multiple cellular processes, including DNA replication, transcription and maintenance of genome stability. Here, we showed that Yin and Yang 1 (YY1) can bind directly to G4 structures. ChIP-seq results revealed that YY1-binding sites overlap extensively with G4 structure loci in chromatin. We also observed that the dimerization of YY1 and its binding with G4 structures contribute to YY1-mediated long-range DNA looping. Displacement of YY1 from G4 structure sites disrupts substantially the YY1-mediated DNA looping. Moreover, treatment with G4-stabilizing ligands modulates the expression of not only those genes with G4 structures in their promoters, but also those associated with distal G4 structures that are brought to close proximity via YY1-mediated DNA looping. Together, we identified YY1 as a DNA G4-binding protein, and revealed that YY1-mediated long-range DNA looping requires its dimerization and occurs, in part, through its recognition of G4 structure.

Inhibiting Matrix Metalloproteinase-2 Activation by Perturbing Protein-Protein Interactions Using a Cyclic Peptide.

We report on a cyclic peptide that inhibits matrix metalloproteinase-2 (MMP2) activation with a low-nM-level potency. This inhibitor specifically binds to the D570-A583 epitope on proMMP2 and interferes with the protein-protein interaction (PPI) between proMMP2 and tissue inhibitor of metalloproteinases-2 (TIMP2), thereby preventing the TIMP2-assisted proMMP2 activation process. We developed this cyclic peptide inhibitor through an epitope-targeted library screening process and validated its binding to proMMP2. Using a human melanoma cell line, we demonstrated the cyclic peptide's ability to modulate cellular MMP2 activities and inhibit cell migration. These results provide the first successful example of targeting the PPI between proMMP2 and TIMP2, confirming the feasibility of an MMP2 inhibition strategy that has been sought after for 2 decades.

NMR determination of pKa values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain.

From the larger set of 191 variants at all the variable contact positions in the turkey ovomucoid third domain, we selected a subset that consists of Asp, Glu, His, and Lys residues at eight of the nine contiguous P6-P3' positions (residues 13-21), the exception being P3-Cys16 which is involved in a conserved disulfide bridge. Two-dimensional [1H,1H]-TOCSY data were collected for each variant as a function of sample pH. This allowed for the evaluation of 31 of the 32 pK(a) values for these residues, the exception being that of P5-Lys14, whose signals at high pH could not be resolved from those of other Lys residues in the molecule. Only two of the titrating residues are present in the wild-type protein (P6-Lys13 and P1'-Glu19); hence, these measurements complement earlier measurements by A. D. Robertson and co-workers. This data set was supplemented with results from the pH dependence of NMR spectra of four additional single mutants, P1-Leu18Gly, P1-Leu18Ala, P2-Thr17Val, and P3'-Arg21Ala, and two double mutants, P2-Thr17Val/P3'-Arg21Ala and P8-Tyr11Phe/P6-Lys13Asp. Probably the most striking result was observation of a P2-Thr17...P1'-Glu19 hydrogen bond and a P1'-Glu19-P3'-Arg21 electrostatic interaction within the triad of P2, P1', and P3' (residues 17, 19, and 21, respectively). In several cases, the pK(a) of a particular residue was sensed by resonances not only in that residue but also in residue(s) with which it interacts. Remarkably, in several interacting systems, resonances from different protons within the same residue yielded different pHmid values.