Reactivity of Zinc Finger Cores:  Analysis of Protein Packing and Electrostatic Screening

Abstract

The chemical stability of 207 zinc fingers, derived from 92 experimental protein structures, is evaluated according to the protein packing and electrostatic screening of their zinc cores. These properties are used as measures of the protein protection of zinc cores, to predictively rank relative zinc finger reactivities and assess differences in function. On average, there is a substantial and concomitant increase in the screening of increasingly anionic core motifs, suggesting zinc fingers have evolved in a manner that promotes shielding of their potentially reactive core thiolates. In contrast, enzymatic zinc cores are functionally differentiated by negative electrostatic screening. Zinc finger cores are predominantly screened by networks of backbone:core NH-S hydrogen bonds that electronically stabilize core thiolates and enhance backbone packing. Stabilizing protein:core interactions can be mapped to conserved residues, including [Arg,Lys]:core salt-bridges in some protein families. Labile zinc fingers are identified by poorly screened cores, possibly indicating redox or metallothionein (MT) regulated function. Consistent with experiment, the cores of the C-terminal finger of the human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein p7 (NCp7) and Escherichia coli Ada protein (Ada) "finger" are identified as reactive. The C-terminal zinc fingers of nuclear receptors are predicted to be the most labile in this study, particularly the human estrogen receptor (hER), which contains a triad of reactive thiolates. We propose that hER DNA binding is redox and MT regulated through the C-terminal finger and that weak electrophilic agents may inhibit hER-mediated transcription, implicated in breast cancer progression.

15-Deoxy-Δ12,14-Prostaglandin J2 Inhibits Transcriptional Activity of Estrogen Receptor-α via Covalent Modification of DNA-Binding Domain

“…In addition, the singly charged NH 2 -terminal fragment (*b 5 ) and the singly (*y 2 -*y 5 ) and doubly (*y 5 +2 ) charged COOHterminal fragments were observed to increase 316.4 Da, suggesting that Cys 240 but not Cys 237 is the target for 15d-PGJ 2 modification. Consistent with the previous studies (27)(28)(29), these results show that 15d-PGJ 2 modifies two cysteines (Cys 227 and Cys 240 ) located in the COOH-terminal zinc finger of ERa DBD that is structurally disordered and susceptible to electrophilic attack (Fig. 4C).…”

“…These two zinc fingers in ERa DBD function cooperatively in ERa dimerization and DNA binding (25,26). In addition, the COOH-terminal zinc finger of ERa is structurally disordered, and the cysteine thiols of this zinc finger have been characterized as particularly susceptible to the attack of electrophilic agents such as 2,2 ¶-dithiobisbenzamide-1 and benzisothiazolone (27)(28)(29).…”

Comparison of the protein–protein interfaces in the p53–DNA crystal structures: Towards elucidation of the biological interface

“…The distances of the three ZnOS bonds and ZnON between the ZnOHis were fixed during the simulation. The charge and van der Waals parameters of the Zn and deprotonated Cys were taken from Maynard and Covell (25).…”

Applications of tripodal [S3] and [Se3] L2X donor ligands to zinc, cadmium and mercury chemistry: organometallic and bioinorganic perspectives

“…As such, it has been postulated that N-H•••S hydrogen bonding interactions between the thiolate sulfur and amide groups of other residues provide a mechanism to modulate the reactivity of the zinc-cysteine thiolate moiety. 74,75 In this regard, the thiolate copmplexes [Tm R ]ZnSCH 2 C(O)N(H)Ph (R = Ph, Bu t ), which incorporate an N-H hydrogen bonding functionality, provide a more refined structural analogue for the Ada protein. 71b, 76 The presence of hydrogen bonding interactions within [Tm R ]ZnSCH 2 C(O)N(H)Ph was confirmed by X-ray diffraction, as illustrated in Figure 13.…”