Zinc finger (ZF) proteins are proteins that use zinc as a structural cofactor. The common feature among all ZFs is that they contain repeats of four cysteine and/or histidine residues within their primary amino acid sequence. With the explosion of genome sequencing in the early 2000s, a large number of proteins were annotated as ZFs based solely upon amino acid sequence. As these proteins began to be characterizedexperimentally, it was discovered that some of these proteins contain iron–sulfur sites either in place of or in addition to zinc. Here, we describe methods to isolate and characterize one such ZF protein, cleavage and polyadenylation specificity factor 30 (CPSF3O) with respect to its metal-loading and RNA-binding activity.
more »
« less
Emerging investigator series: characterization of silver and silver nanoparticle interactions with zinc finger peptides
In biological systems, chemical and physical transformations of engineered silver nanomaterials (AgENMs) are mediated, in part, by proteins and other biomolecules. Metalloprotein interactions with AgENMs are also central in understanding toxicity, antimicrobial, and resistance mechanisms. Despite their readily available thiolate and amine ligands, zinc finger (ZF) peptides have thus far escaped study in reaction with AgENMs and their Ag( i ) oxidative dissolution product. We report spectroscopic studies that characterize AgENM and Ag( i ) interactions with two ZF peptides that differ in sequence, but not in metal binding ligands: the ZF consensus peptide CP-CCHC and the C-terminal zinc finger domain of HIV-1 nucleocapsid protein p7 (NCp7_C). Both ZF peptides catalyze AgENM (10 and 40 nm, citrate coated) dissolution and agglomeration, two important AgENM transformations that impact bioreactivity. AgENMs and their oxidative dissolution product, Ag( i )(aq), mediate changes to ZF peptide structure and metalation as well. Spectroscopic titrations of Ag( i ) into apo-ZF peptides show an Ag( i )–thiolate charge transfer band, indicative of Ag( i )–ZF binding. Fluorescence studies of the Zn( ii )–NCp_7 complex indicate that the Ag( i ) also effectively competes with the Zn( ii ) to drive Zn( ii ) displacement from the ZFs. Upon interaction with AgENMs, Zn( ii ) bound ZF peptides show a secondary structural change in circular dichroism spectroscopy toward an apo-like structure. The results suggest that Ag( i ) and AgENMs may alter ZF protein function within the cell.
more »
« less
- PAR ID:
- 10107347
- Date Published:
- Journal Name:
- Environmental Science: Nano
- ISSN:
- 2051-8153
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Aqueous zinc-ion batteries (AZIBs) are promising candidates for large-scale electrical energy storage due to the inexpensive, safe, and non-toxic nature of zinc. One key area that requires further development is electrode materials that store Zn 2+ ions with high reversibility and fast kinetics. To determine the viability of low-cost organosulfur compounds as OEMs for AZIBs, we investigate how structural modification affects electrochemical performance in Zn-thiolate complexes 1 and 2. Remarkably, modification of one thiolate in 1 to sulfide in 2 reduces the voltage hysteresis from 1.04 V to 0.15 V. While 1 exhibits negligible specific capacity due to the formation of insulating DMcT polymers, 2 delivers a capacity of 107 mA h g −1 with a primary discharge plateau at 1.1 V vs. Zn 2+ /Zn. Spectroscopic studies of 2 suggest a Zn 2+ and H + co-insertion mechanism with Zn 2+ as the predominant charge carrier. Capacity fading in Zn-2 cells likely results from the formation of (i) soluble H + insertion products and (ii) non-redox-active side products. Increasing electrolyte concentration and using a Nafion membrane significantly enhances the stability of 2 by suppressing H + insertion. Our findings provide insight into the molecular design strategies to reduce the polarization potential and improve the cycling stability of the thiolate/disulfide redox couple in aqueous battery systems.more » « less
-
Abstract SH2B1 is a multidomain protein that serves as a key adaptor to regulate numerous cellular events, such as insulin, leptin, and growth hormone signaling pathways. Many of these protein‐protein interactions are mediated by the SH2 domain of SH2B1, which recognizes ligands containing a phosphorylated tyrosine (pY), including peptides derived from janus kinase 2, insulin receptor, and insulin receptor substrate‐1 and −2. Specificity for the SH2 domain of SH2B1 is conferred in these ligands either by a hydrophobic or an acidic side chain at the +3 position C‐terminal to the pY. This specificity for chemically disparate species suggests that SH2B1 relies on distinct thermodynamic or structural mechanisms to bind to peptides. Using binding and structural strategies, we have identified unique thermodynamic signatures for each peptide binding mode, and several SH2B1 residues, including K575 and R578, that play distinct roles in peptide binding. The high‐resolution structure of the SH2 domain of SH2B1 further reveals conformationally plastic protein loops that may contribute to the ability of the protein to recognize dissimilar ligands. Together, numerous hydrophobic and electrostatic interactions, in addition to backbone conformational flexibility, permit the recognition of diverse peptides by SH2B1. An understanding of this expanded peptide recognition will allow for the identification of novel physiologically relevant SH2B1/peptide interactions, which can contribute to the design of obesity and diabetes pharmaceuticals to target the ligand‐binding interface of SH2B1 with high specificity.more » « less
-
Abstract The copper(I), silver(I), and gold(I) metals bind π‐ligands by σ‐bonding and π‐back bonding interactions. These interactions were investigated using bidentate ancillary ligands with electron donating and withdrawing substituents. The π‐ligands span from ethylene to larger terminal and internal alkenes and alkynes. Results of X‐ray crystallography, NMR, and IR spectroscopy and gas phase experiments show that the binding energies increase in the order Agmore » « less
-
Abstract The ability to accurately identify peptide ligands for a given major histocompatibility complex class I (MHC-I) molecule has immense value for targeted anticancer therapeutics. However, the highly polymorphic nature of the MHC-I protein makes universal prediction of peptide ligands challenging due to lack of experimental data describing most MHC-I variants. To address this challenge, we have developed a deep convolutional neural network, HLA-Inception, capable of predicting MHC-I peptide binding motifs using electrostatic properties of the MHC-I binding pocket. By approaching this immunological issue using molecular biophysics, we measure the impact of sidechain arrangement and topology on peptide binding, feature not captured by sequence-based MHC-I prediction methods. Through a combination of molecular modeling and simulation, 5821 MHC-I alleles were modeled, providing extensive coverage across human populations. Predicted peptide binding motifs fell into distinct clusters, each defined with different degrees of submotif heterogeneity. Peptide binding scores generated by HLA-Inception are strongly correlated with quantitative MHC-I binding data, indicating predicted peptides can be ranked, both within and between alleles. HLA-inception also showed high precision when predicting naturally presented peptides and can be used for rapid proteome-scale MHC-I peptide binding predictions. Finally, we show that the binding pocket diversity measured by HLA inception predicts response to checkpoint blockade. Citation Format: Eric A. Wilson, John Kevin Cava, Diego Chowell, Abhishek Singharoy, Karen S. Anderson. Protein structure-based modeling to improve MHC class I epitope predictions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5376.more » « less