Helix Induction by Dirhodium: Access to Biocompatible Metallopeptides with Defined Secondary Structure

Digging into protein metalation differences triggered by fluorine containing-dirhodium tetracarboxylate analogues

Catalytic and biological properties of dirhodium tetracarboxylates ([Rh2(μ-O2CR)4L2], L=axial ligand, R=CH3-, CH3CH2-, etc) largely depend on the nature of the bridging carboxylate equatorial μ-O2CR ligands, which can be easily exchanged...

Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A

Clavanin A (ClavA) is an antimicrobial peptide (AMP) whose antimicrobial activity is enhanced in the presence of Zn(II) ions. The antimicrobial activity of ClavA has been shown to increase 16-fold in the presence of Zn(II) ions. In this study, we investigate the potential sources of this enhancement, namely, the effect of Zn(II) binding on the helical conformation of ClavA and on the ClavA interaction with a model for gram-negative bacterial membranes. In addition, we investigate the effect of Zn(II) on the membrane mechanical properties. We employed all-atom equilibrium molecular dynamics simulations initiated from both fully helical and random coil structures of ClavA. We observe that Zn(II) can stabilize an existing helical conformation in the Zn(II)-binding region, but we do not observe induction of helical conformations in systems initiated in random coil configurations. Zn(II) binding to ClavA provides more favorable electrostatics for membrane association in the C-terminal region. This is evidenced by longer and stronger C-terminal-lipid interactions. Zn(II) is also capable of modulating the membrane properties in a manner which favors ClavA insertion and the potential for enhanced translocation into the cell. This work provides insights into the role of divalent metal cations in the antimicrobial activity of ClavA. This information can be used for the development of synthetic AMPs containing motifs that can bind metals (metalloAMPs) for therapeutic and medical purposes.

Site-selective nitrenoid insertions utilizing postfunctionalized bifunctional rhodium(ii) catalysts

We report a new strategy for the preparation of dirhodium(ii) complexes with the general formula Rh₂(A)₄ that allows the isolation of a dirhodium tetracarboxylate complex with a free amino group available for postfunctionalization. The postfunctionalization of this complex enables the incorporation of a variety of functional groups, including double and triple bonds as well as nucleophilic moieties, thus paving the way to new classes of polymeric as well as bifunctional catalysts, and polymetallic complexes. Furthermore, we demonstrate that a urea containing dirhodium(ii) complex enables site-selective nitrenoid insertions by remote hydrogen bonding control.

Protein metalation by metal-based drugs: X-ray crystallography and mass spectrometry studies

The combined use of X-ray crystallography and mass spectrometry represents a valuable strategy to investigate and characterize protein metalation induced by anticancer metal-based drugs. Here, we summarize a series of significant results recently obtained in our laboratories upon the examination of the structures of several adducts of proteins with representative metallodrugs (mostly containing ruthenium, gold and platinum). The general mechanisms of protein metalation that emerge from a careful comparative analysis of these structures are illustrated and their mechanistic implications are discussed. Possible directions for future work in the field are delineated.

Assessing the intracellular fate of rhodium(ii) complexes

Rhodium(ii)-fluorophore conjugates have strong rhodium-based fluorescence quenching that can be harnessed to report on a conjugate's cellular uptake and the intracellular decomposition rate. Information gleened from this study allowed the design of an improved STAT3 metalloinhibitor.

Influence of reaction conditions on the self-assembly of the natural silk sericin protein

In the past years, the self-assembly of specific proteins has been paid more and more attention due to their significant role in human health and fabrication of new materials. In this article, we explore the effect of reaction conditions on the self-assembly of natural silk sericin protein, including the molecular weight and the concentration of sericin, pH, and metal ions in the reaction system. The results indicate that all these factors, especially species and concentration of metal ions, could influence the self-assembly process of the silk sericin protein. A series of assemblies with various morphologies can be fabricated by modulating the reaction condition. The article may provide some clue for the understanding of the protein self-assembly in the body and a method to fabricate new organic materials with different morphology. Microsc. Res. Tech. 80:298-304, 2017. © 2016 Wiley Periodicals, Inc.

Investigating the role of chain and linker length on the catalytic activity of an H2 production catalyst containing a β-hairpin peptide

Building on our recent report of an active H2 production catalyst [Ni(PPh 2NProp-peptide)2]2+ (Prop = para-phenylpropionic acid, peptide (R10) = WIpPRWTGPR-NH2, p = D-proline and P2N = 1-aza-3,6-diphosphacycloheptane) that contains structured β-hairpin peptides, here we investigate how H2 production is effected by: (1) the length of the hairpin (eight or ten residues) and (2) limiting the flexibility between the peptide and the core complex by altering the length of the linker: para-phenylpropionic acid (three carbons) or para-benzoic acid (one carbon). Reduction of the peptide chain length from ten to eight residues increases or maintains the catalytic current for H2 production for all complexes, suggesting a non-productive steric interaction at longer peptide lengths. While the structure of the hairpin appears largely intact for the complexes, NMR data are consistent with differences in dynamic behavior which may contribute to the observed differences in catalytic activity. Molecular dynamics simulations demonstrate that complexes with a one-carbon linker have the desired effect of restricting the motion of the hairpin relative to the complex; however, the catalytic currents are significantly reduced compared to complexes containing a three-carbon linker as a result of the electron withdrawing nature of the -COOH group. These results demonstrate the complexity and interrelated nature of the outer coordination sphere on catalysis.

Tunable Helicity, Stability and DNA-Binding Properties of Short Peptides with Hybrid Metal Coordination Motifs

Given the prevalent role of α-helical motifs on protein surfaces in mediating protein-protein and protein-DNA interactions, there have been significant efforts to develop strategies to induce α-helicity in short, unstructured peptides to interrogate such interactions. Toward this goal, we have recently introduced hybrid metal coordination motifs (HCMs). HCMs combine a natural metal-binding amino acid side chain with a synthetic chelating group that are appropriately positioned in a peptide sequence to stabilize an α-helical conformation upon metal coordination. Here, we present a series of short peptides modified with HCMs consisting of a His and a phenanthroline group at i and i+7 positions that can induce α-helicity in a metal-tunable fashion as well as direct the formation of discrete dimeric architectures for recognition of biological targets. We show that the induction of α-helicity can be further modulated by secondary sphere interactions between amino acids at the i+4 position and the HCM. A frequently cited drawback of the use of peptides as therapeutics is their propensity to be quickly digested by proteases; here, we observe an enhancement of up to ∼100-fold in the half-lifes of the metal-bound HCM-peptides in the presence of trypsin. Finally, we show that an HCM-bearing peptide sequence, which contains the DNA-recognition domain of a bZIP protein but is devoid of the obligate dimerization domain, can dimerize with the proper geometry and in an α-helical conformation to bind a cognate DNA sequence with high affinities (K_d≥ 65 nM), again in a metal-tunable manner.

Reversible and rapid pH-regulated self-assembly of a poly(ethylene glycol)-peptide bioconjugate

The use of external triggers to manipulate the secondary structure of self-assembling peptides conjugated to flexible synthetic polymers is a challenging problem, particularly in terms of reversibility. Here, we demonstrate, for the first time, sustained rapid and reversible, pH-regulated self-assembly of the peptide ELELELELELF (EL-5F) and its conjugates with 2 and 5 kDa poly(ethylene glycol) (EL-5F-PEG-2K and EL-5F-PEG-5K). Circular dichroism indicated the formation of β-sheet structures at pH < 5.9, 5.8, and 5.4 and disassembly to random coils above those pH values for EL-5F, EL-5F-PEG-2K, and EL-5F-PEG-5K, respectively. β-sheets were confirmed by the thioflavin T assay, while transmission electron microscopy revealed the existence of extended fibrillar structures below the above pH values. pH-induced secondary structure conversion was reproducible for over 15 cycles, even at salt concentrations of up to 200 mM NaCl, and was quantitatively related to the pH. Self-supporting hydrogelation after self-assembly was observed at concentrations as low as 0.2 wt %, which is 15-fold lower than previously reported concentrations. This simple approach to mediate reversible self-assembly of EL-5F-PEG bioconjugates is expected to offer novel functionality relevant to drug delivery and bioseparation systems.

Unusual structural features in the lysozyme derivative of the tetrakis(acetato)chloridodiruthenium(II,III) complex

The reaction between the paddle-wheel tetrakis(acetato)chloridodiruthenium(II,III) complex, [Ru2(μ-O2CCH3)4Cl] and hen egg-white lysozyme (HEWL) was investigated through ESI-MS and UV/Vis spectroscopy and the formation of a stable metal-protein adduct was unambiguously demonstrated. Remarkably, the diruthenium core is conserved in the adduct while two of the four acetate ligands are released. The crystal structure of this diruthenium-protein derivative was subsequently solved through X-ray diffraction analysis to 2.1 Å resolution. The structural data are in agreement with the solution results. It was found that HEWL binds two diruthenium moieties, at Asp101 and Asp119, respectively, with the concomitant release of two acetate ligands from each diruthenium center.

Enzyme design from the bottom up: an active nickel electrocatalyst with a structured peptide outer coordination sphere

Catalytic, peptide-containing metal complexes with a well-defined peptide structure have the potential to enhance molecular catalysts through an enzyme-like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide-based metal complex built upon the well-characterized hydrogen production catalyst [Ni(P(Ph)2N(Ph))2](2+) (P(Ph)2N(Ph)=1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane). The incorporated peptide maintains its β-hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide-based metal complex (≈100,000 s(-1)) is enhanced compared to the parent complex ([Ni(P(Ph)2N(APPA))2](2+); ≈50,500 s(-1)). The combination of an active molecular catalyst with a structured peptide provides a scaffold that permits the incorporation of features of an enzyme-like outer-coordination sphere necessary to create molecular electrocatalysts with enhanced functionality.

Designing functional metalloproteins: from structural to catalytic metal sites

Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.

Functional, metal-based crosslinkers for α-helix induction in short peptides

Many protein-protein interactions that play a central role in cellular processes involve α-helical domains. Consequently, there has been great interest in developing strategies for stabilizing short peptides in α-helical conformations toward the inhibition and interrogation of protein-protein interactions. Here, we show that tridentate Hybrid Coordination Motifs (HCMs), which consist of a natural (histidine, His) and an unnatural (8-hydroxyquinoline, Quin) metal binding functionality, can bind divalent metal ions with high affinity and thereby induce/stabilize an α-helical configuration in short peptide sequences. The Quin functionality is readily introduced onto peptide platforms both during or after solid-state peptide synthesis, demonstrating the preparative versatility of HCMs. A systematic study involving a series of HCM-bearing peptides has revealed the critical importance of the length of the linkage between the Quin moiety and the peptide backbone as well as the metal coordination geometry in determining the extent of α-helix induction. Through ZnII coordination or modification with ReI(Quin)(CO)3, the HCM-bearing peptides can be rendered luminescent in the visible region, thus showing that HCMs can be exploited to simultaneously introduce structure and functionality into short peptides.

Oxime side-chain cross-links in an α-helical coiled-coil protein: structure, thermodynamics, and folding-templated synthesis of bicyclic species

Covalent side-chain cross-links are a versatile method to control peptide folding, particularly when α-helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein-protein complex. A series of sequence variants of the dimeric coiled coil GCN4-p1 bearing oxime bridges at solvent-exposed positions were prepared and biophysically characterized. Triggered unmasking of a side-chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X-ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an α-helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.

Designing enzyme-like catalysts: a rhodium(II) metallopeptide case study

Chemists have long been fascinated by metalloenzymes and their chemistry. Because enzymes are essential for biological processes and to life itself, they present a key to understanding the world around us. At the same time, if chemists could harness the reactivity and selectivity of enzymes in designed transition-metal catalysts, we would have access to a powerful practical advance in chemistry. But the design of enzyme-like catalysts from scratch presents enormous challenges. Simplified, designed systems often don't provide the opportunity to mimic the complex features of enzymes such as selectivity in polyfunctional environments and access to reactive intermediates incompatible with bulk aqueous solution. Extensive efforts by numerous groups have led to remarkable designed metalloproteins that contain complex folds, including well-defined secondary and tertiary structure surrounding complex polymetallic centers. These structural achievements, however, have not yet led to general approaches to useful catalysts; continued efforts and new insights are needed. Our efforts have combined the attributes of enzymatic and traditional catalysis, bringing the benefits of polypeptide ligands to bear on completely nonbiological transition-metal centers. With a focus on designing useful catalytic activity, we have examined rhodium(II) carboxylates, bound to peptide chains through carboxylate side chains. Among other advantages, these complexes are stable and catalytically active in water. Our efforts have centered on two main interests: (1) understanding how Nature's ligand of choice, polypeptides, can be used to control the chemistry of nonbiological metal centers, and (2) mimicking metalloenzyme characteristics in designed, nonbiological catalysts. This Account conveys our motivation and goals for these studies, outlines progress to date, and discusses the future of enzyme-like catalyst design. In particular, these studies have resulted in on-bead, high-throughput screens for asymmetric metallopeptide catalysts. In addition, peptide-based molecular recognition strategies have facilitated the site-specific modification of protein substrates. Molecular recognition enables site-specific, proximity-driven modification of a broad range of amino acids, and the concepts outlined here are compatible with natural protein substrates and with complex, cell-like environments. We have also explored rhodium metallopeptides as hybrid organic-inorganic inhibitor molecules that block protein-protein interactions.

Hybrid organic-inorganic inhibitors of a PDZ interaction that regulates the endocytic fate of CFTR

Together strong: Cooperative binding of organic (see picture, red) and inorganic fragments provides a strategy for the potent inhibition of protein-protein interactions. By targeting specific Lewis basic side chains in peripheral regions of the binding site for coordination to a rhodium(II) center, the affinity of otherwise weak ligands is improved.

Site-specific protein modification with a dirhodium metallopeptide catalyst

A new method for chemical protein modification is presented utilizing a dirhodium metallopeptide catalyst. The combination of peptide-based molecular recognition and a dirhodium catalyst with broad side-chain scope enables site-specific protein functionalization. The scope and utility of dirhodium-catalyzed biomolecule modification is expanded to allow reaction at physiological pH and in biologically relevant buffer solutions. Specific protein modification is possible directly in E. coli lysate, demonstrating the remarkable activity and specificity of the designed metallopeptide catalyst. Furthermore, a new biotin-diazo conjugate 1b is presented that allows affinity tagging of target proteins.

A general synthesis of dirhodium metallopeptides as MDM2 ligands

A synthesis of multifunctional dirhodium metallopeptide ligands for MDM2 is presented. An orthogonal protection scheme of palladium-catalyzed de-allylation on a metallopeptide substrate allows specific dirhodium incorporation in a complex peptide. Sequence effects on MDM2 binding are discussed.

Covalent Anchor Positions Play an Important Role in Tuning Catalytic Properties of a Rationally Designed MnSalen-containing Metalloenzyme

Two questions important to the success in metalloenzyme design are how to attach or anchor metal cofactors inside protein scaffolds, and in what way such positioning affects enzymatic properties. We have previously reported a dual anchoring method to position a nonnative cofactor, MnSalen (1), inside the heme cavity of apo sperm whale myoglobin (Mb) and showed that the dual anchoring can increase both the activity and enantioselectivity over the single anchoring methods, making this artificial enzyme an ideal system to address the above questions. Here we report systematic investigations of the effect of different covalent attachment or anchoring positions on reactivity and selectivity of sulfoxidation by the MnSalen-containing Mb enzymes. We have found that changing the left anchor from Y103C to T39C has an almost identical effect of increasing rate by 1.8-fold and increasing selectivity by +14% for S, whether the right anchor is L72C or S108C. At the same time, regardless of the identity of the left anchor, changing the right anchor from S108C to L72C increases rate by 4-fold and selectivity by +66%. The right anchor site was observed to have a greater influence than the left anchor site on the reactivity and selectivity in sulfoxidation of a wide scope of other ortho-, meta- and para- substituted substrates. The 1•Mb(T39C/L72C) showed the highest reactivity (TON up to 2.31 min(-1)) and selectivity (ee% up to 83%) among the different anchoring positions examined. Molecular dynamic simulations indicate that these changes in reactivity and selectivity may be due to the steric effects of the linker arms inside the protein cavity. These results indicate that small differences in the anchor positions can result in significant changes in reactivity and enantioselectivity, probably through steric interactions with substrates when they enter the substrate-binding pocket, and that the effects of right and left anchor positions are independent and additive in nature. The finding that the anchoring arms can influence both the positioning of the cofactor and steric control of substrate entrance will help design better functional metalloenzymes with predicted catalytic activity and selectivity.