A phage-displayed disulfide constrained peptide discovery platform yields novel human plasma protein binders.

Disulfide constrained peptides (DCPs) show great potential as templates for drug discovery. They are characterized by conserved cysteine residues that form intramolecular disulfide bonds. Taking advantage of phage display technology, we designed and generated twenty-six DCP phage libraries with enriched molecular diversity to enable the discovery of ligands against disease-causing proteins of interest. The libraries were designed based on five DCP scaffolds, namely Momordica charantia 1 (Mch1), gurmarin, Asteropsin-A, antimicrobial peptide-1 (AMP-1), and potato carboxypeptidase inhibitor (CPI). We also report optimized workflows for screening and producing synthetic and recombinant DCPs. Examples of novel DCP binders identified against various protein targets are presented, including human IgG Fc, serum albumin, vascular endothelial growth factor-A (VEGF-A) and platelet-derived growth factor (PDGF). We identified DCPs against human IgG Fc and serum albumin with sub-micromolar affinity from primary panning campaigns, providing alternative tools for potential half-life extension of peptides and small protein therapeutics. Overall, the molecular diversity of the DCP scaffolds included in the designed libraries, coupled with their distinct biochemical and biophysical properties, enables efficient and robust identification of de novo binders to drug targets of therapeutic relevance.

Cellular uptake of a cystine-knot peptide and modulation of its intracellular trafficking.

Cyclotides or cyclic cystine-knot peptides have emerged as a promising class of pharmacological ligands that modulate protein function. Interestingly, very few cyclotides have been shown to enter into cells. Yet, it remains unknown whether backbone cyclization is required for their cellular internalization. In this report, we studied the cellular behavior of EETI-II, a model acyclic cystine-knot peptide. Even though synthetic methods have been used to generate EETI-II, recombinant methods that allow efficient large scale biosynthesis of EETI-II have been lagging. Here, we describe a novel protocol for recombinant generation of folded EETI-II in high yields and to near homogeneity. We also uncover that EETI-II is efficiently uptaken via an active endocytic pathway to early endosomes in mammalian cells, eventually accumulating in late endosomes and lysosomes. Notably, co-incubation with a cell-penetrating peptide enhanced the cellular uptake and altered the trafficking of EETI-II, leading to its evasion of lysosomes. Our results demonstrate the feasibility of modulating the subcellular distribution and intracellular targeting of cystine-knot peptides, and hence enable future exploration of their utility in drug discovery and delivery.

Copper regulates cyclic-AMP-dependent lipolysis.

Cell signaling relies extensively on dynamic pools of redox-inactive metal ions such as sodium, potassium, calcium and zinc, but their redox-active transition metal counterparts such as copper and iron have been studied primarily as static enzyme cofactors. Here we report that copper is an endogenous regulator of lipolysis, the breakdown of fat, which is an essential process in maintaining body weight and energy stores. Using a mouse model of genetic copper misregulation, in combination with pharmacological alterations in copper status and imaging studies in a 3T3-L1 white adipocyte model, we found that copper regulates lipolysis at the level of the second messenger, cyclic AMP (cAMP), by altering the activity of the cAMP-degrading phosphodiesterase PDE3B. Biochemical studies of the copper-PDE3B interaction establish copper-dependent inhibition of enzyme activity and identify a key conserved cysteine residue in a PDE3-specific loop that is essential for the observed copper-dependent lipolytic phenotype.

Backbone cyclization of a recombinant cystine-knot peptide by engineered Sortase A.

Cyclotides belong to the family of cyclic cystine-knot peptides and have shown promise as scaffolds for protein engineering and pharmacological modulation of cellular protein activity. Cyclotides are characterized by a cystine-knotted topology and a head-to-tail cyclic polypeptide backbone. While they are primarily produced in plants, cyclotides have also been obtained by chemical synthesis. However, there is still a need for methods to generate cyclotides in high yields to near homogeneity. Here, we report a biomimetic approach which utilizes an engineered version of the enzyme Sortase A to catalyze amide backbone cyclization of the recombinant cyclotide MCoTI-II, thereby allowing the efficient production of active homogenous species in high yields. Our results provide proof of concept for using engineered Sortase A to produce cyclic MCoTI-II and should be generally applicable to generating other cyclic cystine-knot peptides.

Metal transfer within the Escherichia coli HypB-HypA complex of hydrogenase accessory proteins.

The maturation of [NiFe]-hydrogenase in Escherichia coli is a complex process involving many steps and multiple accessory proteins. The two accessory proteins HypA and HypB interact with each other and are thought to cooperate to insert nickel into the active site of the hydrogenase-3 precursor protein. Both of these accessory proteins bind metal individually, but little is known about the metal-binding activities of the proteins once they assemble together into a functional complex. In this study, we investigate how complex formation modulates metal binding to the E. coli proteins HypA and HypB. This work lead to a re-evaluation of the HypA nickel affinity, revealing a KD on the order of 10(-8) M. HypA can efficiently remove nickel, but not zinc, from the metal-binding site in the GTPase domain of HypB, a process that is less efficient when complex formation between HypA and HypB is disrupted. Furthermore, nickel release from HypB to HypA is specifically accelerated when HypB is loaded with GDP, but not GTP. These results are consistent with the HypA-HypB complex serving as a transfer step in the relay of nickel from membrane transporter to its final destination in the hydrogenase active site and suggest that this complex contributes to the metal fidelity of this pathway.

Nickel binding and [NiFe]-hydrogenase maturation by the metallochaperone SlyD with a single metal-binding site in Escherichia coli.

SlyD (sensitive to lysis D) is a nickel metallochaperone involved in the maturation of [NiFe]-hydrogenases in Escherichia coli (E. coli) and specifically contributes to the nickel delivery step during enzyme biosynthesis. This protein contains a C-terminal metal-binding domain that is rich in potential metal-binding residues that enable SlyD to bind multiple nickel ions with high affinity. The SlyD homolog from Thermus thermophilus does not contain the extended cysteine- and histidine-rich C-terminal tail of the E. coli protein, yet it binds a single Ni(II) ion tightly. To investigate whether a single metal-binding motif can functionally replace the full-length domain, we generated a truncation of E. coli SlyD, SlyD155. Ni(II) binding to SlyD155 was investigated by using isothermal titration calorimetry, NMR and electrospray ionization mass spectrometry measurements. This in vitro characterization revealed that SlyD155 contains a single metal-binding motif with high affinity for nickel. Structural characterization by X-ray absorption spectroscopy and NMR indicated that nickel was coordinated in an octahedral geometry with at least two histidines as ligands. Heterodimerization between SlyD and another hydrogenase accessory protein, HypB, is essential for optimal hydrogenase maturation and was confirmed for SlyD155 via cross-linking experiments and NMR titrations, as were conserved chaperone and peptidyl-prolyl isomerase activities. Although these properties of SlyD are preserved in the truncated version, it does not modulate nickel binding to HypB in vitro or contribute to the maturation of [NiFe]-hydrogenases in vivo, unlike the full-length protein. This study highlights the importance of the unusual metal-binding domain of E. coli SlyD in hydrogenase biogenesis.

Escherichia coli SlyD, more than a Ni(II) reservoir.

SlyD interacts with HypB and contributes to nickel insertion during [NiFe]-hydrogenase biogenesis. Herein, we provide evidence of SlyD acting as a nickel storage determinant in Escherichia coli and show that this Ni(II) can be mobilized to HypB in vitro even under competitive conditions. Furthermore, SlyD enhances the GTPase activity of HypB, and acceleration of release of Ni(II) from HypB is more pronounced when HypB is GDP-bound. The data support a model in which a HypB-SlyD complex establishes communication between GTP hydrolysis and nickel delivery and provide insight into the role of the HypB-SlyD complex during [NiFe]-hydrogenase biosynthesis.

Metal selectivity of the Escherichia coli nickel metallochaperone, SlyD.

SlyD is a Ni(II)-binding protein that contributes to nickel homeostasis in Escherichia coli. The C-terminal domain of SlyD contains a rich variety of metal-binding amino acids, suggesting broader metal binding capabilities, and previous work demonstrated that the protein can coordinate several types of first-row transition metals. However, the binding of SlyD to metals other than Ni(II) has not been previously characterized. To improve our understanding of the in vitro metal-binding activity of SlyD and how it correlates with the in vivo function of this protein, the interactions between SlyD and the series of biologically relevant transition metals [Mn(II), Fe(II), Co(II), Cu(I), and Zn(II)] were examined by using a combination of optical spectroscopy and mass spectrometry. Binding of SlyD to Mn(II) or Fe(II) ions was not detected, but the protein coordinates multiple ions of Co(II), Zn(II), and Cu(I) with appreciable affinity (K(D) values in or below the nanomolar range), highlighting the promiscuous nature of this protein. The order of affinities of SlyD for the metals examined is as follows: Mn(II) and Fe(II) < Co(II) < Ni(II) ~ Zn(II) ≪ Cu(I). Although the purified protein is unable to overcome the large thermodynamic preference for Cu(I) and exclude Zn(II) chelation in the presence of Ni(II), in vivo studies reveal a Ni(II)-specific function for the protein. Furthermore, these latter experiments support a specific role for SlyD as a [NiFe]-hydrogenase enzyme maturation factor. The implications of the divergence between the metal selectivity of SlyD in vitro and the specific activity in vivo are discussed.

Relationship between the GTPase, metal-binding, and dimerization activities of E. coli HypB.

Biosynthesis of the metallocenter in the active site of the [NiFe] hydrogenase enzyme requires the accessory protein HypB, which is a metal-binding GTPase. In this study, the interplay between the individual activities of Escherichia coli HypB was examined. The full-length protein undergoes nucleotide-responsive dimerization that is disrupted upon mutation of L242 and L246 to alanine. This mutant HypB is monomeric under all of the conditions investigated but the inability of L242A/L246A HypB to dimerize does not abolish its GTPase activity and the monomeric protein has metal-binding behavior similar to that of wild-type HypB. Furthermore, expression of L242A/L246A HypB in vivo results in hydrogenase activity that is approximately half of the activity produced by the wild-type control, suggesting that dimerization of HypB does not have a critical role in the hydrogenase maturation pathway. In contrast, the GTPase activity of HypB is modulated by metal loading of the protein. These results provide insight into the role of HypB in hydrogenase biosynthesis.

Microbial nickel proteins.

Microorganisms have evolved to utilize nickel ions in several different enzyme systems that enable these organisms to survive and proliferate in various environments. Typically the biosynthesis of these nickel containing enzymes are multi-step processes involving a number of accessory proteins, with one or more proteins dedicated to the delivery of the cognate nickel ion to the active site of the enzyme. This review highlights the nickel proteins dedicated to the biogenesis of [NiFe]-hydrogenase, urease, and carbon monoxide dehydrogenase, and aims to summarize our current knowledge of these unique proteins. Putative proteins that function in excess nickel storage and/or detoxification, through sequestration of considerable amount of nickel, are also discussed.

The Ni(II)-binding properties of the metallochaperone SlyD.

Metallochaperones are essential for the safe and targeted delivery of necessary yet toxic metal cofactors to their respective protein partners. In this study we examine the nickel-binding properties of the Escherichia coli protein SlyD, a factor that contributes to optimal nickel accumulation in this organism. This protein is also required for E. coli energy metabolism because it participates in the nickel insertion step during [Ni-Fe]-hydrogenase metallocenter assembly. Our study demonstrates that SlyD is a multiple nickel ion binding protein. The analysis of noncovalent metal-protein complexes via electrospray ionization mass spectrometry revealed that SlyD binds up to seven nickel ions in a noncooperative manner with submicromolar affinity (<2 microM, upper limit) and that the protein exists in a dynamic mixture of metalloforms that is dependent on the availability of nickel ions in solution. Structural analysis indicates that this metallochaperone undergoes small but distinct changes in the structure upon metal binding and that the nickel-binding sites are assembled through beta-turn formation. Although the C-terminal metal-binding domain is primarily responsible for metal chelation, we find that metal binding also perturbs the structure of the N-terminal domains. An investigation of the nickel sites by using X-ray absorption spectroscopy shows that SlyD binds nickel ions by adapting several different geometries and coordination numbers. Finally, the characterization of SlyD mutants demonstrates that the cysteine residues in the C-terminal domain confer tighter affinity as well as increased binding capacity to SlyD. On the basis of the presented data a model for nickel binding to SlyD as well as its role in nickel homeostasis is discussed.

Spectroscopic, electrochemical, and computational aspects of the charge distribution in Ru(acac)2(R-o-benzoquinonediimine) complexes.

The syntheses and properties are reported for five Ru(acac)2(R-bqdi) species where acac is acetylacetonate, and R-bqdi is the non-innocent ligand ortho-benzoquinonediimine substituted with R = H (1), 4,5-dimethyl (2), 4-Cl (3), or 4-NO2 (4), and N,N''-dimethylsulfonyl (5). Their identities and purities were confirmed by NMR, mass spectra, IR and analytical data. The large degree of metal-to-ligand pi-back-donation was analyzed by spectroscopic (UV/visible, IR, Raman) and electrochemical data, supported by molecular orbital composition computations using density functional theory (DFT), with the polarizable continuum model (PCM) to mimic the presence of solvent, and prediction of electronic spectra using time-dependent DFT methods. Extended charge decomposition analysis (ECDA) and natural population analysis (NPA) both produced a detailed picture of the bonding between the non-innocent bqdi ligand and the metal center, allowing correlations to be drawn between the nature of the R substituents and the quantitative extent of pi-back-donation and sigma-forward donation. In conclusion, the issue of whether these species are best regarded as Ru(II)(quinonediimine) or coupled Ru(III)(semiquinonediiminate) species is discussed.

Structural and spectroscopic impact of tuning the stereochemical activity of the lone pair in lead(II) cyanoaurate coordination polymers via ancillary ligands.

The reaction of Pb(ClO4)2 x xH2O, an ancillary ligand L, and two equivalents of Au(CN)2(-) gave a series of crystalline coordination polymers, which were structurally characterized. The ligands were chosen to represent a range of increasing basicity, to influence the stereochemical activity (i.e., p-orbital character) of the Pb(II) lone pair. The Pb(II) center in [Pb(1,10-phenanthroline)2][Au(CN)2]2 (1) is 8-coordinate, with a stereochemically inactive lone pair; all 8 Pb-N bonds are similar. The Au(CN)2(-) units propagate a 2-D brick-wall structure. In [Pb(2,2'-bipyridine)2][Au(CN)2]2 (2), the 8-coordinate Pb(II) center has asymmetric Pb-N bond lengths, indicating moderate lone pair stereochemical activity; the supramolecular structure forms a 1-D chain/ribbon motif. For [Pb(ethylenediamine)][Au(CN)2]2 (3), the Pb(II) is only 5-coordinate and extremely asymmetric, with Pb-N bond lengths from 2.123(7) to 3.035(9) A; a rare Pb-Au contact of 3.5494(5) A is also observed. The Au(CN)2(-) units connect the Pb(ethylenediamine) centers to form 1-D zigzag chains which stack via Au-Au interactions of 3.3221(5) A to yield a 2-D sheet. (207)Pb MAS NMR of the polymers indicates an increase in both the chemical shielding span and isotropic chemical shift with increasing Pb(II) coordination sphere anisotropy (from delta iso = -2970 and Omega = 740 for 1 to delta iso = -448 and Omega = 3980 for 3). The shielding anisotropy is positively correlated with Pb(II) p-character, and reflects a direct connection between the NMR parameters and lone-pair activity. Solid-state variable-temperature luminescence measurements indicate that the emission bands at 520 and 494 nm, for 1 and 2, respectively, can be attributed to Pb --> L transitions, by comparison with simple [Pb(L)2](ClO4)2 salts. In contrast, two emission bands for 3 at 408 and 440 nm are assignable to Au-Au and Pb-Au-based transitions, respectively, as supported by single-point density-functional theory calculations on models of 3.