Carboxypeptidase A: native, zinc-removed and mercury-replaced forms

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF_1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.

Heteroleptic Coordination Environments in Metal-Mediated DNA G-Quadruplexes

The presence of metal centers with often highly conserved coordination environments is crucial for roughly half of all proteins, having structural, regulatory, or enzymatic function. To understand and mimic the function of metallo-enzymes, bioinorganic chemists pursue the challenge of synthesizing model compounds with well-defined, often heteroleptic metal sites. Recently, we reported the design of tailored homoleptic coordination environments for various transition metal cations based on unimolecular DNA G-quadruplex structures, templating the regioselective positioning of imidazole ligandosides L^I. Here, we expand this modular system to more complex, heteroleptic coordination environments by combining L^I with a new benzoate ligandoside L^B within the same oligonucleotide. The modifications still allow the correct folding of parallel tetramolecular and antiparallel unimolecular G-quadruplexes. Interestingly, the incorporation of L^B results in strong destabilization expressed in lower thermal denaturation temperatures T_m. While no transition metal cations could be bound by G-quadruplexes containing only L^B, heteroleptic derivatives containing both L^I and L^B were found to complex Cu^II, Ni^II, and Zn^II. Especially in case of Cu^II we found strong stabilizations of up to ΔT_m = +34°C. The here shown system represents an important step toward the design of more complex coordination environments inside DNA scaffolds, promising to culminate in the preparation of functional metallo-DNAzymes.

pH-Dependent reactivity for glycyl-L-tyrosine in carboxypeptidase-A-catalyzed hydrolysis

The dipeptide glycyl-L-tyrosine (GY) can be either a substrate for carboxypeptidase A (CPA) or an inhibitor, depending on pH. In this work, we investigate the pH-dependent reactivity of this dipeptide in CPA-catalyzed hydrolysis using a combined quantum mechanical and molecular mechanical method. It is shown that the monoionic form of the dipeptide, prevalent at high pH, chelates the active site zinc ion, rendering the enzyme inactive. This inhibitory form is consistent with an earlier X-ray structure of the CPA-GY complex. On the other hand, the prevailing di-ionic form of the dipeptide at low pH was found to undergo hydrolysis via a nucleophilic mechanism, leading to an acyl-enzyme complex. The stability of this reaction intermediate is consistent with previous low-temperature solid-state NMR results. The calculated overall free-energy barrier of 20.1 kcal/mol is in excellent agreement with the experimental value of 19.9 kcal/mol.

Catalysis of carboxypeptidase A: promoted-water versus nucleophilic pathways

The catalytic mechanism of carboxypeptidase A (CPA) for the hydrolysis of ester substrates is investigated using hybrid quantum mechanical/molecular mechanical (QM/MM) methods and high-level density functional theory. The prevailing mechanism was found to utilize an active-site water molecule assisted by Glu270, and this so-called promoted-water pathway is similar to that in the CPA catalyzed proteolytic reaction (D. Xu and H. Guo, J. Am. Chem. Soc. 2009, 131, 9780). On the other hand, our simulations indicated the existence of an alternative pathway due to direct nucleophilic attack of Glu270 on the scissile carbonyl carbon. This so-called nucleophilic pathway, which is not viable in proteolytic reactions, leads to a stable acyl-enzyme complex. However, the nucleophilic pathway is nonproductive as it is blocked by a high barrier in the deacylation step. On the basis of results reported here and in our earlier publication, a unified model is proposed to account for nearly all experimental observations concerning the catalysis of CPA.

On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes

Zinc metalloenzymes play a major role in key biological processes and carboxypeptidase-A (CPA) is a major prototype of such enzymes. The present work quantifies the energetics of the catalytic reaction of CPA and its mutants using the empirical valence bond (EVB) approach. The simulations allow us to quantify the origin of the catalytic power of this enzyme and to examine different mechanistic alternatives. The first step of the analysis used experimental information to determine the activation energy of each assumed mechanism of the reference reaction without the enzyme. The next step of the analysis involved EVB simulations of the reference reaction and then a calibration of the simulations by forcing them to reproduce the energetics of the reference reaction, in each assumed mechanism. The calibrated EVB was then used in systematic simulations of the catalytic reaction in the protein environment, without changing any parameter. The simulations reproduced the observed rate enhancement in two feasible general acid-general base mechanisms (GAGB-1 and GAGB-2), although the calculations with the GAGB-2 mechanism underestimated the catalytic effect in some treatments. We also reproduced the catalytic effect in the R127A mutant. The mutation calculations indicate that the GAGB-2 mechanism is significantly less likely than the GAGB-1 mechanism. It is also found, that the enzyme loses all its catalytic effect without the metal. This and earlier studies show that the catalytic effect of the metal is not some constant electrostatic effect, that can be assessed from gas phase studies, but a reflection of the dielectric effect of the specific environment.

Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism

Carboxypeptidase A is a zinc-containing enzyme that cleaves the C-terminal residue in a polypeptide substrate. Despite much experimental work, there is still a significant controversy concerning its catalytic mechanism. In this study, the carboxypeptidase A-catalyzed hydrolysis of the hippuryl-L-Phe molecule (k(cat) = 17.7 +/- 0.7 s(-1)) is investigated using both density functional theory and a hybrid quantum mechanical/molecular mechanical approach. The enzymatic reaction was found to proceed via a promoted-water pathway with Glu270 serving as the general base and general acid. Free-energy calculations indicate that the first nucleophilic addition step is rate-limiting, with a barrier of 17.9 kcal/mol. Besides activating the zinc-bound water nucleophile, the zinc cofactor also serves as an electrophilic catalyst that stabilizes the substrate carbonyl oxygen during the formation of the tetrahedral intermediate. In the Michaelis complex, Arg127, rather than Zn(II), is responsible for the polarization of the substrate carbonyl and it also serves as the oxyanion hole. As a result, its mutation leads to a higher free-energy barrier, in agreement with experimental observations.

De novo ligand design to partially flexible active sites: application of the ReFlex algorithm to carboxypeptidase A, acetylcholinesterase, and the estrogen receptor

Reflex is a recent algorithm in the de novo ligand design software, SkelGen, that allows the flexibility of amino acid side chains in a protein to be taken into account during the drug-design process. In this paper the impact of flexibility on the solutions generated by the de novo design algorithm, when applied to carboxypeptidase A, acetylcholinesterase, and the estrogen receptor (ER), is investigated. The results for each of the targets indicate that when allowing side-chain movement in the active site, solutions are generated that were not accessible from the multiple static protein conformations available for these targets. Furthermore, an analysis of structures generated in a flexible versus a static ER active site suggests that these additional solutions are not merely noise but contain many interesting chemotypes.

Identification of the zinc binding ligands and the catalytic residue in human aspartoacylase, an enzyme involved in Canavan disease

Canavan disease is an autosomal-recessive neurodegenerative disorder caused by a lack of aspartoacylase, the enzyme that degrades N-acetylaspartate (NAA) into acetate and aspartate. With a view to studying the mechanisms underlying the action of human aspartoacylase (hASP), this enzyme was expressed in a heterologous Escherichia coli system and characterized. The recombinant protein was found to have a molecular weight of 36 kDa and kinetic constants K(m) and k(cat) of 0.20 +/- 0.03 mM and 14.22 +/- 0.48 s(-1), respectively. Sequence alignment showed that this enzyme belongs to the carboxypeptidase metalloprotein family having the conserved motif H(21)xxE(24)(91aa)H(116). We further investigated the active site of hASP by performing modelling studies and site-directed mutagenesis. His21, Glu24 and His116 were identified here for the first time as the residues involved in the zinc-binding process. In addition, mutations involving the Glu178Gln and Glu178Asp residues resulted in the loss of enzyme activity. The finding that wild-type and Glu178Asp have the same K(m) but different k(cat) values confirms the idea that the carboxylate group contributes importantly to the enzymatic activity of aspartoacylase.

Self-assembly of the 2-His-1-carboxylate facial triad in mononuclear iron(II) and zinc(II) models of metalloenzyme active sites

A synthetic strategy involving the use of sterically hindered N-donor and terphenylcarboxylate ligands has been used to prepare complexes of iron(II) and zinc(II) that feature N2(carboxylate) donors. X-ray crystallographic and NMR data show that the 2-His-1-carboxylate facial triad found in metalloenzyme active sites is closely modeled by the mononuclear complexes. In addition, by virtue of the flexibility of the ligands used, the geometries and coordination environments of the complexes display carboxylate binding mode differences such as those seen in the enzymes.

Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks

Accurate predictions of metal-binding sites in proteins by using sequence as the only source of information can significantly help in the prediction of protein structure and function, genome annotation, and in the experimental determination of protein structure. Here, we introduce a method for identifying histidines and cysteines that participate in binding of several transition metals and iron complexes. The method predicts histidines as being in either of two states (free or metal bound) and cysteines in either of three states (free, metal bound, or in disulfide bridges). The method uses only sequence information by utilizing position-specific evolutionary profiles as well as more global descriptors such as protein length and amino acid composition. Our solution is based on a two-stage machine-learning approach. The first stage consists of a support vector machine trained to locally classify the binding state of single histidines and cysteines. The second stage consists of a bidirectional recurrent neural network trained to refine local predictions by taking into account dependencies among residues within the same protein. A simple finite state automaton is employed as a postprocessing in the second stage in order to enforce an even number of disulfide-bonded cysteines. We predict histidines and cysteines in transition-metal-binding sites at 73% precision and 61% recall. We observe significant differences in performance depending on the ligand (histidine or cysteine) and on the metal bound. We also predict cysteines participating in disulfide bridges at 86% precision and 87% recall. Results are compared to those that would be obtained by using expert information as represented by PROSITE motifs and, for disulfide bonds, to state-of-the-art methods.

Flexibility of metal binding sites in proteins on a database scale

Protein metal binding sites in the pre-bound (apo) state, and their rearrangements upon metal binding were not analyzed previously at a database scale. Such a study may provide valuable information for metal binding site prediction and design. A high resolution, nonredundant dataset of 210 metal binding sites was created, containing all available representatives of apo-holo pairs for the most populated metals in the PDB. More than 40% of the sites underwent rearrangements upon metal binding. In 30 cases rearrangements involved the backbone. The tendency for side-chain rearrangement inversely correlates with the number of first-shell residues. Analysis of side-chain reorientations as a result of metal binding showed that in 95% of the rigid-backbone binding sites at most one side chain moved. Thus, in general, part of the first coordination shell is already in place in the pre-bound form. The frequencies of side-chain reorientation directly correlated with metal ligand flexibility and solvent accessibility in the apo state.

Native carboxypeptidase A in a new crystal environment reveals a different conformation of the important tyrosine 248

Native carboxypeptidase A has been crystallized in a new crystal form, and the structure has been refined with X-ray data to 2.0 A resolution. In contrast to the previously published structure [Rees, D. C., Lewis, M., and Lipscomb, W. N. (1983) J. Mol. Biol. 168, 367-387], no active-site amino acids are involved in the crystal packing. The important Tyr248 is stabilized inside the active site by a hydrogen bond and by interactions with Ile247. The proposed role of Tyr248 in the induced fit mechanism is therefore not supported by the findings in this structure of native carboxypeptidase A. The structure has a partly populated inhibitory Zn2+ site in close proximity to the catalytic Zn2+ as evident from X-ray anomalous dispersion data. A hydroxo bridge is found between the catalytic Zn2+ and the inhibitory Zn2+ with a Zn2+-Zn2+ distance of 3.48 A. In addition, the inhibitory Zn2+ has Glu270 as a monodentate ligand. No other protein ligands to the inhibitory Zn2+ are seen. The crystals were grown at 0.3 M LiCl and weak evidence for a binding site for partly competitive inhibitory anions is observed.