In silico design of mimosine containing peptides as new efficient chelators of aluminum.

The design of new and efficient chelators that can remove aluminium(iii), a metal with increasing recognition as a potential toxic agent, from biological systems is an area of high therapeutic relevance. In the present paper, we present an extensive computational study of a new promising type of these chelators based on mimosine containing peptides. The reason to choose mimosine is that the sidechain of this residue is similar to deferiprone, a ligand known to tightly interact with highly-valent metals, and in particular with Al(iii). In this article we analyze systematically, using a combination of methods that include QM/MM MD simulations, how the size and sequence of the polypeptides can alter the fundamental binding patterns to aluminum, in comparison with the binding to deferiprone. Particular attention is given towards the identification of the smallest peptide that interacts efficiently with aluminum, since polypeptide size is a fundamental factor to allow a given polypeptide to efficiently cross the cell membrane. The results indicate that the longest peptides, with 8 or 9 amino acids, show no difficulties interacting with Al(iii) in an optimum arrangement. By contrast, when the peptide contains five or six amino acids Al(iii) is pentacoordinated, reducing the stability of the resultant complex. In summary, our study demonstrates that the mimosine containing peptides can efficiently coordinate highly valent metals such as Al(iii), with a subtle dependence of the binding on the specific chain-lengths of the polypeptide. We believe that the present study sheds light on the adequacy of this new type of chelator towards aluminum binding.

Unveiling the Catalytic Role of B-Block Histidine in the N-S Acyl Shift Step of Protein Splicing.

Protein splicing is a post-translational modification that involves the excision of a segment denoted as "intein" and the joining of its two flanking segments. The process is autocatalytic, making inteins appealing for many applications in biotechnology, bioengineering, or medicine. The canonical mechanism of protein splicing is composed of four sequential steps, and is initialized by an N-S or N-O acyl shift to form a linear ester. It is well-established that a histidine, the most conserved amino acid in all inteins, catalyzes this initial step, even though its role remains to be understood. In this study, we combine molecular dynamics simulations and quantum mechanics/molecular mechanics (QM/MM) hybrid calculations to investigate the alternative reaction pathways proposed for the N-S acyl shift in Mycobacterium tuberculosis RecA intein. The results rule out the histidine acting as a base and activating the side chain of Cys1; instead, an aspartate performs this action. In the reaction mechanism proposed herein, denoted as the "Asp422 activated" mechanism, two sequential roles are attributed to the histidine: (i) ground-state destabilization by straining the scissile peptide bond and (ii) protonation of the leaving amide group. In summary, the study provides relevant data to understand the catalytic role of this histidine, and proposes a reaction pathway for the N-S acyl shift reaction in protein splicing that fits with the available experimental data.

Aluminum interaction with glutamate and α-ketoglutarate: a computational study.

Aluminum, although a nonessential element in the human body, has been found to be involved in a variety of diseases. Thus, it has recently been reported that aluminum interferes with the metabolic tricarboxylic acid cycle, in which α-ketoglutarate (α-KG) is involved. α-KG is transformed to glutamate (or vice versa) by glutamate dehydrogenase (GDH). Al(III) inhibits the normal function of GDH, and it was speculated that the reason for this inhibition is triggered by the Al(III)-assisted tautomerization of α-KG from keto to enol. In the present study, we investigate the interaction of both tautomers of α-KG with Al(III) as well the complexation of glutamate to the metal. The results confirm that Al(III) indeed displaces the tautomerization reaction and favors the enol form of α-KG by 28 kcal/mol. However, when citrate is included in the system, the stabilization of the enol tautomer decreases, as this tautomer is only 1.5 kcal/mol more stable than the keto form of α-KG. Finally, possible routes for the complexation of these molecules to Al(III) in a biological environment are discussed; we propose that the ternary complexes formed by Al(III), citrate, and α-KG or glutamate can be the more likely species.

Computational study on the attack of ·OH radicals on aromatic amino acids.

The attack of hydroxyl radicals on aromatic amino acid side chains, namely phenylalanine, tyrosine, and tryptophan, have been studied by using density functional theory. Two reaction mechanisms were considered: 1) Addition reactions onto the aromatic ring atoms and 2) hydrogen abstraction from all of the possible atoms on the side chains. The thermodynamics and kinetics of the attack of a maximum of two hydroxyl radicals were studied, considering the effect of different protein environments at two different dielectric values (4 and 80). The obtained theoretical results explain how the radical attacks take place and provide new insight into the reasons for the experimentally observed preferential mechanism. These results indicate that, even though the attack of the first (·)OH radical on an aliphatic C atom is energetically favored, the larger delocalization and concomitant stabilization that are obtained by attack on the aromatic side chain prevail. Thus, the obtained theoretical results are in agreement with the experimental evidence that the aromatic side chain is the main target for radical attack and show that the first (·)OH radical is added onto the aromatic ring, whereas a second radical abstracts a hydrogen atom from the same position to obtain the oxidized product. Moreover, the results indicate that the reaction can be favored in the buried region of the protein.

Pro-oxidant activity of aluminum: promoting the Fenton reaction by reducing Fe(III) to Fe(II).

The possibility for an Al-superoxide complex to reduce Fe(III) to Fe(II), promoting oxidative damage through the Fenton reaction, is investigated using highly accurate ab initio methods and density functional theory in conjunction with solvation continuum methods to simulate bulk solvent effects. It is found that the redox reaction between Al-superoxide and Fe(III) to produce Fe(II) is exothermic. Moreover, the loss of an electron from the superoxide radical ion in the Al-superoxide complex leads to a spontaneous dissociation of molecular oxygen from aluminum, recovering therefore an Al(3+) hexahydrated complex. As demonstrated in previous studies, this complex is again prone to stabilize another superoxide molecule, suggesting a catalytic cycle that augments the concentration of Fe(II) in the presence of Al(III). Similar results are found for Al(OH)(2+) and Al(OH)(2)(+) hydrolytic species. Our work reinforces the idea that the presence of aluminum in biological systems could lead to an important pro-oxidant activity through a superoxide formation mechanism.

Molecular dynamics simulations of iron- and aluminum-loaded serum transferrin: protonation of Tyr188 is necessary to prompt metal release.

Serum transferrin (sTf) carries iron in blood serum and delivers it into cells by receptor-mediated endocytosis. The protein can also bind other metals, including aluminum. The crystal structures of the metal-free and metal-loaded protein indicate that the metal release process involves an opening of the protein. In this process, Lys206 and Lys296 lying in the proximity of each other form the dilysine pair or, so-called, dilysine trigger. It was suggested that the conformational change takes place due to variations of the protonation state of the dilysine trigger at the acidic endosomal pH. In 2003, Rinaldo and Field (Biophys. J. 85, 3485-3501) proposed that the dilysine trigger alone can not explain the opening and that the protonation of Tyr188 is required to prompt the conformational change. However, no evidence was supplied to support this hypothesis. Here, we present several 60 ns molecular dynamics simulations considering various protonation states to investigate the complexes formed by sTf with Fe(III) and Al(III). The calculations demonstrate that only in those systems where Tyr188 has been protonated does the protein undergo the conformational change and that the dilysine trigger alone does not lead to the opening. The simulations also indicate that the metal release process is a stepwise mechanism, where the hinge-bending motion is followed by the hinge-twisting step. Therefore, the study demonstrates for the first time that the protonation of Tyr188 is required for the release of metal from the metal loaded sTf and provides valuable information about the whole process.

Aluminum speciation in biological environments. The deprotonation of free and aluminum bound citrate in aqueous solution.

Citrate is the main low mass molecule chelator of aluminum in serum, and knowledge of the interaction mode of this organic molecule with this cation is necessary to understand aluminum speciation in biosystems. However, the 1:1 complexation of citric acid to Al(III) is a complex process due to the myriad of coordination sites and protonation states of this molecule. Moreover, due to the acidic character of the complex, its entire experimental characterization is elusive. The system is also challenging from a computational point of view, due to the difficulties in getting a balanced estimation of the large range of solvation free energies encountered for the different protonation states of a multiprotic acid in both situations, complexed and uncomplexed with a trivalent cation. Herein, the deprotonation process of the free citric acid in solution and that interacting with Al(III) have been investigated considering all possible coordination modes and protonation states of the citric acid. All the structures were optimized in solution combining the B3LYP density function method with the polarizable continuum IEFPCM model. In addition, different schemes have been employed to obtain reliable solvation energies. Taking into account the most stable isomer of each protonation state, the pK(a) values were computationally estimated for the free citric acid and that interacting with Al(III), showing a good agreement with the experimental data. All these results shed light on how the deprotonation process of the citric acid takes place, and show that Al(III) not only increases the acidity of the molecule, but also changes qualitatively the deprotonation pattern of the citric acid. This information is highly relevant to understand aluminum speciation in biological environments, for which citrate is the main low molecular weight chelator, and responsible for its cellular in-take.

A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH.

Serum transferrin (sTf) transports iron in serum and internalizes in cells via receptor mediated endocytosis. Additionally, sTf has been identified as the predominant aluminum carrier in serum. Some questions remain unclear about the exact mechanism for the metal release or whether the aluminum and iron show the same binding mode during the entire process. In the present work, simulation techniques at quantum and atomic levels have been employed in order to gain access into a molecular level understanding of the metal-bound sTf complex, and to describe the binding of Al(III) and Fe(III) ions to sTf. First, hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations were carried out in order to analyze the dynamics of the aluminum-loaded complex, taking into account the different pH conditions in blood and into the cell. Moreover, the complexes formed by transferrin with Al(III) and Fe(III) were optimized with high level density functional theory (DFT)/MM methods. All these results indicate that the interaction mode of Al(III) and Fe(III) with sTf change upon different pH conditions, and that the coordination of Al(III) and Fe(III) is not equivalent during the metal intake, transport and release processes. Our results emphasize the importance of the pH on the metal binding and release mechanism and suggest that Al(III) can follow the iron pathway to get access into cells, although once there, it may show a different binding mode, leading to a different mechanism for its release.

Pro-oxidant activity of aluminum: stabilization of the aluminum superoxide radical ion.

The pro-oxidant activity of aluminum, a nonredox metal, through superoxide formation is studied by theoretical methods, determining the ESR g-tensor values of O2(•­) with a variety of metals and the reaction energies for Al3+ superoxide affinity in solution. First, the intrinsic ability of aluminum to induce a splitting of the πg levels is compared to that of other significant biological metals, such as Na+, K+, Mg2+, and Ca2+. Additional properties such as bond lengths, ionization potentials, and electron affinities are also determined, and the coherency with the trends observed from ESR g-tensor values is analyzed. As it corresponds to the high charge and its small size, there is a strong interaction between Al3+ and the superoxide. We predict that this strong inherent interaction remains when aluminum is microsolvated. Finally, we analyze the possibility of Al3+ superoxide formation in solution, leading to the conclusion that substitution of the first coordination shell water molecules is plausible, but not of hydroxides. This points to the possibility of Al3+ superoxide formation in solution, which would be pH-dependent. Taking into account the earlier established linear relationship between metal­superoxide interactions and promoting effects in electron-transfer reactions, our work reinforces the idea that the presence of aluminum in biological systems could lead to an important pro-oxidant activity through a superoxide formation mechanism.