A survey of methionine-aromatic interaction geometries in the oxidoreductase class of enzymes: What could Met-aromatic interactions be doing near metal sites?

Amino acid positions near the active site determine the reduced activity of human ACOD1 compared to murine ACOD1

cis-Aconitate decarboxylase (ACOD1, IRG1) converts cis-aconitate to the immunomodulatory and antibacterial metabolite itaconate. Although the active site residues of human and mouse ACOD1 are identical, the mouse enzyme is about fivefold more active. Aiming to identify the cause of this difference, we mutated positions near the active site in human ACOD1 to the corresponding residues of mouse ACOD1 and measured resulting activities in vitro and in transfected cells. Interestingly, Homo sapiens is the only species with methionine instead of isoleucine at residue 154 and introduction of isoleucine at this position increased the activity of human ACOD1 1.5-fold in transfected cells and 3.5-fold in vitro. Enzyme activity of gorilla ACOD1, which is almost identical to the human enzyme but has isoleucine at residue 154, was similar to the mouse enzyme in vitro. Met154 in human ACOD1 forms a sulfur-π bond to Phe381, which is positioned to impede access of the substrate to the active site. It appears that the ACOD1 sequence has changed at position 154 during human evolution, resulting in a pronounced decrease in activity. This change might have offered a selective advantage in diseases such as cancer.

Proximal Methionine Amino Acid Residue Affects the Properties of Redox-Active Tryptophan in an Artificial Model Protein

Redox-active amino acid residues are at the heart of biological electron-transfer reactions. They play important roles in natural protein functions and are implicated in disease states (e.g., oxidative-stress-associated disorders). Tryptophan (Trp) is one such redox-active amino acid residue, and it has long been known to serve a functional role in proteins. Broadly speaking, there is still much to learn about the local features that make some Trp redox active and others inactive. Herein, we describe a new protein model system where we investigate how a methionine (Met) residue proximal to a redox-active Trp affects its reactivity and spectroscopy. We use an artificial variant of azurin from Pseudomonas aeruginosa to produce these models. We employ a series of UV-visible spectroscopy, electrochemistry, electron paramagnetic resonance, and density functional theory experiments to demonstrate the effect that placing Met near Trp radicals has in the context of redox proteins. The introduction of Met proximal to Trp lowers its reduction potential by ca. 30 mV and causes clear shifts in the optical spectra of the corresponding radicals. While the effect may be small, it is significant enough to be a way for natural systems to tune Trp reactivity.

Photodynamic Activation of Cholecystokinin 1 Receptor Is Conserved in Mammalian and Avian Pancreatic Acini

Cholecystokinin 1 receptor (CCK1R) is the only G protein coupled receptor that is activated in type II photodynamic action, but whether this is a property common to both mammalian and avian species is not known. In this work, pancreatic acini were isolated from the rat, mouse, and Peking duck, and photodynamic CCK1R activation was examined. Isolated pancreatic acini were exposed to photosensitizer sulphonated aluminum phthalocyanine (SALPC) and photodynamic action elicited by a brief light-emitting diode (LED 675 nm) pulse (1.5 min); photodynamic CCK1R activation was assessed by Fura-2 fluorescent calcium imaging. Photodynamic action was found to induce persistent calcium oscillations in rat, mouse, and Peking duck pancreatic acini, with the sensitivity order of mouse > rat > Peking duck. Photodynamically-activated CCK1R could be inhibited reversibly by CCK1R antagonist devazepide (1 μM); photodynamic CCK1R activation was blocked by pre-incubation with 1O2 quencher Trolox C (300 µM). The sensitivity of photodynamic CCK1R activation was correlated with the increasing size of the disordered region in intracellular loop 3. These data suggest that photodynamic CCK1R activation is conserved in both mammalian and avian species, as evidenced by the presence of the photodynamic activation motif “YFM” in transmembrane domain 3.

Photodynamic Activation of Cholecystokinin 1 Receptor Is Conserved in Mammalian and Avian Pancreatic Acini

Cholecystokinin 1 receptor (CCK1R) is the only G protein coupled receptor that is activated in type II photodynamic action, but whether this is a property common to both mammalian and avian species is not known. In this work, pancreatic acini were isolated from the rat, mouse, and Peking duck, and photodynamic CCK1R activation was examined. Isolated pancreatic acini were exposed to photosensitizer sulphonated aluminum phthalocyanine (SALPC) and photodynamic action elicited by a brief light-emitting diode (LED 675 nm) pulse (1.5 min); photodynamic CCK1R activation was assessed by Fura-2 fluorescent calcium imaging. Photodynamic action was found to induce persistent calcium oscillations in rat, mouse, and Peking duck pancreatic acini, with the sensitivity order of mouse > rat > Peking duck. Photodynamically-activated CCK1R could be inhibited reversibly by CCK1R antagonist devazepide (1 μM); photodynamic CCK1R activation was blocked by pre-incubation with 1O2 quencher Trolox C (300 µM). The sensitivity of photodynamic CCK1R activation was correlated with the increasing size of the disordered region in intracellular loop 3. These data suggest that photodynamic CCK1R activation is conserved in both mammalian and avian species, as evidenced by the presence of the photodynamic activation motif “YFM” in transmembrane domain 3.

On the roles of methionine and the importance of its microenvironments in redox metalloproteins

The amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.

Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases

We report the measurement and analysis of sulfonium-π, thioether-π, and ammonium-π interactions in a β-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-π interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-π interaction. In comparing sulfonium-π versus sulfur-π interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-π interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-π interaction in going from SAM to SAH may contribute to turnover of the cofactor.

Clustering of Aromatic Amino Acid Residues around Methionine in Proteins

Short-range, non-covalent interactions between amino acid residues determine protein structures and contribute to protein functions in diverse ways. The interactions of the thioether of methionine with the aromatic rings of tyrosine, tryptophan, and/or phenylalanine has long been discussed and such interactions are favorable on the order of 1–3 kcal mol⁻¹. Here, we carry out a new bioinformatics survey of known protein structures where we assay the propensity of three aromatic residues to localize around the [-CH₂-S-CH₃] of methionine. We term these groups “3-bridge clusters”. A dataset consisting of 33,819 proteins with less than 90% sequence identity was analyzed and such clusters were found in 4093 structures (or 12% of the non-redundant dataset). All sub-classes of enzymes were represented. A 3D coordinate analysis shows that most aromatic groups localize near the CH₂ and CH₃ of methionine. Quantum chemical calculations support that the 3-bridge clusters involve a network of interactions that involve the Met-S, Met-CH₂, Met-CH₃, and the π systems of nearby aromatic amino acid residues. Selected examples of proposed functions of 3-bridge clusters are discussed.