The importance of the helical structure of a MamC-derived magnetite-interacting peptide for its function in magnetite formation

Abstract

Biomineralization is the process of mineral formation by organisms and involves the uptake of ions from the environment in order to produce minerals, with the process generally being mediated by proteins. Most proteins that are involved in mineral interactions are predicted to contain disordered regions containing large numbers of negatively charged amino acids. Magnetotactic bacteria, which are used as a model system for iron biomineralization, are Gram-negative bacteria that can navigate through geomagnetic fields using a specific organelle, the magnetosome. Each organelle comprises a membrane-enveloped magnetic nanoparticle, magnetite, the formation of which is controlled by a specific set of proteins. One of the most abundant of these proteins is MamC, a small magnetosome-associated integral membrane protein that contains two transmembrane α-helices connected by an ∼21-amino-acid peptide. In vitro studies of this MamC peptide showed that it forms a helical structure that can interact with the magnetite surface and affect the size and shape of the growing crystal. Our results show that a disordered structure of the MamC magnetite-interacting component (MamC-MIC) abolishes its interaction with magnetite particles. Moreover, the size and shape of magnetite crystals grown in in vitro magnetite-precipitation experiments in the presence of this disordered peptide were different from the traits of crystals grown in the presence of other peptides or in the presence of the helical MIC. It is suggested that the helical structure of the MamC-MIC is important for its function during magnetite formation.

The Catalytic Mechanisms of the Reactions between Tryptophan Indole-Lyase and Nonstandard Substrates: The Role of the Ionic State of the Catalytic Group Accepting the Cα Proton of the Substrate

“…We may assume that serine conformation in the active site is analogous to that of tryptophan in the sense that the position of hydroxylic oxygen strictly corresponds to the position of the Cγ atom of the indole ring. In this case, according to the X-ray data [20], hydroxylic oxygen of L-serine should be located in close proximity to the phenol group of the Tyr74 residue, which is connected to the amino group of the Lys270 residue by a chain of hydrogen bonds [20]. In the course of α,β-elimination, a proton from the ammonium group of Lys270 is transferred to Tyr74 through the chain of hydrogen bonds.…”

“…The three-dimensional structure was established by X-ray analysis for TIL from Escherichia coli [8, 9, 10] and for the enzyme from Proteus vulgaris [11]. The catalytic mechanism of TIL was studied in detail in [12-16]; the role of specific residues in the mechanism of TIL was elucidated in [17-20].…”

“…Therefore, the observed intramolecular transfer [21] might be a result of the existence of a chain of hydrogen bonds between several residues, which renders the observed transfer possible. Convincing X-ray evidence of the existence of such a chain was presented in [20]. In α,β-elimination reactions with substrates containing bad leaving groups (e.g., L-serine), general acid catalysis is required at the stage of the leavinggroup elimination.…”

Tuning properties of biomimetic magnetic nanoparticles by combining magnetosome associated proteins

“…Therefore, as in the case of Mms6, ionotropic effects could induce magnetite nucleation on those specific negatively charged areas. However, some authors 29,30,41 also claim a template effect that rules magnetite nucleation based on: a) the distance between the Glu66 and Asp70 (8 Å) is similar (within the helix elasticity) to the 6 Å distance between the Fe cations in specific crystal faces, namely (111), (100), (110) and (311), that become expressed in the final morphology of MamC-mediated magnetites, and b) when MamC was not correctly folded, the size of the resulting crystals was equal to that from crystals precipitated in protein-free experiments, so an extended protein structure was needed for MamC to control the size and/or morphology of magnetite.…”

“…Conversely, it was MamC, and not Mms6, the protein that had more input determining the size of the crystals. Several studies 26,29,30,41,44,45 have shown the effect of MamC on the size of the magnetite crystals formed in the presence of the protein and had demonstrated the importance of the conformation of MamC loop in properly controlling such a size. Therefore, the template effect, rather than the ionotropic effect seems to stand as the key factor controlling nucleation and the size of the final crystals under limited iron conditions.…”