Conserved glycine residues in the P-loop of ATP synthases form a doorframe for nucleotide entrance

Synthetic and Computational Design Insights toward Mimicking Protein Binding of Phosphate

The unique and precise capabilities of proteins are renowned for their specificity and range of application. Effective mimicking of protein-binding offers enticing potential to direct their abilities toward useful applications, but it is nevertheless quite difficult to realize this characteristic of protein behavior in a synthetic material. Here, we design, synthesize, and evaluate experimentally and computationally a series of multicomponent phosphate-binding peptide amphiphile micelles to derive design insights into how protein binding behavior translates to synthetic materials. By inserting the Walker A P-loop binding motif into this peptide synthetic material, we successfully implemented the protein-binding design parameters of hydrogen-bonding and electrostatic interaction to bind phosphate completely and selectively in this highly tunable synthetic platform. Moreover, in this densely arrayed peptide environment, we use molecular dynamics simulations to identify an intriguing mechanistic shift of binding that is inaccessible in traditional proteins, introducing two corresponding new design elements─flexibility and minimization of the loss of entropy due to ion binding, in protein-analogous synthetic materials. We then translate these new design factors to de novo peptide sequences that bind phosphate independent of protein-extracted sequence or conformation. Overall, this work reveals that traditional complex conformational restrictions of binding by proteins can be replaced and repurposed in a multicomponent peptide amphiphile synthetic material, opening up opportunities for future enhanced protein-inspired design.

Directed proton transfer from Fo to F1 extends the multifaceted proton functions in ATP synthase

The role of protons in ATP synthase is typically considered to be energy storage in the form of an electrochemical potential, as well as an operating element proving rotation. However, this review emphasizes that protons also act as activators of conformational changes in F1 and as direct participants in phosphorylation reaction. The protons transferred through Fo do not immediately leave to the bulk aqueous phase, but instead provide for the formation of a pH gradient between acidifying Fo and alkalizing F1. It facilitates a directed inter-subunit proton transfer to F1, where they are used in the ATP synthesis reaction. This ensures that the enzyme activity is not limited by a lack of protons in the alkaline mitochondrial matrix or chloroplast stroma. Up to one hundred protons bind to the carboxyl groups of the F1 subunit, altering the electrical interactions between the amino acids of the enzyme. This removes the inhibition of ATP synthase caused by the electrostatic attraction of charged amino acids of the stator and rotor and also makes the enzyme more prone to conformational changes. Protonation occurs during ATP synthesis initiation and during phosphorylation, while deprotonation blocks the rotation inhibiting both synthesis and hydrolysis. Thus, protons participate in the functioning of all main components of ATP synthase molecular machine making it effectively a proton-driven electric machine. The review highlights the key role of protons as a coupling factor in ATP synthase with multifaceted functions, including charge and energy transport, torque generation, facilitation of conformational changes, and participation in the ATP synthesis reaction.

Stability assessment and improvement of a Lactobacillus plantarum mutant with low post-fermentation acidification characteristics

Intracellular pH homeostasis through the extrusion of a proton by F₀F₁-ATPase is one of the key mechanisms used by lactic acid bacteria in response to acid stress, and also influences their post-fermentation acidification. In this study, the genotypic and phenotypic stability of a low post-fermentation acidification (LPA) mutant (designated as DGCC12411^m) of Lactobacillus plantarum DGCC12411 was assessed. Compared with its mother strain, the pH of DGCC12411^m in De Man, Rogosa, and Sharpe (MRS) broth after 48-h cultivation was 0.35 pH units higher. Incorporation of DGCC12411^m in yogurt stored at ambient temperature (ambient yogurt) showed a reduced post-fermentation acidification during storage at 25°C for 120 d. Whole-genome sequencing analysis showed a SNP mutation (GGT > GAT at positions 505 to 507) in DGCC12411^m, which resulted in the substitution of a highly conserved glycine residue by aspartic acid at the Walker A motif of the F₀F₁-ATPase α-subunit. However, degeneration of the LPA phenotype was observed after 5 passages of DGCC12411^m in MRS broth. Analysis of DNA sequencing on both the whole population and the isolates showed that a back mutation occurred at the SNP site (GAT changed back to GGT) over the passaging, and the reversion gradually increased from a ratio of 10.8% at P5 to 60.0% at P10. We also found that the LPA phenotype stability of DGCC12411^m was improved by supplementing 0.1 M potassium phosphate buffer to the growth medium as well as by reducing the inoculation rate of DGCC12411^m to 2% (vol/vol). Such LPA Lactobacillus strains have potential for use as starter cultures in fermented foods with less change in acidity during shelf-life storage.

Crystallographic and enzymatic insights into the mechanisms of Mg-ADP inhibition in the A1 complex of the A1AO ATP synthase

F-ATP synthases are described to have mechanisms which regulate the unnecessary depletion of ATP pool during an energy limited state of the cell. Mg-ADP inhibition is one of the regulatory features where Mg-ADP gets entrapped in the catalytic site, preventing the binding of ATP and further inhibiting ATP hydrolysis. Knowledge about the existence and regulation of the related archaeal-type A₁A_O ATP synthases (A₃B₃CDE₂FG₂ac) is limited. We demonstrate MgADP inhibition of the enzymatically active A₃B₃D- and A₃B₃DF complexes of Methanosarcina mazei Gö1 A-ATP synthase and reveal the importance of the amino acids P235 and S238 inside the P-loop (GPFGSGKTV) of the catalytic A subunit. Substituting these two residues by the respective P-loop residues alanine and cysteine (GAFGCGKTV) of the related eukaryotic V-ATPase increases significantly the ATPase activity of the enzyme variant and abolishes MgADP inhibition. The atomic structure of the P235A, S238C double mutant of subunit A of the Pyrococcus horikoshii OT3 A-ATP synthase provides details of how these critical residues affect nucleotide-binding and ATP hydrolysis in this molecular engine. The qualitative data are confirmed by quantitative results derived from fluorescence correlation spectroscopy experiments.

Mechanisms of apoptosis by the tumor suppressor Par-4

Par-4 is a pro-apoptotic, tumor suppressor protein that induces apoptosis selectively in cancer cells. Endoplasmic reticulum-stress and higher levels of protein kinase A in tumor cells confer the coveted feature of cancer selective response to extracellular and intracellular Par-4, respectively. Recent studies have shown that systemic Par-4 confers resistance to tumor growth in mice, and that tumor-resistance is transferable by bone-marrow transplantation. Moreover, recombinant Par-4 inhibits the growth of tumors in mice. As systemic Par-4 induces apoptosis via cell surface GRP78, strategies that promote GRP78 trafficking to the cell surface are expected sensitize cancer cells to circulating levels of Par-4. This review illustrates the domains and mechanisms by which Par-4 orchestrates the apoptotic process in both cell culture models and in physiological settings.