Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

Synergizing multiresolution simulations, interface redesign, and hotspot mapping to decipher pathogenic mutation-driven structural modulation in VCP

Valosin-containing protein (VCP/p97), a pivotal AAA+ ATPase, orchestrates proteostasis via ER-associated degradation (ERAD), ubiquitin-mediated proteolysis, and organelle surveillance. Pathogenic missense mutations, notably Arg95Gly (R95G) within the evolutionarily conserved double-ψ β-barrel (DPBB) of its N-terminal domain, are implicated in proteinopathies including IBMPFD and ALS. To decode the structural-dynamics perturbations underpinning R95G-driven dysfunction, we integrated AlphaFold3-based modeling, protein-peptide docking, and multiscale enhanced-sampling molecular dynamics (MD) simulations-spanning 1.2 μs all-atom, 12 μs coarse-grained, and umbrella sampling regimes. Our findings reveal that R95G disrupts the β-barrel integrity, destabilizes long-range domain coupling, and engenders conformational heterogeneity deleterious to gp78 cofactor recruitment. Free-energy landscapes of the mutant highlight enthalpically disfavored, low-occupancy binding conformers, corroborated by MM/PBSA-based end-state binding free energy and potential of mean force (PMF) analyses, which indicate impaired binding thermodynamics. Interface hotspot mapping pinpoints dynamic perturbations at critical residues that propagate allosteric decoupling and morphological distortion of the binding interface. Collectively, our results delineate a mechanistic cascade-from local β-barrel destabilization to global interaction network disruption-underlying VCP's functional impairment in disease states. This work provides a computationally derived structural framework to inform targeted biophysical validation and the rational design of therapeutic strategies aimed at rescuing VCP function in IBMPFD and ALS.

Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases

At the heart of many nucleoside triphosphatases is a conserved phosphate-binding sequence motif. A current model of early enzyme evolution proposes that this six to eight residue motif could have sparked the emergence of the very first nucleoside triphosphatases-a striking example of evolutionary continuity from simple beginnings, if true. To test this provocative model, seven disembodied Walker A-derived peptides were extensively computationally characterized. Although dynamic flickers of nest-like conformations were observed, significant structural similarity between the situated peptide and its disembodied counterpart was not detected. Simulations suggest that phosphate binding is nonspecific, with a preference for GTP over orthophosphate. Control peptides with the same amino acid composition but different sequences and situated conformations behaved similarly to the Walker A peptides, revealing no indication that the Walker A sequence is privileged as a disembodied peptide. We conclude that the evolutionary history of the P-loop NTPase family is unlikely to have started with a disembodied Walker A peptide in an aqueous environment. The limits of evolutionary continuity for this protein family must be reconsidered. Finally, we argue that motifs such as the Walker A motif may represent incomplete or fragmentary molecular fossils-the true nature of which has been eroded by time.

A Puccinia striiformis f. sp. tritici Effector with DPBB Domain Suppresses Wheat Defense

Wheat (Triticum aestivum L.) is a primary crop globally. Among the numerous pathogens affecting wheat production, Puccinia striiformis f. sp. tritici (Pst) is a significant biotic stress agent and poses a major threat to world food security by causing stripe rust or yellow rust disease. Understanding the molecular basis of plant-pathogen interactions is crucial for developing new means of disease management. It is well established that the effector proteins play a pivotal role in pathogenesis. Therefore, studying effector proteins has become an important area of research in plant biology. Our previous work identified differentially expressed candidate secretory effector proteins of stripe rust based on transcriptome sequencing data from susceptible wheat (Avocet S) and resistant wheat (Avocet YR10) infected with Pst. Among the secreted effector proteins, PSTG_14090 contained an ancient double-psi beta-barrel (DPBB) fold, which is conserved in the rare lipoprotein A (RlpA) superfamily. This study investigated the role of PSTG_14090 in plant immune responses, which encodes a protein, here referred to as Pst-DPBB, having 131 amino acids with a predicted signal peptide (SP) of 19 amino acids at the N-terminal end, and the DNA sequence of this effector is highly conserved among different stripe rust races. qRT-PCR analysis indicated that expression levels are upregulated during the early stages of infection. Subcellular localization studies in Nicotiana benthamiana leaves and wheat protoplasts revealed that it is distributed in the cytoplasm, nucleus, and apoplast. We demonstrated that Pst-DPBB negatively regulates the immune response by functioning in various compartments of the plant cells. Based on Co-IP and structural predictions and putative interaction analyses by AlphaFold 3, we propose the probable biological function(s). Pst-DPBB behaves as a papain inhibitor of wheat cysteine protease; Pst-DPBB has high structural homology to kiwellin, which is known to interact with chorismate mutase, suggesting that Pst-DPBB inhibits the native function of the host chorismate mutase involved in salicylic acid synthesis. The DPBB fold is also known to interact with DNA and RNA, which may suggest its possible role in regulating the host gene expression.

Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity

The archaeal ribosome is of the eukaryotic type. TACK and Asgard superphyla, the closest relatives of eukaryotes, have ribosomes containing eukaryotic ribosomal proteins not found in other archaea, eS25, eS26 and eS30. Here, we investigate the case of Saccharolobus solfataricus, a TACK crenarchaeon, using mainly leaderless mRNAs. We characterize the small ribosomal subunit of S. solfataricus bound to SD-leadered or leaderless mRNAs. Cryo-EM structures show eS25, eS26 and eS30 bound to the small subunit. We identify two ribosomal proteins, aS33 and aS34, and an additional domain of eS6. Leaderless mRNAs are bound to the small subunit with contribution of their 5'-triphosphate group. Archaeal eS26 binds to the mRNA exit channel wrapped around the 3' end of rRNA, as in eukaryotes. Its position is not compatible with an SD:antiSD duplex. Our results suggest a positive role of eS26 in leaderless mRNAs translation and possible evolutionary routes from archaeal to eukaryotic translation.

Integrated computational characterization of valosin-containing protein double-psi β-barrel domain: Insights into structural stability, binding mechanisms, and evolutionary significance

Valosin-containing protein (VCP) plays a crucial role in various cellular processes, yet the molecular mechanisms and structural dynamics of its double-psi β-barrel (DPBB) domain, particularly in human, remain insufficiently explored. While previous studies have characterized the VCP_DPBB domain in other organisms, such as thermoplasma acidophilum and methanopyrus kandleri, its evolutionary conservation, binding potential, and stability in human require further investigation. To address this gap, we first employed all-atom molecular dynamics (AAMD) simulations to examine the structural dynamics of the human VCP_DPBB domain. We also assessed its amino acid interaction energies, stability, folding enthalpy, evolutionary conservation, solubility, and crystallizability using various computational frameworks. Additionally, to uncover the plausible biological function, protein-peptide docking was performed to evaluate the interactions between the DPBB domain and the C-terminal gp78 peptide of the E3 ubiquitin ligase. Further, AAMD and coarse-grained molecular dynamics (CGMD) simulations explored the binding preferences, fluctuations, and stability of human VCP_DPBB-gp78 complexes. Our findings indicate that, while thermoplasma acidophilum VCP_DPBB-gp78 showed stronger initial binding, the human VCP_DPBB-gp78 complex exhibited superior stability, binding affinity, and more stabilizing interactions. This integrated analysis provides valuable insights into the evolutionary significance and functionality of the DPBB domain, with potential therapeutic implications for VCP-related diseases.

Origins of Life: The Protein Folding Problem all over again?

How did specific useful protein sequences arise from simpler molecules at the origin of life? This seemingly needle-in-a-haystack problem has remarkably close resemblance to the old Protein Folding Problem, for which the solution is now known from statistical physics. Based on the logic that Origins must have come only after there was an operative evolution mechanism-which selects on phenotype, not genotype-we give a perspective that proteins and their folding processes are likely to have been the primary driver of the early stages of the origin of life.

An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins

Numerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which these numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by double-psi β-barrels (DPBBs) conserved in DNA and RNA polymerases, and similar but topologically distinct six-stranded β-barrel RIFT or five-stranded β-barrel folds such as OB and SH3 in ribosomal proteins. Here, we discover that the previously reconstructed ancient DPBB sequence could also adopt a β-barrel fold named Double-Zeta β-barrel (DZBB), as a metamorphic protein. The DZBB fold is not found in any modern protein, although its structure shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be further converted into SH3 by circular-permutation as previously predicted. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution.

The prebiotic emergence of biological evolution

The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. We find that cooperative autocatalysts, i.e. autocatalysts whose per-unit reproductive rate grows as their population increases, have the special property of being able to cross a barrier that separates their initial degradation-dominated state from a growth-dominated state with evolutionary dynamics. For some model parameters, this leap to persistent propagation is likely, not rare. We apply this analysis to the Foldcat Mechanism, wherein peptides fold and help catalyse the elongation of each other. Foldcats are found to have cooperative autocatalysis and be capable of emergent evolutionary dynamics.

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

An unresolved question in the origin and evolution of life is whether a continuous path from geochemical precursors to the majority of molecules in the biosphere can be reconstructed from modern-day biochemistry. Here we identified a feasible path by simulating the evolution of biosphere-scale metabolism, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, which can be alleviated by non-autocatalytic phosphoryl coupling agents. Early phases of the expansion are enriched with enzymes that are metal dependent and structurally symmetric, supporting models of early biochemical evolution. This expansion trajectory suggests distinct hypotheses regarding the tempo, mode and timing of metabolic pathway evolution, including a late appearance of methane metabolisms and oxygenic photosynthesis consistent with the geochemical record. The concordance between biological and geological analyses suggests that this trajectory provides a plausible evolutionary history for the vast majority of core biochemistry.

The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15

In CASP15, 87 predictors submitted around 11 000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact predictions, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2-Multimer approach into custom-built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2-Multimer predictor. In over 1/3 of cases, the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom-built multiple sequence alignments, optimized AF2-Multimer sampling, and the manual assembly of AF2-Multimer-built subcomplexes. The best three groups, in order, are Zheng, Venclovas, and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody-antigen, antibody-antigen, and viral complexes. Expectedly, modeling large complexes also remains challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved a 76.5% success rate, with the UM-TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.

From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics

The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated response to the pandemic highlights how technological advancements can accelerate the detection, monitoring, and treatment of the disease. Robust surveillance systems have been established to understand the clinical characteristics of new variants, although the unpredictable nature of these variants presents significant challenges. Some variants have shown resistance to current treatments, but innovative technologies like computational protein design (CPD) offer promising solutions and versatile therapeutics against SARS-CoV-2. Advances in computing power, coupled with open-source platforms like AlphaFold and RFdiffusion (employing deep neural network and diffusion generative models), among many others, have accelerated the design of protein therapeutics with precise structures and intended functions. CPD has played a pivotal role in developing peptide inhibitors, mini proteins, protein mimics, decoy receptors, nanobodies, monoclonal antibodies, identifying drug-resistance mutations, and even redesigning native SARS-CoV-2 proteins. Pending regulatory approval, these designed therapies hold the potential for a lasting impact on human health and sustainability. As SARS-CoV-2 continues to evolve, use of such technologies enables the ongoing development of alternative strategies, thus equipping us for the "New Normal".

The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15

In CASP15, 87 predictors submitted around 11,000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact prediction, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2-Multimer approach into custom-built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2-Multimer predictor. In over 1/3 of cases the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom-built multiple sequence alignments, optimized AF2-Multimer sampling, and the manual assembly of AF2-Multimer-built subcomplexes. The best three groups, in order, are Zheng, Venclovas and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody-antigen, antibody-antigen, and viral complexes. Expectedly, modeling large complexes remains also challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved the 76.5% success rate, with the UM-TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.

Protein salvage and repurposing in evolution: Phospholipase D toxins are stabilized by a remodeled scrap of a membrane association domain

The glycerophosphodiester phosphodiesterase (GDPD)-like SMaseD/PLD domain family, which includes phospholipase D (PLD) toxins in recluse spiders and actinobacteria, evolved anciently in bacteria from the GDPD. The PLD enzymes retained the core (β/α)8 barrel fold of GDPD, while gaining a signature C-terminal expansion motif and losing a small insertion domain. Using sequence alignments and phylogenetic analysis, we infer that the C-terminal motif derives from a segment of an ancient bacterial PLAT domain. Formally, part of a protein containing a PLAT domain repeat underwent fusion to the C terminus of a GDPD barrel, leading to attachment of a segment of a PLAT domain, followed by a second complete PLAT domain. The complete domain was retained only in some basal homologs, but the PLAT segment was conserved and repurposed as the expansion motif. The PLAT segment corresponds to strands β7-β8 of a β-sandwich, while the expansion motif as represented in spider PLD toxins has been remodeled as an α-helix, a β-strand, and an ordered loop. The GDPD-PLAT fusion led to two acquisitions in founding the GDPD-like SMaseD/PLD family: (1) a PLAT domain that presumably supported early lipase activity by mediating membrane association, and (2) an expansion motif that putatively stabilized the catalytic domain, possibly compensating for, or permitting, loss of the insertion domain. Of wider significance, messy domain shuffling events can leave behind scraps of domains that can be salvaged, remodeled, and repurposed.

Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life

Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).

Boron-assisted abiotic polypeptide synthesis

The emergence of proteins and their interactions with RNAs were a key step in the origin and early evolution of life. The abiotic synthesis of peptides has been limited in short amino acid length and is favored in highly alkaline evaporitic conditions in which RNAs are unstable. This environment is also inconsistent with estimated Hadean Earth. Prebiotic environments rich in boron are reportedly ideal for abiotic RNA synthesis. However, the effects of boron on amino acid polymerization are unclear. We report that boric acid enables the polymerization of amino acids at acidic and near-neutral pH levels based on simple heating experiments of amino acid solutions containing borate/boric acid at various pH levels. Our study provides evidence for the boron-assisted synthesis of polypeptides in prebiotically plausible environments, where the same conditions would allow for the formation of RNAs and interactions of primordial proteins and RNAs that could be inherited by RNA-dependent protein synthesis during the evolution of life.

Ancestral Sequence Reconstruction of the Ribosomal Protein uS8 and Reduction of Amino Acid Usage to a Smaller Alphabet

Understanding the origin and early evolution of proteins is important for unveiling how the RNA world developed into an RNA-protein world. Because the composition of organic molecules in the Earth's primitive environment was plausibly not as diverse as today, the number of different amino acids used in early protein synthesis is likely to be substantially less than the current 20 proteinogenic residues. In this study, we have explored the thermal stability and RNA binding of ancestral variants of the ribosomal protein uS8 constructed from a reduced-alphabet of amino acids. First, we built a phylogenetic tree based on the amino acid sequences of uS8 from multiple extant organisms and used the tree to infer two plausible amino acid sequences corresponding to the last bacterial common ancestor of uS8. Both ancestral proteins were thermally stable and bound to an RNA fragment. By eliminating individual amino acid letters and monitoring thermal stability and RNA binding in the resulting proteins, we reduced the size of the amino acid set constituting one of the ancestral proteins, eventually finding that convergent sequences consisting of 15- or 14-amino acid alphabets still folded into stable structures that bound to the RNA fragment. Furthermore, a simplified variant reconstructed from a 13-amino-acid alphabet retained affinity for the RNA fragment, although it lost conformational stability. Collectively, RNA-binding activity may be achieved with a subset of the current 20 amino acids, raising the possibility of a simpler composition of RNA-binding proteins in the earliest stage of protein evolution.

Selective Synthesis of Lysine Peptides and the Prebiotically Plausible Synthesis of Catalytically Active Diaminopropionic Acid Peptide Nitriles in Water

Why life encodes specific proteinogenic amino acids remains an unsolved problem, but a non-enzymatic synthesis that recapitulates biology's universal strategy of stepwise N-to-C terminal peptide growth may hold the key to this selection. Lysine is an important proteinogenic amino acid that, despite its essential structural, catalytic, and functional roles in biochemistry, has widely been assumed to be a late addition to the genetic code. Here, we demonstrate that lysine thioacids undergo coupling with aminonitriles in neutral water to afford peptides in near-quantitative yield, whereas non-proteinogenic lysine homologues, ornithine, and diaminobutyric acid cannot form peptides due to rapid and quantitative cyclization that irreversibly blocks peptide synthesis. We demonstrate for the first time that ornithine lactamization provides an absolute differentiation of lysine and ornithine during (non-enzymatic) N-to-C-terminal peptide ligation. We additionally demonstrate that the shortest lysine homologue, diaminopropionic acid, undergoes effective peptide ligation. This prompted us to discover a high-yielding prebiotically plausible synthesis of the diaminopropionic acid residue, by peptide nitrile modification, through the addition of ammonia to a dehydroalanine nitrile. With this synthesis in hand, we then discovered that the low basicity of diaminopropionyl residues promotes effective, biomimetic, imine catalysis in neutral water. Our results suggest diaminopropionic acid, synthesized by peptide nitrile modification, can replace or augment lysine residues during early evolution but that lysine's electronically isolated sidechain amine likely provides an evolutionary advantage for coupling and coding as a preformed monomer in monomer-by-monomer peptide translation.

Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance spectroscopy (EPR) to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif revealed the presence of dimers, even in the absence of RNA. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. DEER measurements of spin-diluted, doubly labeled peptides in solution indicated transient α-helical character. The distance distributions between spin labels in the dimer and the signatures of α-helical folding are consistent with the symmetric (HhH)₂-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.

Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion

Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg²⁺-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K₂V₆: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl₂, while enhancing it significantly at 400 mM MgCl₂. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.

Probing the Role of Cysteine Thiyl Radicals in Biology: Eminently Dangerous, Difficult to Scavenge

Thiyl radicals are exceptionally interesting reactive sulfur species (RSS), but rather rarely considered in a biological or medical context. We here review the reactivity of protein thiyl radicals in aqueous and lipid phases and provide an overview of their most relevant reaction partners in biological systems. We deduce that polyunsaturated fatty acids (PUFAs) are their preferred reaction substrates in lipid phases, whereas protein side chains arguably prevail in aqueous phases. In both cellular compartments, a single, dominating thiyl radical-specific antioxidant does not seem to exist. This conclusion is rationalized by the high reaction rate constants of thiyl radicals with several highly concentrated substrates in the cell, precluding effective interception by antioxidants, especially in lipid bilayers. The intractable reactivity of thiyl radicals may account for a series of long-standing, but still startling biochemical observations surrounding the amino acid cysteine: (i) its global underrepresentation on protein surfaces, (ii) its selective avoidance in aerobic lipid bilayers, especially the inner mitochondrial membrane, (iii) the inverse correlation between cysteine usage and longevity in animals, (iv) the mitochondrial synthesis and translational incorporation of cysteine persulfide, and potentially (v) the ex post introduction of selenocysteine into the genetic code.