NAD+, nicotinamide adenine dinucleotide, is a dinucleotide coenzyme built from nicotinamide and adenine ribonucleotides joined through a pyrophosphate bridge. It is not a peptide, has no amino acid residues and no residue count, and no molecular record is held for it in our peptide dataset, so it is described here qualitatively. MOTS-c, CAS 1627580-64-6, is a mitochondrial derived peptide, meaning it is encoded by a short open reading frame within the mitochondrial 12S ribosomal RNA gene rather than by nuclear DNA. SS-31, CAS 736992-21-5, also catalogued as elamipretide and MTP-131, is a fully synthetic tetrapeptide from the Szeto-Schiller series.
Structure separates them further. MOTS-c is recorded as C101H152N28O22S2 with an average mass of 2174.6 and the sixteen residue sequence H-Met-Arg-Trp-Gln-Glu-Met-Gly-Tyr-Ile-Phe-Tyr-Pro-Arg-Lys-Leu-Arg-OH. SS-31 is recorded as C32H49N9O5 with an average mass of 639.79 and the sequence H-D-Arg-Dmt-Lys-Phe-NH2, four residues alternating between basic and aromatic side chains, one of them the unnatural residue dimethyltyrosine and one in the D configuration. NAD+ has no sequence to give. The mass spread across the three is wide, so identity confirmation by mass spectrometry is unambiguous for each.
The published literature places them at different points inside the organelle. Work on NAD+ concerns its role as a redox carrier in electron transport and as the substrate consumed by sirtuins, poly ADP ribose polymerases and CD38 in cell models. Work on MOTS-c reports effects on AMP activated protein kinase signaling and on folate and methionine cycle metabolites in rodent and cell studies, with the peptide described as translocating to the nucleus under metabolic stress. Work on SS-31 centres on its association with cardiolipin, the phospholipid of the inner mitochondrial membrane, where binding is described as affecting cristae architecture and electron transport chain efficiency in isolated mitochondria.
Handling differences are the most practically important part of this comparison. NAD+ is strongly hygroscopic and is unstable in aqueous solution, degrading faster at alkaline pH and at room temperature, so it is weighed quickly, protected from moisture and prepared fresh rather than held in solution. MOTS-c contains two methionines and a tryptophan, making it both oxidation prone and light sensitive, so its solutions are protected from air and light and are not warmed. SS-31 is the most robust of the three, since its D configured arginine, its dimethyltyrosine and its carboxy terminal amide make it a poor peptidase substrate, although its strongly cationic character means it adsorbs to glass and to some plastics, so low binding tubes are preferred.
Storage otherwise follows the same framework for all three. Lyophilized material is held at minus 20 degrees Celsius protected from light and moisture. Reconstituted material is refrigerated at 2 to 8 degrees Celsius, aliquoted into single use volumes and kept out of repeated freeze thaw. The coenzyme is the exception that deserves the shortest solution life of the three. Selection between them is dictated by the layer of mitochondrial biology under question, whether that is redox cofactor availability, retrograde signaling from the organelle to the nucleus, or the physical integrity of the inner membrane.
What remains unsettled spans all three. Cellular uptake is the recurring problem, since an extracellular dinucleotide, a sixteen residue peptide and a cationic tetrapeptide each face different barriers before reaching the organelle, and published results differ on how much of each arrives at mitochondria in intact cells.