SS-31 Molecular Weight, Sequence & CAS Reference

Chemical Identification and Structural Overview of SS-31

SS-31, also designated in scientific literature as Elamipretide or Bendavia, is a synthetic tetrapeptide engineered specifically for targeted interaction with inner mitochondrial membrane components. Unlike larger naturally occurring peptides, SS-31 exhibits an optimized structural footprint that facilitates rapid cell permeability and selective partitioning into the lipid bilayer of mitochondria.

For investigators sourcing reference material across our all-peptides catalog, maintaining absolute precision regarding structural identity is paramount. As a synthetic research compound supplied exclusively for laboratory research use only, SS-31 must be quantified using its verified molecular parameters to ensure exact molar concentrations during assay preparation.

Amino Acid Sequence and Molecular Architecture

The primary amino acid sequence of SS-31 features an alternating aromatic-cationic motif containing a modified residue. Specifically, the sequence is written as: D-Arg-Dmt-Lys-Phe-NH2 (or H-D-Arg-Dmt-Lys-Phe-NH2 in expanded form). The inclusion of D-arginine at the N-terminus and an amidated C-terminus confers enhanced enzymatic stability against exopeptidases in experimental media.

A key chemical feature of SS-31 is the incorporation of 2',6'-dimethyl-L-tyrosine (Dmt) at position 2 rather than standard L-tyrosine. The addition of methyl groups at the 2' and 6' positions on the aromatic ring significantly alters the electron density and steric properties of the phenol moiety. This modification is critical to the radical-scavenging and cardiolipin-binding properties observed in preclinical evaluations.

SS-31 Molecular Weight, Formula, and CAS Registry

To perform accurate stoichiometric calculations, researchers must distinguish between the free base formula and the synthesized salt form. The fundamental chemical properties for the free base of SS-31 are defined as follows:

Molecular Formula (Free Base): C32H49N9O5 Exact / Monoisotopic Mass: 639.3857 Da Average Molecular Weight: 639.80 g/mol CAS Registry Number: 736992-21-2 (free base) / 1000279-69-5 (acetate salt form) Chemical Name: D-arginyl-2',6'-dimethyl-L-tyrosyl-L-lysyl-L-phenylalaninamide

When purchasing high-purity SS-31, the mass stated on the analytical certificate corresponds to the peptide mass, but gravimetric measurements in the laboratory must account for counterion contributions to determine absolute peptide content.

Salt Counterions (TFA vs. Acetate) and Net Peptide Content

Synthetic peptides generated via solid-phase peptide synthesis (SPPS) are cleaved from resins using trifluoroacetic acid (TFA), leaving residual TFA counterions associated with basic amino acid side chains (such as Arginine and Lysine) and the N-terminus. SS-31 contains multiple basic sites, resulting in a multi-TFA salt unless subjected to acetate exchange.

Net peptide content (NPC) represents the actual percentage of the dry mass that consists of the active peptide chain, as opposed to counterions (TFA or acetate) and bound water. For example, a batch of SS-31 trifluoroacetate salt may exhibit a net peptide content of 75% to 85%. If an investigator weighs out 1.0 mg of lyophilized powder with an 80% NPC, the actual amount of SS-31 peptide present is 0.80 mg (1.25 micromoles based on a 639.80 g/mol molecular weight).

PX1 Research provides comprehensive batch-specific analysis. Every lot is supplied with a lot-specific certificate of analysis detailing the net peptide content, counterion profile, and residual moisture levels to ensure total transparency in experimental dosing calculations.

Reconstitution Metrics and Molar Calculations for In Vitro Assays

Preparing exact stock solutions of SS-31 requires adjusting for the peptide's molecular weight and purity profile. Because SS-31 is highly hydrophilic due to its cationic charges, it dissolves readily in standard aqueous buffers including sterile water for injection, phosphate-buffered saline (PBS, pH 7.4), and cell culture media.

To convert dry mass to micromolar (µM) concentrations for cell culture or isolated mitochondria assays, researchers can utilize our interactive reconstitution calculator or apply the following standard formula: Concentration (mM) = [Mass (mg) × Net Peptide Content (%)] / [Molecular Weight (g/mol) × Volume (mL)].

For instance, dissolving 5.0 mg of SS-31 powder (assuming 80% net peptide content, yielding 4.0 mg net peptide) into 6.25 mL of buffer results in a stock concentration of 1.0 mM (1000 µM). This stock can then be serially diluted down to working ranges (typically 10 nM to 1 µM) for in vitro bioenergetic assays.

Quality Control: HPLC, Mass Spectrometry, and Endotoxin Limits

Given that SS-31 is heavily utilized in sensitive mitochondrial respiration assays and preclinical microvascular models, chemical purity and low endotoxin burdens are essential to prevent confounding cellular stress responses. High-performance liquid chromatography (HPLC) is employed to confirm chemical purity, ensuring that related peptide impurities (such as deletion sequences or un-capped fragments) remain under strict thresholds.

Electrospray ionization mass spectrometry (ESI-MS) confirms the correct molecular weight by measuring the mass-to-charge ratio (m/z) of the ionized peptide. Because SS-31 possesses basic groups, ESI-MS in positive mode routinely displays dominant ions such as [M+H]+ at m/z 640.4, [M+2H]2+ at m/z 320.7, and [M+3H]3+ at m/z 214.1. PX1 Research manufactures peptides in ISO 17025 accredited, GMP-compliant facilities in the USA, testing every lot for purity (>98% by HPLC) and certifying endotoxin levels below 0.01 EU/mg.

Biological Mechanism in Preclinical Mitochondrial Research

In vitro and animal model studies indicate that SS-31 targets cardiolipin, an essential polyunsaturated phospholipid localized almost exclusively to the inner mitochondrial membrane (IMM). Cardiolipin plays a structural role in organizing respiratory chain supercomplexes (electron transport chain complexes I–IV) and maintaining membrane curvature.

Preclinical data suggest that SS-31 electrostatic interactions with the negatively charged headgroups of cardiolipin prevent cardiolipin peroxidation and help preserve cristae structure under oxidative stress conditions. Research models exploring ischemia-reperfusion injury, neurodegenerative pathways, and metabolic dysfunction utilize SS-31 to evaluate changes in mitochondrial membrane potential (ΔΨm), ATP production efficiency, and mitochondrial reactive oxygen species (mtROS) generation.

Comparative Analysis: SS-31 vs. MOTS-c and Humanin

When designing protocols around mitochondrial bioenergetics, researchers frequently compare SS-31 to other mitochondrially active peptides, such as MOTS-c and Humanin. While all three compounds modulate cellular metabolism and oxidative stress in preclinical models, their molecular weights, origins, and targets differ significantly.

SS-31 is a fully synthetic 4-amino-acid tetrapeptide (MW 639.80 g/mol) that acts via direct lipid membrane physical association (cardiolipin binding). Conversely, MOTS-c is a 16-amino-acid mitochondrial-derived peptide (MW ~2174.5 g/mol) that regulates nuclear gene expression involved in metabolic homeostasis, and Humanin is a 24-amino-acid mitochondrial peptide (MW ~2687.1 g/mol) known for cytoprotective signaling via surface receptor interactions. Understanding these molecular distinctions helps laboratories select the appropriate compound for specific pathway inquiries.

Laboratory Storage, Handling, and Solution Stability

Lyophilized SS-31 powder should be stored at -20°C or -80°C in a desiccated container protected from light. Under these conditions, the dry peptide remains stable for up to 24 months. Frequent freeze-thaw cycles must be avoided, as moisture condensation can induce hydrolytic cleavage or aggregation over time.

Once reconstituted in sterile neutral aqueous buffers, working aliquots should be stored at -80°C for long-term stability or kept at 4°C for short-term use (up to 7 days). For high-throughput screening or multi-center research, institutional laboratories purchasing through our wholesale program can request custom bulk packaging configurations to minimize aliquot handling and atmospheric exposure.

Sourcing Certified SS-31 Standards for Research

Analytical accuracy in peptide research depends on using fully characterized, unadulterated standards. PX1 Research synthesizes and packages all research peptides within the USA (shipping directly from facilities in California and Arizona), guaranteeing rapid dispatch and chain-of-custody control.

To review additional mechanistic data or access our repository of compound specifications, visit the PX1 research library. Every vial of SS-31 is verified for sequence fidelity, exact mass, HPLC purity, and endotoxin compliance to provide consistent performance in demanding laboratory applications.