Enzymatic Peptide Research Articles

Kinetically Controlled Carboxypeptidase-Catalyzed Synthesis of Novel Antioxidant Dipeptide Precursor BOC-Tyr-Ala

Recently, enzymatic peptide synthesis has drawn increasing attention due to its eco-friendly reagents and mild conditions, as compared to traditional chemical peptide synthesis. In this study, we successfully produced an important antioxidant dipeptide precursor, BOC-Tyr-Ala, via a kinetically controlled enzymatic peptide synthesis reaction, catalyzed by the recombinant carboxypeptidase Y (CPY) expressed in P. pastoris GS115. In this reaction, the enzyme activity was 95.043 U/mL, and we used t-butyloxycarbonyl-l-tyrosine-methyl ester (BOC-Tyr-OMe) as the acyl donor and l-alanine (l-Ala) was the amino donor. We optimized the reaction conditions to be: 30 °C, pH 9.5, organic phase (methanol)/aqueous phase = 1:20, BOC-Tyr-OMe 0.05 mol/L, Ala 0.5 mol/L, and a reaction time of 12 h. Under these conditions, the dipeptide yield reached 49.84%. Then, we established the kinetic model of the synthesis reaction in the form of Michaelis–Menten equation according to the concentration–time curve during the process and the transpeptidation mechanism. We calculated the apparent Michaelis constant $$K_{\text{m}}^{\text{app}}$$ and the apparent maximum reaction rate $$r_{\hbox{max} }^{\text{app}}$$ to be $$2.9946 \times 10^{{^{ - 2} }} {\text{ mol/L}}$$ and $$2.0406 \times 10^{ - 2} {\text{ mmol/(mL}}\,{\text{h)}}$$ , respectively.

Multispectral Photoacoustic Imaging of Tumor Protease Activity with a Gold Nanocage-Based Activatable Probe.

Tumor proteases have been recognized as significant regulators in the tumor microenvironment, but the current strategies for in vivo protease imaging have tended to focus on the development of a probe design rather than the investigation of a novel imaging strategy by leveraging the imaging technique and probe. Herein, it is the first report to investigate the ability of multispectral photoacoustic imaging (PAI) to estimate the distribution of protease cleavage sites inside living tumor tissue by using an activatable photoacoustic (PA) probe. The protease MMP-2 is selected as the target. In this probe, gold nanocages (GNCs) with an absorption peak at ~ 800nm and fluorescent dye molecules with an absorption peak at ~ 680nm are conjugated via a specific enzymatic peptide substrate. Upon enzymatic activation by MMP-2, the peptide substrate is cleaved and the chromophores are released. Due to the different retention speeds of large GNCs and small dye molecules, the probe alters its intrinsic absorption profile and produces a distinct change in the PA signal. A multispectral PAI technique that can distinguish different chromophores based on intrinsic PA spectral signatures is applied to estimate the signal composition changes and indicate the cleavage interaction sites. Finally, the multispectral PAI technique with the activatable probe is tested in solution, cultured cells, and a subcutaneous tumor model in vivo. Our experiment in solution with enzyme ± inhibitor, cell culture ± inhibitor, and in vivo tumor model with administration of the developed probe ± inhibitor demonstrated the probe was cleaved by the targeted enzyme. Particularly, the in vivo estimation of the cleavage site distribution was validated with the result of ex vivo immunohistochemistry analysis. This novel synergy of the multispectral PAI technique and the activatable probe is a potential strategy for the distribution estimation of tumor protease activity in vivo.

Thermodynamics of a Ca2+ dependent, highly thermostable and detergent compatible purified alkaline serine protease from Nocardiopsis xinjiangensis strain OM-6

Extracellular alkaline protease producing salt tolerant alkaliphilic actinobacteria, Nocardiopsis xinjiangensis strain OM-6 was isolated from Okha Madi (OM) site of coastal Gujarat, India. The purified protease was stable even at 70°C in 100mM Ca2+ with Kd=20×10−3 and t1/2=34min. The activation energies (E), enthalpy (∆H*) and entropy (∆S*) for protease deactivation were 29.35kJ/mol, 26.68kJ/mol and −186.22J/mol, respectively in 200mM Ca2+. The ∆G* for protease deactivation was 97.63kJ/mol at 50°C in 100mM Ca2+. OM-6 protease exhibited enhanced residual activities up to 103%, 70%, 144% and 119% with SDS, CTAB, Tween 80 and Triton X-100, respectively after 2h of incubation at 40°C. Interestingly, residual activity of OM-6 protease increased by 450% and 559% in 50mM H2O2 and 10mM β-mercaptoethanol respectively even after 2h of incubation. Moreover, protease retained 100% of its original activity with H2O2 and β-mercaptoethanol at highest concentration after 24h. The protease retained more than 60% of original activity with 1% w/v of each commercial detergent even after 2h at 40°C. These unique properties of protease make it an ideal choice for application in detergent formulations and enzymatic peptide synthesis.

Co-solvent effects on reaction rate and reaction equilibrium of an enzymatic peptide hydrolysis.

This work presents an approach that expresses the Michaelis constant KaM and the equilibrium constant Kth of an enzymatic peptide hydrolysis based on thermodynamic activities instead of concentrations. This provides KaM and Kth values that are independent of any co-solvent. To this end, the hydrolysis reaction of N-succinyl-l-phenylalanine-p-nitroanilide catalysed by the enzyme α-chymotrypsin was studied in pure buffer and in the presence of the co-solvents dimethyl sulfoxide, trimethylamine-N-oxide, urea, and two salts. A strong influence of the co-solvents on the measured Michaelis constant (KM) and equilibrium constant (Kx) was observed, which was found to be caused by molecular interactions expressed as activity coefficients. Substrate and product activity coefficients were used to calculate the activity-based values KaM and Kth for the co-solvent free reaction. Based on these constants, the co-solvent effect on KM and Kx was predicted in almost quantitative agreement with the experimental data. The approach presented here does not only reveal the importance of understanding the thermodynamic non-ideality of reactions taking place in biological solutions and in many technological applications, it also provides a framework for interpreting and quantifying the multifaceted co-solvent effects on enzyme-catalysed reactions that are known and have been observed experimentally for a long time.

Highly improved enzymatic peptide synthesis by using biphasic reactors

The synthesis of hydrophobic peptide as Leu-enkephalin derivatives (N-acetyl phenyl-l leucinamide) from hydrophobic esters (N-acetyl phenylalanine methyl ester) plus a high excess hydrophilic nucleophile (l-leucinamide) catalyzed by immobilized chymotrypsin (α-CT) was studied. By using biphasic systems, the biocatalyst and the necessary high excess of nucleophile remain in the aqueous phase. The hydrophobic acyl donor in the organic phase is partially partitioned into the aqueous phase allowing the synthesis of the peptide. Then the highly hydrophobic reaction product is completely partitioned to the organic phase and it cannot be hydrolyzed by the biocatalyst. Under these conditions, synthetic yields of 95% with respect to the acyl donor were obtained. The excess of nucleophile does not need to be recovered at the end of the synthesis because it remains “immobilized” in the aqueous phase and it can be re-used as well as the immobilized biocatalyst. In such biphasic systems, in each reaction cycle, the synthesis proceeded according to this interesting mass balance: 50 mM N-acetyl phenylalanine methyl ester plus 47.5 mM l-leucinamide were converted into 47.5 mM peptide derivative, that precipitated in the organic phase as a fluffy solid, and 2.5 mM N-acetyl phenyl acid as side product in the aqueous phase. The immobilized biocatalyst (inside a porous structure) is not in contact with the organic phase. Three consecutive reaction cycles were performed, and 95% of peptide was always obtained.

Efficacy of L-Cysteine as an Anti-Oxidant in Papain Catalyzed Synthesis of Oligopeptides in Organic Solvent System

Enzymatic peptide synthesis has drawn considerable attention for synthesis of high by-pass oligopeptide feed supplements in animal nutrition. A hardy protease, (papain) with a cysteine moiety at the active site requires the presence of an anti-oxidant in the reaction medium to ensure that the thiol group remains intact. Free cysteine has been the antioxidant of choice for papain-catalyzed synthesis of oligopeptides in aqueous systems. However, due to limited solubility of cysteine in organic solvents, it is generally not a suitable antioxidant for the synthesis of oligopeptides in biphasic solvent systems; instead, mercaptoethanol is often used. Lysine and Methionine is couple of well-known limiting amino acids that find application in cattle feed and poultry. Synthesis of co-oligopeptides of Lysine and Methionine has generally been attempted in bi-phasic solvent systems with Mercaptoethanol as an anti-oxidant. The inherent toxicity of mercaptoethanol when present even in trace amounts make its use undesirable during synthesis of oligopeptides to be used as feed supplements. Use of non-toxic antioxidants such as Cysteine would make the end product more amenable as a nutritional supplement for animal feed. Therefore efficacy of L-cysteine as an anti-oxidant was investigated during papain catalyzed oligomerization of Lys, Arg, Glu and Asp in two organic systems: a three phase micro-aqueous media consisting of n-octane, DFP and water, as well as homogeneous ACN/water mixtures. Reactions were also carried out under an argon atmosphere in the presence and absence of anti-oxidants. The results of the experiments showed that L-cysteine facilitated oligomer synthesis in both the three phase system and the ACN/water mixture. The overall oligomer yields were found to be better than 75% in the presence of L-Cysteine. Oligopeptide yields obtained through reactions carried out under the argon atmosphere were less than 20%.

Alkaline proteases from a newly isolated Micromonospora chaiyaphumensis S103: Characterization and application as a detergent additive and for chitin extraction from shrimp shell waste

The present study was undertaken to characterize the extracellular thermostable serine alkaline proteases from newly actinomycete strain Micromonospora chaiyaphumensis S103 and to describe their evaluation in commercial detergents and shrimp waste deproteinization. This proteolytic crude extract was active and stable in alkaline solution. It was extremely stable in the pH range of 5.0–12.0. The optimum pH and temperature were 8.0 and 70°C, respectively, using casein as a substrate. The thermoactivity and thermostability of proteases were enhanced by the addition of 5mM Ca2+. Proteases from S103 were also used for shrimp wastes deproteinization in the process of chitin preparation. The percent of protein removal after 3h hydrolysis at 45°C with an enzyme/substrate ratio of 20U/mg had reached 93%. Furthermore, S103 crude enzyme was stable towards several organic solvents and retained 100% of its original activity after 90days of incubation in the presence of methanol, hexane, acetone, and DMSO. These properties make S103 proteases an ideal choice for application in detergent formulations, chitin production, and enzymatic peptide synthesis.

Sequence Determination of an Antioxidant Peptide Obtained by Enzymatic Hydrolysis of Oyster Crassostrea madrasensis (Preston)

Soft tissue from cultured farm fresh oysters (Crassostrea madrasensis) was subjected to two standard enzymatic peptide extraction procedures using pepsin and papain. The crude extracts obtained were partially purified by column chromatography and were freeze-dried. The hydrolysates obtained were compared with respect to their degree of hydrolysis (DH), antioxidant potential (AP) and total phenolic content (TPC). The hydrolysate showing better antioxidant property was further subjected to purification by high performance liquid chromatography and characterized by LC-MS/MS. Papain-digested oyster protein (OPHpap) hydrolysate showed higher DH, AP and TPC. OPHpap was further subjected to ultrafiltration and fractionated into 3 sizes namely, above 10, 3–10 and 1–3 kDa according to the molecular size. Antioxidant capacity of <3 kDa fraction OPHpap-3 evaluated by DPPH free radical scavenging assay, metal chelating activity, linoleic acid autoxidation assay showed maximum effectiveness. Of the seven fractions collected by purification of OPH-pap-3 on semi-preparative RP-HPLC, fraction 7 that showed the highest antioxidant activity was further characterized by LC-ESI-MS/MS and its sequence determined. An antioxidant peptide molecule with thirteen amino acids was identified in oyster protein hydrolysate obtained by papain digestion that may find application as a nutraceutical or may be utilized in food industry for prevention of rancidity in foods.

Enzymatic activatable self-assembled peptide nanowire for targeted therapy and fluorescence imaging of tumors.

We developed novel activatable probe using self-assembled peptide nanowires with low affinity and toxicity to tumor cells in the absence of matrix metalloproteinase that showed activated high affinity and toxicity and provided a highly selective and efficient platform for targeted therapy and tumor imaging.

Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling.

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase-2 (MMP-2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all-atom three-dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace-Gln-Gly∼Ile-Ala-Gly-Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four-step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C-N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5-10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate-limiting step in MMP-2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations.

&amp;lt;i&amp;gt;Arthrobacter arilaitensis&amp;lt;/i&amp;gt; Re117 as a Source of Solvent-Stable Proteases: Production, Characteristics, Potential Application in the Deproteinization of Shrimp Wastes and Evaluation in Liquid Laundry Commercial Detergents

The present study describes the characterization of crude protease extract from Arthrobacter arilaitensis Re117 and its evaluation in solid and liquid detergent. One caseinolytic protease clear band was observed in zymogram. The crude alkaline protease showed optimum activity at pH 9.0 and 50&degC, and it was highly stable over a wide range of pH from 8.0 to 9.0. Proteolytic enzymes showed extreme stability towards non-ionic surfactants (Tween 80, Tween 20 and Triton X-100) and stimulate activity towards oxidizing agents such as sodium perborate. They also showed high stability and compatibility with various laundry solid detergents from Tunisian market. The protease of A. arilaitensis Re117, was also tested for shrimp waste deproteinization to produce chitin. The protein removal with a ratio E/S of 20 was about 83%. The novelties of the Re117 protease include its high stability to organic solvents and surfactants. These unique properties make it an ideal choice for application in detergent formulations and enzymatic peptide synthesis. In addition, the enzyme may find potential applications in the deproteinization of shrimp wastes to produce chitin.

Core‐multishell nanotransporters enhance skin penetration of the cell‐penetrating peptide low molecular weight protamine

Several peptides may enable innovative, sophisticated therapeutic approaches. Their hydrophilic nature and high molecular weight, however, often limit the applicability to topical and transdermal treatment. Aiming to enhance drug delivery to the skin, we examined the loading of two model peptides—the Cell‐Penetrating Peptides (CPPs) Low Molecular Weight Protamine (LMWP) and penetratin—to Core‐Multishell (CMS) nanotransporters which are well tolerated and known to enhance skin penetration most efficiently. Furthermore, we followed skin penetration of dye‐tagged LMWP in the presence of CMS nanotransporters taking enzymatic peptide cleavage into account. As expected, Isothermal Titration Calorimetry indicated that the large peptides do not interact with CMS nanotransporters. Additionally, size exclusion chromatography and Dynamic Light Scattering confirmed no loading of CPPs to CMS nanoparticles. Due to less LMWP aggregation, concomitant topical application of LMWP and CMS nanotransporters did not enhance the penetration of intact LWMP but enhanced the penetration of peptide fragments in viable layers of human skin ex vivo. Conclusively, our results indicate that CMS nanotransporters impair the skin barrier function leading to increased skin penetration of less voluminous peptides, which may be of future clinical relevance—in particular with those failing to be CPPs. Copyright © 2014 John Wiley &amp; Sons, Ltd.

The Novel Caspase-3 Substrate Gap43 is Involved in AMPA Receptor Endocytosis and Long-Term Depression

The cysteine protease caspase-3, best known as an executioner of cell death in apoptosis, also plays a non-apoptotic role in N-methyl-d-aspartate receptor-dependent long-term depression of synaptic transmission (NMDAR-LTD) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor endocytosis in neurons. The mechanism by which caspase-3 regulates LTD and AMPA receptor endocytosis, however, remains unclear. Here, we addressed this question by using an enzymatic N-terminal peptide enrichment method and mass spectrometry to identify caspase-3 substrates in neurons. Of the many candidates revealed by this proteomic study, we have confirmed BASP1, Dbn1, and Gap43 as true caspase-3 substrates. Moreover, in hippocampal neurons, Gap43 mutants deficient in caspase-3 cleavage inhibit AMPA receptor endocytosis and LTD. We further demonstrated that Gap43, a protein well-known for its functions in axons, is also localized at postsynaptic sites. Our study has identified Gap43 as a key caspase-3 substrate involved in LTD and AMPA receptor endocytosis, uncovered a novel postsynaptic function for Gap43 and provided new insights into how long-term synaptic depression is induced.

Isolation, Purification and Characterisation of an Organic Solvent-Tolerant Ca2+-Dependent Protease from Bacillus megaterium AU02

A new organic solvent-tolerant strain Bacillus megaterium AU02 which secretes an organic solvent-tolerant protease was isolated from milk industry waste. Statistical methods were employed to achieve optimum protease production of 43.6 U/ml in shake flask cultures. The productivity of the protease was increased to 53 U/ml when cultivated under controlled conditions in a 7-L fermentor. The protease was purified to homogeneity by a three-step process with 24 % yield and specific activity of 5,375 U/mg. The molecular mass of the protease was found to be 59 kDa. The enzyme was active over a wide range of pH (6.0–9.0), with an optimum activity at pH 7.0 and temperature from 40 to 70 °C having an optimum activity at 50 °C. The thermal stability of the enzyme increased significantly in the presence of CaCl2, and it retained 90 % activity at 50 °C for 3 h. The Km and Vmax values were determined as 0.722 mg/ml and 0.018 U/mg respectively. The metalloprotease exhibited significant stability in the presence of organic solvents with log P values more than 2.5, nonionic detergents and oxidising agent. An attempt was made to test the synthesis of aspartame precursor (Cbz-Asp-Phe-NH2) which was catalysed by AU02 protease in the presence of 50 % DMSO. These properties of AU02 protease make it an ideal choice for enzymatic peptide synthesis in organic media.

Process design for enzymatic peptide synthesis in near-anhydrous organic media

This work is a case study on a process design for enzymatic peptide synthesis, which is based on and inspired by previously established data about the Alcalase-catalyzed coupling of an amino acid amide and a chemically synthesized activated N-protected amino acid carbamoylmethyl ester in near-anhydrous tetrahydrofuran. The choices with regard to Alcalase formulation, the type of reactor, method of controlling the water content, and whether or not to recycle the enzyme, are discussed. In addition, an estimate is given for the reactor size, volumes of solvent, amount of substrate, enzyme and molecular sieves, needed in order to meet a specific demand for peptides. We believe that this case study gives a good indication of the various choices that have to be made when designing a process for enzymatic peptide synthesis and the implications of these choices.

Newly Discovered Components and Actions of the Renin–Angiotensin System

The renin–angiotensin system (RAS) is the best understood and arguably most important hormonal system in the control of blood pressure (BP) and the pathophysiology of hypertension.1 In the classical RAS, the enzyme renin cleaves its substrate angiotensinogen (Agt) forming the decapeptide angiotensin I that is in turn cleaved by angiotensin-converting enzyme (ACE) to produce the angiotensin II (Ang II), the biologically active peptide of the system. Although several other peptide products of Agt had been identified and studied, Ang II was generally accepted as the physiological and pathophysiological driving force of the classical RAS.2 Ang II activates its AT1 receptor (AT1R) to induce a large array of biological responses, including vasoconstriction, renal sodium (Na+) reabsorption, cell proliferation, dedifferentiation, and growth and aldosterone secretion, increasing BP and contributing to the development of hypertension. However, we appreciate that the RAS is far more complex than the simple hormonal cascade represented by the classical system. In recent years, we have recognized several essential components and actions of the RAS, including those of local tissue RASs functioning independently of the circulating system, the (pro)renin receptor as a potential direct biological target for renin and prorenin, and 2 counter-regulatory pathways, the ACE-2–angiotensin (1–7)– Mas receptor cascade and the Ang type-2 receptor (AT2R) pathway, that generally oppose the actions of Ang II via AT1Rs (Figure).1 Indeed, our understanding of the RAS has been transformed into one of the most complex hormonal systems known with internal balance and interplay among its multiple enzymatic peptide and receptor constituents. This brief review will encompass selected recent publications identifying additional new components and actions of the RAS. Figure. Schematic depiction of the renin–angiotensin system components and selected actions. The enzymes of the system are shown in red. Newly described …

Racemization‐Free Chemoenzymatic Peptide Synthesis Enabled by the Ruthenium‐Catalyzed Synthesis of Peptide Enol Esters via Alkyne‐Addition and Subsequent Conversion Using Alcalase‐Cross‐Linked Enzyme Aggregates

AbstractThe C‐terminal activation of peptides as prerequisite for the formation or ligation of peptide fragments is often associated with the problem of epimerization. We report that ruthenium‐catalyzed alkyne addition with (+)‐2,3‐O‐isopropylidene‐2,3‐dihydroxy‐1,4‐bis(diphenylphosphino)butane as ligand allows the racemization‐free synthesis of peptide enol esters tolerating a wide range of functional groups. The transformation can be performed in a variety of different solvents addressing the solubility issues imposed by peptides with varying amino acid side chain patterns. We show that peptide enol esters with an amide motif in the enol moiety are excellent acyl donors for the peptide condensation with other peptide fragments in organic solvents using serine endopeptidase subtilisin A as catalyst. The reported combination of transition metal catalysis with enzymatic peptide ligations adds an important tool for the racemization‐free synthesis and ligation of peptides which is compatible even with unprotected amino acid side chains.

Ultrasensitive dual-channel detection of matrix metalloproteinase-2 in human serum using gold-quantum dot core–satellite nanoprobes

We have developed a robust enzymatic peptide cleavage-based assay for the ultrasensitive dual-channel detection of matrix metalloproteinase-2 (MMP-2) in human serum using gold-quantum dot (Au-QD) core-satellite nanoprobes.

Solvent selection and optimization of α‐chymotrypsin‐catalyzed synthesis of N‐Ac‐Phe‐Tyr‐NH2 using mixture design and response surface methodology

A peptide, N-Ac-Phe-Tyr-NH(2) , with angiotensin I-converting enzyme (ACE) inhibitor activity was synthesized by an α-chymotrypsin-catalyzed condensation reaction of N-acetyl phenylalanine ethyl ester (N-Ac-Phe-OEt) and tyrosinamide (Tyr-NH(2) ). Three kinds of solvents: a Tris-HCl buffer (80 mM, pH 9.0), dimethylsulfoxide (DMSO), and acetonitrile were employed in this study. The optimum reaction solvent component was determined by simplex centroid mixture design. The synthesis efficiency was enhanced in an organic-aqueous solvent (Tris-HCl buffer: DMSO: acetonitrile = 2:1:1) in which 73.55% of the yield of N-Ac-Phe-Tyr-NH(2) could be achieved. Furthermore, the effect of reaction parameters on the yield was evaluated by response surface methodology (RSM) using a central composite rotatable design (CCRD). Based on a ridge max analysis, the optimum condition for this peptide synthesis included a reaction time of 7.4 min, a reaction temperature of 28.1°C, an enzyme activity of 98.9 U, and a substrate molar ratio (Phe:Tyr) of 1:2.8. The predicted and the actual (experimental) yields were 87.6 and 85.5%, respectively. The experimental design and RSM performed well in the optimization of synthesis of N-Ac-Phe-Tyr-NH(2) , so it is expected to be an effective method for obtaining a good yield of enzymatic peptide. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012.

Subtyping Botulinum Neurotoxins by Sequential Multiple Endoproteases In-Gel Digestion Coupled with Mass Spectrometry

Botulinum neurotoxin (BoNT) is one of the most toxic substances known. BoNT is classified into seven distinct serotypes labeled A-G. Among individual serotypes, researchers have identified subtypes based on amino acid variability within a serotype and toxin variants with minor amino acid sequence differences within a subtype. BoNT subtype identification is valuable for tracing and tracking bacterial pathogens. A proteomics approach is useful for BoNT subtyping since botulism is caused by botulinum neurotoxin and does not require the presence of the bacteria or its DNA. Enzymatic digestion and peptide identification using tandem mass spectrometry determines toxin protein sequences. However, with the conventional one-step digestion method, producing sufficient numbers of detectable peptides to cover the entire protein sequence is difficult, and incomplete sequence coverage results in uncertainty in distinguishing BoNT subtypes and toxin variants because of high sequence similarity. We report here a method of multiple enzymes and sequential in-gel digestion (MESID) to characterize the BoNT protein sequence. Complementary peptide detection from toxin digestions has yielded near-complete sequence coverage for all seven BoNT serotypes. Application of the method to a BoNT-contaminated carrot juice sample resulted in the identification of 98.4% protein sequence which led to a confident determination of the toxin subtype.