Proteases

What Are Proteases?

Proteases (also called proteinases or peptidases) catalyze the hydrolysis of peptide bonds in proteins and polypeptides. They are classified by their catalytic mechanism into serine proteases (Proteinase K, trypsin, chymotrypsin, subtilisin), cysteine proteases (papain, calpain), aspartic proteases (pepsin), metalloproteases (thermolysin, carboxypeptidase A), and threonine proteases. In research applications, proteases serve roles that span nucleic acid purification, proteomics sample preparation, cell culture maintenance, recombinant protein processing, and structural biology. Trypsin cleaves at the carboxyl side of lysine and arginine residues and generates peptides in the 500-3,000 Da mass range ideal for LC-MS/MS peptide identification. Select a protease based on substrate specificity (broad-spectrum vs. site-specific), compatibility with your lysis or reaction buffer, and the need for downstream inactivation.

What you will find:

• Proteinase K: A robust serine protease (available in lyophilized or liquid formats) designed for rapid protein digestion and the inactivation of nucleases during sensitive nucleic acid isolation.

• Aprotinin, A high-purity competitive inhibitor of serine proteases, is essential for preventing unwanted proteolytic activity during delicate protein purification and extraction steps.

• Protease Inhibitor Cocktail, A pre-formulated, multi-component blend engineered to provide immediate, broad-range protection against a variety of endogenous proteases in cellular lysates.

• TEV Protease, A specialized endopeptidase with ultra-fine specificity, is utilized for the precise, site-directed cleavage of affinity tags from recombinant fusion proteins.

How to Choose Proteases

Nucleic acid purification

Proteinase K is the first choice for nucleic acid extraction because it is a broad-spectrum serine endopeptidase that digests nucleases (DNases, RNases), histones, and structural proteins in the presence of SDS, urea, EDTA, and most detergents. It is active from pH 4.0 to 12.5 with optimal activity at pH 8.0, and at temperatures from 20 to 60 degrees C. Inactivation at 95 degrees C for 5 minutes or by proteinase K inhibitors (PMSF) is required before downstream enzymatic steps.

Proteomics and mass spectrometry

Trypsin (sequencing grade) is the industry standard for bottom-up proteomics: it generates predictable lysine/arginine-terminated peptides of 6-25 amino acids, well-suited for LC-MS/MS analysis on Orbitrap and Q-TOF platforms. Chymotrypsin (cleaves after Phe, Tyr, Trp, Leu) and Glu-C/V8 protease (cleaves after Glu in phosphate buffer, or Glu+Asp in bicarbonate) are used for orthogonal digestions to improve protein sequence coverage. Lys-C protease (cleaves after Lys only) is stable in 8 M urea and is used for denatured or hard-to-digest proteins.

Cell culture dissociation

Trypsin at 0.25% (w/v) with 0.53 mM EDTA is the standard reagent for detaching adherent mammalian cells from culture surfaces. Recombinant trypsin formulations avoid the lot variability and animal-derived pathogen concerns of porcine pancreatic trypsin. Collagenase (types I, II, III, IV) is used for tissue dissociation, particularly for primary cell isolation from solid tissues, including liver, pancreas, breast, and adipose.

Recombinant protein processing

Site-specific proteases are used to remove N-terminal affinity tags (His6, GST, MBP) from purified recombinant proteins without leaving extra residues. Thrombin cleaves after Arg in the sequence LVPR/GS; Factor Xa cleaves after Arg in IE/DGR; TEV protease cleaves between Gln and Ser in ENLYFQ/S. TEV is the most commonly used because of its stringent 7-amino-acid recognition sequence, which minimizes off-target cleavage.

Buffer compatibility

Confirm protease compatibility with your lysis buffer before use. Proteinase K retains activity in 1% SDS, 4 M urea, 1% Triton X-100, and 10 mM EDTA. Trypsin is inhibited by EDTA (chelates the Ca2+ that stabilizes trypsin structure) and by soybean trypsin inhibitor (SBTI). Chymotrypsin is inhibited by PMSF (an irreversible serine protease inhibitor). Factor Xa is inhibited by benzamidine.

Specifications Context

Trypsin activity for proteomics is expressed in TAME units (N-alpha-p-tosyl-L-arginine methyl ester esterase units); 1 TAME unit hydrolyzes 1 micromol of TAME per minute at 25 degrees C, pH 8.1. Sequencing-grade trypsin is treated with TPCK (tosylphenylalanyl chloromethyl ketone) to irreversibly inactivate contaminating chymotrypsin activity, which would otherwise generate non-tryptic peptides that complicate database searches. Proteinase K activity is expressed as mAnson units per mL or mg, where 1 mAnson unit releases 1 micromol of tyrosine equivalents per minute from hemoglobin at pH 7.5 and 35.5 degrees C. Single-pot, solid-phase-enhanced sample preparation (SP3) using magnetic bead-bound proteases is increasingly adopted in proteomics to reduce sample loss and processing time for low-input samples. 

Secure your sample stability—contact the MBP team today to request a quote for our professional-grade proteases.