Selectively controllable cleavable linkers include electrochemically-cleavable linkers, photolabile linkers, thermolabile linkers, chemically-labile linkers, and enzymatically-cleavable linkers. Selective cleavage of individual linkers may be controlled by changing local conditions. Local conditions may be changed by activating electrodes in proximity to the linkers, exposing the linkers to light, heating the linkers, or applying chemicals. Selective cleaving of enzymatically-cleavable linkers may be controlled by designing the sequences of different sets of the individual linkers to respond to different enzymes. Cleavable linkers may be used to attach polymers to a solid substrate. Selective cleavage of the linkers enables release of specific polymers from the solid substrate. Cleavable linkers may also be used to attach protecting groups to the ends of growing polymers. The protecting groups may be selectively removed by cleavage of the linkers to enable growth of specific polymers.

Provided herein are methods, reagents, and kits for isolating polypeptides, such as a proteome. Also provided herein is a modified trypsin polypeptide that is resistant to autolysis, and that can be selectively-separated from a biological sample once digestion is complete.

Provided herein are methods, reagents, and kits for isolating polypeptides, such as a proteome. Also provided herein is a modified trypsin polypeptide that is resistant to autolysis, and that can be selectively-separated from a biological sample once digestion is complete.

A polypeptide or protein directional modification method based on sulfhydryl-alkenyl azide coupling is provided. The method uses a sulfhydryl group-containing compound and a compound containing alkenyl azide group as reactants to generate an amino acid containing β-carbonyl sulfide, a polypeptide containing β-carbonyl sulfide and a protein bioconjugate containing β-carbonyl sulfide, thereby achieving a chemical modification. The method is mild in conditions and wide in solvent selectivity, a reaction temperature is in a range of 37 degrees Celsius (° C.) to 40° C., and a reaction time is in a range of 10 minutes to 48 hours. The method is promising in preparing functional polypeptides or functional proteins, protein labeling, and biological medicine.

A polypeptide or protein directional modification method based on sulfhydryl-alkenyl azide coupling is provided. The method uses a sulfhydryl group-containing compound and a compound containing alkenyl azide group as reactants to generate an amino acid containing β-carbonyl sulfide, a polypeptide containing β-carbonyl sulfide and a protein bioconjugate containing β-carbonyl sulfide, thereby achieving a chemical modification. The method is mild in conditions and wide in solvent selectivity, a reaction temperature is in a range of 37 degrees Celsius (° C.) to 40° C., and a reaction time is in a range of 10 minutes to 48 hours. The method is promising in preparing functional polypeptides or functional proteins, protein labeling, and biological medicine.

Provided herein are methods for design of engineered polypeptides that recapitulate molecular structure features of a predetermined portion of a reference protein structure, e.g., an antibody epitope or a protein binding site. A Machine Learning (ML) model is trained by labeling blueprint records generated from a reference target structure with scores calculated based on computational protein modeling of polypeptide structures generated by the blueprint records. The method may include training an ML model based on a first set of blueprint records, or representations thereof, and a first set of scores, each blueprint record from the first set of blueprint records associated with each score from the first set of scores. After the training, the machine learning model may be executed to generate a second set of blueprint records. A set of engineered polypeptides are then generated based on the second set of blueprint records.

Methods are provided that, for example, include (a) combining ssDNA containing a modified nucleotide (e.g., a ssDNA with a modified nucleotide proximate to its 5′ end) with a DNA cleavage enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate a first ssDNA fragment having a 3′OH and a second ssDNA fragment having the modified nucleotide); wherein the ratio of enzyme to DNA substrate is less than 1:1 molar ratio (m/m); and (b) cleaving at least 95% of the ssDNA at the modified nucleotide. In some embodiments, a method may comprise (a) combining (i) a ssDNA comprising a modified nucleotide (e.g., proximate to its 5′ end) with (ii) a DNA cleavage enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate (after cleavage) a first ssDNA fragment having a 3′OH and a second ssDNA fragment comprising the modified nucleotide) wherein the ratio of enzyme to DNA substrate is less than 1:1 molar ratio and cleaving at least 95% of the ssDNA at the modified nucleotide. In some embodiments, methods provided herein may include (a) combining (i) a ssDNA (1) immobilized on a substrate and (2) comprising a modified nucleotide with (ii) a ssDNA cleaving enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate (after cleavage) a first ssDNA fragment having a 3′OH and a second ssDNA fragment comprising the modified nucleotide) ; and (b) cleaving the immobilized ssDNA to release the second single stranded DNA fragment from the substrate. At least 95% (m/m) of an ssDNA comprising a modified nucleotide may be cleaved in less than 60 minutes.

Methods are provided that, for example, include (a) combining ssDNA containing a modified nucleotide (e.g., a ssDNA with a modified nucleotide proximate to its 5′ end) with a DNA cleavage enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate a first ssDNA fragment having a 3′OH and a second ssDNA fragment having the modified nucleotide); wherein the ratio of enzyme to DNA substrate is less than 1:1 molar ratio (m/m); and (b) cleaving at least 95% of the ssDNA at the modified nucleotide. In some embodiments, a method may comprise (a) combining (i) a ssDNA comprising a modified nucleotide (e.g., proximate to its 5′ end) with (ii) a DNA cleavage enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate (after cleavage) a first ssDNA fragment having a 3′OH and a second ssDNA fragment comprising the modified nucleotide) wherein the ratio of enzyme to DNA substrate is less than 1:1 molar ratio and cleaving at least 95% of the ssDNA at the modified nucleotide. In some embodiments, methods provided herein may include (a) combining (i) a ssDNA (1) immobilized on a substrate and (2) comprising a modified nucleotide with (ii) a ssDNA cleaving enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate (after cleavage) a first ssDNA fragment having a 3′OH and a second ssDNA fragment comprising the modified nucleotide) ; and (b) cleaving the immobilized ssDNA to release the second single stranded DNA fragment from the substrate. At least 95% (m/m) of an ssDNA comprising a modified nucleotide may be cleaved in less than 60 minutes.

The present invention has an object of shortening the process time and reducing use of a poor solvent for solidifying a carrier (Tag)-peptide component, by removing impurities without conducting solid-liquid separation (condensation, solid-liquid separation and drying operation) of a Tag-peptide component, in an Fmoc method using a Tag for liquid phase peptide synthesis. Provided is the peptide synthesis method that includes the following steps a-d: step a: a carrier-protected amino acid, carrier-protected peptide, or a carrier-protected amino acid amide, and an N-Fmoc-protected amino acid or an N-Fmoc-protected peptide are condensed in an organic solvent or a mixed solution of organic solvents, to obtain an N-Fmoc-carrier-protected peptide, step b: a water-soluble amine is added to the reaction solution after the condensation reaction, step c: the Fmoc group is deprotected from the protected amino group in the presence of a water-soluble amine, and step d: the reaction solution is neutralized by adding an acid, and further, by adding and washing with an acidic aqueous solution, then, by liquid-liquid separation an aqueous layer is removed to obtain an organic layer.

A method for preparing peptides is disclosed, the method comprising a step of forming a peptide bond wherein the carboxyl group of a first amino acid or first peptide is activated and an amino group of the first activated amino acid or first peptide is protected by a protecting group having a water-solubility enhancing group and the activated carboxyl group of the first amino acid or first peptide is reacted with an amino group of a second amino acid or second peptide wherein said carboxyl group of the first amino acid or first peptide is activated in the absence of the second amino acid or second peptide. Peptides comprising a protecting group having a water-solubility enhancing group being bound to the amino group and an activated or free carboxyl group are also disclosed.