Systems and methods for engineering enzymes using identified energy transfer networks

A method of engineering a target enzyme to modify its catalytic activity, the method comprising:

• accessing biophysical and dynamics data for the target enzyme;
• analyzing, using a computing device, the biophysical and dynamics data to identify at least one energy transfer network within the target enzyme, the at least one energy transfer network comprising a series of residues spanning from a surface of the target enzyme to a catalytic site of the target enzyme;
• identifying one or more residues within the energy transfer network that are not on the surface of the target enzyme;
• iteratively modifying at least one of the one or more residues of the energy transfer network to produce a plurality of candidate engineered enzyme sequences such that each of the plurality of candidate engineered enzyme sequences comprises a different residue at the location of the at least one residue, wherein at least one surface loop or neighboring region has longer side chains as a result of the modifying;
• for each candidate engineered enzyme sequence of the plurality of candidate engineered enzyme sequences:
• determining a modified network conductance of the engineered enzyme sequence exceeds a baseline network conductance of the target enzyme and provides an increase in energy flow to the catalytic site, via the at least one energy transfer network by:
• calculating a residue energy conductance for each residue of the at least one energy transfer network for each of the target enzyme and the engineered enzyme sequence;
• and
• combining the residue energy conductance for each residue of the at least one energy transfer network for each of the baseline network conductance and the modified network conductance;
• calculating the change in thermo-dynamical coupling with an external environment or solvent by calculating the surface area of interaction due to the modified residue;
• calculating the changes in conformations in functionally important sub-states related to the enzyme activity due to the changes in energy conductance through the network;
• assigning a score or ranking of each candidate engineered enzyme sequence of the plurality of candidate engineered enzyme sequences using the modified network conductance, the change in thermo-dynamical coupling, and the changes in conformations;
• selecting a subset of top ranking candidates of the plurality of candidate engineered enzyme sequences;
• and
• constructing an engineered enzyme with increased catalytic activity by transfecting cells with nucleic acids encoding the engineered enzyme sequence selected from the subset of top ranking candidates and purifying the engineered enzyme.

A method of immobilizing an enzyme to preserve naturally occurring activity, the method comprising:

• accessing biophysical and dynamics data for the target enzyme;
• analyzing, using a computing device, the biophysical and dynamics data to identify at least one energy transfer network within the target enzyme, the at least one energy transfer network comprising a series of residues spanning from a surface of the target enzyme to a catalytic site of the target enzyme;
• identifying one or more residues that are not within the energy transfer network and are not on the surface of the target enzyme, wherein the one or more residues show higher energy conductance than an average values of all the enzyme residues, wherein each residue energy conductance is determined by:
• calculating a residue energy conductance for each residue of the at least one energy transfer network for each of the target enzyme and the engineered enzyme sequence;
• and
• combining the residue energy conductance for each residue of the at least one energy transfer network for each of the baseline network conductance and the modified network conductance;
• calculating the change in thermo-dynamical coupling with an external environment or solvent by calculating the surface area of interaction due to the modified residue;
• and
• immobilizing the target enzyme using the one or more residues identified as not part of the energy network.

A method of engineering a target enzyme to modify its catalytic activity, the method comprising:

• accessing biophysical and dynamics data for the target enzyme;
• analyzing, using a computing device, the biophysical and dynamics data to identify at least one energy transfer network within the target enzyme, the at least one energy transfer network comprising a series of residues spanning from a surface of the target enzyme to a catalytic site of the target enzyme;
• identifying at least one surface loop within the energy transfer network, the at least one surface loop or neighboring region comprising one or more residues showing demoting dynamical motions coupled to the catalytic activity of the target enzyme;
• iteratively modifying one or more residues out of the at least one surface loop or neighboring region to produce a plurality of candidate engineered enzyme sequences such that each of the plurality of candidate engineered enzyme comprises a different residue at the location of the at least one residue, wherein the at least one surface loop or neighboring region has shorter side chains as a result of the modifying;
• for each candidate engineered enzyme sequence of the plurality of candidate engineered enzyme sequences:
• determining a modified network conductance of the engineered enzyme sequence exceeds a baseline network conductance of the target enzyme and provides a decrease in energy flow with decreased dynamics and decreased energy transfer directed into the active site via the at least one energy transfer network by:
• calculating a residue energy conductance for each residue of the at least one energy transfer network for each of the target enzyme and the engineered enzyme sequence;
• and
• combining the residue energy conductance for each residue of the at least one energy transfer network for each of the baseline network conductance and the modified network conductance;
• calculating the change in thermo-dynamical coupling with an external environment or solvent by calculating the surface area of interaction due to the modified residue;
• calculating the changes in conformations in the functionally important sub-states related to the enzyme activity due to the changes in energy conductance through the network;
• assigning a score or ranking of each candidate engineered enzyme sequence of the plurality of candidate engineered enzyme sequences using the modified network conductance, the change in thermo-dynamical coupling, and the changes in conformations;
• selecting a subset of top ranking candidates of the plurality of candidate engineered enzyme sequences;
• and
• constructing an engineered enzyme with decreased catalytic activity by transfecting cells with nucleic acids encoding the engineered enzyme sequence selected from the subset of top ranking candidates and purifying the engineered enzyme.