Systems and methods for identifying protein stabilizers

Abstract

A device for studying protein conformation transformation can include a macroscopic substrate, and chaperonin proteins bound to the substrate, each chaperonin protein being capable of binding to a protein of interest during or after undergoing protein conformation transformation. The device may also include the proteins of interest bound to the substrate, where the substrate is included in a label-free assay system. A method of studying protein conformation transformation can include: providing a macroscopic substrate bound with the chaperonin protein and immersing the chaperonin protein in a study composition having the protein of interest, or include providing a macroscopic substrate bound with the protein of interest; and immersing the protein in a study composition having the chaperonin. Such a method can be done with and without a potential stabilizer in order to determine whether the potential stabilizer stabilizes the protein of interest.

1 . A device for studying protein conformation transformation, the device comprising:
 a macroscopic substrate; and   one or more chaperonin proteins or functional portion thereof bound to the substrate, each chaperonin protein being capable of binding to a protein of interest during or after undergoing protein conformation transformation, the protein of interest being capable of undergoing protein conformation transformation at physiological conditions.   
     
     
         2 . The device of  claim 1 , comprising the macroscopic substrate being immersed in a composition having a protein susceptible of undergoing protein conformation transformation. 
     
     
         3 . The device of  claim 1 , wherein the device is configured for:
 biolayer interferometry (BLI); or   surface plasmon resonance (SPR); or   any label-free system device.   
     
     
         4 . (canceled) 
     
     
         5 . (canceled) 
     
     
         6 . The device of  claim 1 , wherein a nonfunctional portion of the chaperonin protein is bound to the substrate, wherein
 optionally the chaperonin protein is bound to the substrate through direct amine coupling, antibody capture, or biotin/streptavidin affinity.   
     
     
         7 . (canceled) 
     
     
         8 . The device of  claim 1 , wherein the substrate is:
 a probe; or   biolayer interferometry (BLI) probe; or   a biochemical chip; or   an assay surface of an assay surface array plate; or   a well surface of a plate; or   an assay surface array plate.   
     
     
         9 . (canceled) 
     
     
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         13 . A device for studying protein conformation transformation, the device comprising:
 a macroscopic substrate;   one or more proteins of interest or functional portion thereof bound to the substrate, the protein being susceptible of undergoing protein conformation transformation at physiological conditions; and   a label-free assay system having the one or more proteins of interest bound to the macroscopic substrate.   
     
     
         14 . The device of  claim 13 , comprising the macroscopic substrate being immersed in a composition having one or more chaperonin proteins each capable of binding to the protein of interest during or after undergoing protein conformation transformation. 
     
     
         15 . (canceled) 
     
     
         16 . The device of  claim 13 , wherein the protein of interest is bound to the macroscopic substrate through a linker, the linker optionally selected from the group consisting of a polymer, hydrocarbon, antibody, chimeric construct, GST domain, histidine tag, SUMO tag, or combination thereof. 
     
     
         17 . (canceled) 
     
     
         18 . The device of  claim 13 , wherein:
 a nonfunctional portion of the protein of interest is bound to the substrate; or   the protein of interest is bound to the substrate through direct amine coupling, antibody capture, or biotin/streptavidin affinity.   
     
     
         19 . (canceled) 
     
     
         20 . The device of  claim 13 , wherein the substrate is:
 a probe; or   biolayer interferometry (BLI) probe; or   a biochemical chip; or   an assay surface of an assay surface array plate; or   a well surface of a plate; or   an assay surface array plate.   
     
     
         21 . (canceled) 
     
     
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         31 . A system for studying protein conformation transformation, the system comprising:
 the device of  claim 1 ; and   a liquid composition having the protein of interest soluble in the liquid.   
     
     
         32 . A system for studying protein conformation transformation, the system comprising:
 the device of  claim 13 ; and   a liquid composition having the chaperonin soluble in the liquid.   
     
     
         33 . The system of  claim 31 , comprising one or more of:
 one or more potential protein stabilizers;   a control composition having dihydrofolate reductase (DHFR) as a control;   one or more potential protein destabilizers;   a positive control protein stabilizer;   a composition including an osmolyte; or   a composition including a denaturant.   
     
     
         34 . The system of  claim 32 , comprising one or more of:
 one or more potential protein destabilizers;   a control composition having dihydrofolate reductase (DHFR) as a control;   one or more potential protein stabilizers;   a positive control protein stabilizer;   a composition including an osmolyte; or   a composition including a denaturant.   
     
     
         35 . (canceled) 
     
     
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         41 . (canceled) 
     
     
         42 . (canceled) 
     
     
         43 . (canceled) 
     
     
         44 . (canceled) 
     
     
         45 . A method of studying protein conformation transformation, the method comprising:
 providing the device of  claim 1  having the macroscopic substrate bound with the chaperonin protein; and   immersing the chaperonin protein in a study composition having the protein of interest.   
     
     
         46 . The method of studying protein conformation transformation, the method comprising:
 providing the device of  claim 13  having the macroscopic substrate bound with the protein of interest; and   immersing the protein in a study composition having the chaperonin.   
     
     
         47 . The method of  claim 45 , comprising:
 introducing a potential protein stabilizer into the study composition; and   determining whether the potential protein stabilizer is a protein stabilizer for the protein of interest.   
     
     
         48 . The method of  claim 45 , comprising:
 monitoring kinetics of interaction between the chaperonin and the protein of interest with or without presence of potential protein stabilizer.   
     
     
         49 . The method of  claim 45 , comprising:
 determining a potential protein stabilizer to be a protein stabilizer for the protein of interest at a desired pH value or range.   
     
     
         50 . (canceled) 
     
     
         51 . (canceled) 
     
     
         52 . The method of  claim 45 , comprising:
 monitoring dynamic folding and/or unfolding of the protein of interest with or without the potential protein stabilizer.   
     
     
         53 . (canceled) 
     
     
         54 . (canceled) 
     
     
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         56 . The method of  claim 45 , comprising:
 introducing a potential protein destabilizer into the study composition; and   determining whether the potential protein destabilizer is a protein destabilizer for the protein of interest.   
     
     
         57 . (canceled) 
     
     
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         66 . The method of  claim 45 , comprising:
 determining whether or not a potential protein stabilizer inhibits aggregation of the protein of interest.   
     
     
         67 . (canceled) 
     
     
         68 . (canceled) 
     
     
         69 . (canceled) 
     
     
         70 . A method of studying protein aggregation, the method comprising:
 providing the device of  claim 1  having the macroscopic substrate bound with the chaperonin protein;   immersing the chaperonin protein in a study composition having the protein of interest and a potential protein stabilizer; and   determining whether or not the potential protein stabilizer inhibits aggregation of the protein of interest.   
     
     
         71 . A method of studying protein aggregation, the method comprising:
 providing the device of  claim 13  having the macroscopic substrate bound with the protein of interest; and   immersing the protein of interest in an study composition having the chaperonin and a potential protein stabilizer; and   determining whether or not the potential protein stabilizer inhibit aggregation of the protein of interest.   
     
     
         72 . (canceled) 
     
     
         73 . The method of  claim 46 , comprising:
 introducing a potential protein stabilizer into the study composition; and   determining whether the potential protein stabilizer is a protein stabilizer for the protein of interest.   
     
     
         74 . The method of  claim 46 , comprising:
 monitoring kinetics of interaction between the chaperonin and the protein of interest with or without presence of potential protein stabilizer.   
     
     
         75 . The method of  claim 46 , comprising:
 determining a potential protein stabilizer to be a protein stabilizer for the protein of interest at a desired pH value or range.   
     
     
         76 . The method of  claim 46 , comprising:
 monitoring dynamic folding and/or unfolding of the protein of interest with or without the potential protein stabilizer.   
     
     
         77 . The method of  claim 46 , comprising:
 introducing a potential protein destabilizer into the study composition; and   determining whether the potential protein destabilizer is a protein destabilizer for the protein of interest.