Simplifying residue relationships in protein design
The invention provides a method of determining changes in a first set of residues r 1 due to changes in a second set of residues r 2 in a protein system comprising one or more proteins comprising r 1 and r 2 . In exemplary embodiments, the method comprises optimizing a quality function Q by modifying one or more properties of r 1 and r 2 in a constrained environment in which all degrees of freedom of the system except those directly involved in the potential coupling between r 1 and r 2 are removed.
1. A computer implemented method of determining changes in a property value of a first set of residues r 1 due to perturbations in a second set of residues r 2 in a protein system comprising one or more proteins, the protein system comprising r 1 and r 2 , the method comprising:
for each respective perturbation p i in a first set of perturbations P 1 ={p 1 , . . . , p n }, wherein n is a user-defined number of perturbations of value 2 or greater, performing the method of:
(a) applying the respective perturbation p i to r 2 ,wherein the respective perturbation is an alteration to the structure of one or more residues of r 2 ;
(b) optimizing, responsive to the applying (a) and using an atomistic force field for the entire protein system, a quality function Q by modifying the conformation of residues of r 1 and r 2 in a constrained environment in which the backbone of all residues in the protein system apart from the residues in r 2 and r 1 are fixed during the optimization and in which C β atoms of all residues, other than glycine residues and proline residues, in the protein system apart from the residues in r 2 and r 1 are fixed during the optimization and, wherein the quality function Q comprises a free energy term for r 1 and r 2 ; and
(c) applying, upon completion of the optimizing (b), a measure M to r 1 thereby providing a physical property value v i of r 1 , wherein the physical property value is a side-chain conformation value, a backbone conformation value, or a rotamer conformation value, and wherein the measure M comprises an enumeration of the residues in r 1 that exhibit an altered property after application of one or more perturbations to the residues of r 2 and optimization of Q, thereby obtaining a first set of property values V 1 ={v 1 , . . . , v n } for r 1 , and thereby determining changes in the property values of r 1 due to perturbations to r 2 , wherein the method is performed on a computer system.
2. The method of claim 1 wherein the protein system comprises a receptor and a ligand, and wherein the constrained environment is a mixed background wherein the receptor provides a full background and the ligand provides a zero background.
3. The method of claim 2 wherein all of the residues of the receptor apart from r 1 and r 2 have their backbone and side-chain fixed, and all of the residues of the ligand apart from r 1 , r 2 , glycine, and proline are mutated to alanine during the optimizing (b).
4. The method of claim 1 wherein the free energy term is selected from a free energy of stability of r 1 and r 2 and a free energy of interaction of r 1 and r 2 .
5. The method of claim 1 wherein the quality function comprises one or more measures selected from a measure of protein volume, a measure of protein surface area, a measure of relative particle coordinates and atom types, a measure of contact between multiple proteins or parts of a protein, a measure of protein system surface area exposed to a solvent, and a measure of protein shape.
6. The method of claim 1 wherein r 1 and r 2 comprise common elements.
7. The method of claim 1 further comprising calculating a first coupling measure M c1 based on two or more property values selected from V 1 , wherein the coupling measure M c1 is a mean, a total, an extremum, an entropy, a variance, an absolute deviation, or a variability measure of V 1 .
8. The method of claim 7 wherein r 1 is a residue at a position s 1 and r 2 is a residue at a position s 2 of the protein system in the applying (a), the optimizing (b), and the applying (c), the method further comprising, with r 1 being a residue at the position s 2 and r 2 being a residue at the position s 1 , repeating the applying (a), the optimizing (b) and the applying (c) for each respective perturbation p i in a second set of perturbations P 2 until all perturbations in the second set of perturbations have been applied, thereby providing a second set of property values V 2 for r 1 and,
calculating a second coupling measure M c2 based on two or more property values selected from V 2 .
9. The method of claim 8 wherein the second set of perturbations comprise one or more residue mutations.
10. The method of claim 7 further comprising:
making a variant of the protein characterized by a mutation selected based on M c1 .
11. The method of claim 1 , the method further comprising evaluating the first set of property values V 1 ={v 1 , . . . , v n } to determine a degree of side-chain flexibility in a first residue position in the protein system as a function of a residue type in a second residue position in the protein system.
12. The method of claim 1 , the method further comprising evaluating the first set of property values V 1 ={v 1 , . . . , v n } to characterize non-hydrogen atom clashes between a side-chain in a first residue position in the protein system and a residue in the second residue position in the protein system.
13. The method of claim 1 , the method further comprising evaluating the first set of property values V 1 ={v 1 , . . ., v n } to identify an optimal rotamer position for a side-chain in a first residue position in the protein system.
14. A computer readable medium comprising nontransitory instructions that perform the method of claim 1 .
15. A computer system comprising a clock, a memory and a processor, the memory comprising nontransitory instructions that performs the method of claim 1 .