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Anchored design of protein-protein interfaces.

Lewis SM, Kuhlman BA - PLoS ONE (2011)

Bottom Line: The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space.This protocol was implemented within the Rosetta3 software suite.This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

ABSTRACT

Background: Few existing protein-protein interface design methods allow for extensive backbone rearrangements during the design process. There is also a dichotomy between redesign methods, which take advantage of the native interface, and de novo methods, which produce novel binders.

Methodology: Here, we propose a new method for designing novel protein reagents that combines advantages of redesign and de novo methods and allows for extensive backbone motion. This method requires a bound structure of a target and one of its natural binding partners. A key interaction in this interface, the anchor, is computationally grafted out of the partner and into a surface loop on the design scaffold. The design scaffold's surface is then redesigned with backbone flexibility to create a new binding partner for the target. Careful choice of a scaffold will bring experimentally desirable characteristics into the new complex. The use of an anchor both expedites the design process and ensures that binding proceeds against a known location on the target. The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space.

Conclusions and significance: This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.

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Best scoring prediction for 8 complexes.This figure demonstrates the relaxed crystal structure input and AnchoredDesign's lowest-score prediction for 8 of the 16 structures. The first and third rows show whole structures, and the second and fourth zoom in on the predicted loops. The nonmoving side of the interface is in green, the actual partner in cyan and the prediction in yellow. The predicted loop is red and the anchor is white. Structures are labeled with their PDB code in the lower right of each cell. For most structures, the predicted rigid-body placement and loop is indistinguishable from the relaxed crystal structure; 3cgc (lower left) is the exception. The other 8 structures are shown similarly in Figure S2.
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pone-0020872-g005: Best scoring prediction for 8 complexes.This figure demonstrates the relaxed crystal structure input and AnchoredDesign's lowest-score prediction for 8 of the 16 structures. The first and third rows show whole structures, and the second and fourth zoom in on the predicted loops. The nonmoving side of the interface is in green, the actual partner in cyan and the prediction in yellow. The predicted loop is red and the anchor is white. Structures are labeled with their PDB code in the lower right of each cell. For most structures, the predicted rigid-body placement and loop is indistinguishable from the relaxed crystal structure; 3cgc (lower left) is the exception. The other 8 structures are shown similarly in Figure S2.

Mentions: Table 3 lists the RMSD metrics for the lowest-score structure predicted by AnchoredDesign for each input (compared to the minimized crystal structure used as input). In most cases, AnchoredDesign produces extremely accurate models for which each metric is below 1 Å RMSD; exceptions are further discussed below. Figures 5 and S2 show each of the 16 complexes, including the minimized crystal structure and lowest-scoring result from AnchoredDesign. For most cases, the prediction is indistinguishable from the correct structure. Note that lowest-scoring is defined purely by Rosetta's standard Score12 scorefunction, plus a chainbreak term used in CCD loop modeling; these weights are listed in Table S1.


Anchored design of protein-protein interfaces.

Lewis SM, Kuhlman BA - PLoS ONE (2011)

Best scoring prediction for 8 complexes.This figure demonstrates the relaxed crystal structure input and AnchoredDesign's lowest-score prediction for 8 of the 16 structures. The first and third rows show whole structures, and the second and fourth zoom in on the predicted loops. The nonmoving side of the interface is in green, the actual partner in cyan and the prediction in yellow. The predicted loop is red and the anchor is white. Structures are labeled with their PDB code in the lower right of each cell. For most structures, the predicted rigid-body placement and loop is indistinguishable from the relaxed crystal structure; 3cgc (lower left) is the exception. The other 8 structures are shown similarly in Figure S2.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3117852&req=5

pone-0020872-g005: Best scoring prediction for 8 complexes.This figure demonstrates the relaxed crystal structure input and AnchoredDesign's lowest-score prediction for 8 of the 16 structures. The first and third rows show whole structures, and the second and fourth zoom in on the predicted loops. The nonmoving side of the interface is in green, the actual partner in cyan and the prediction in yellow. The predicted loop is red and the anchor is white. Structures are labeled with their PDB code in the lower right of each cell. For most structures, the predicted rigid-body placement and loop is indistinguishable from the relaxed crystal structure; 3cgc (lower left) is the exception. The other 8 structures are shown similarly in Figure S2.
Mentions: Table 3 lists the RMSD metrics for the lowest-score structure predicted by AnchoredDesign for each input (compared to the minimized crystal structure used as input). In most cases, AnchoredDesign produces extremely accurate models for which each metric is below 1 Å RMSD; exceptions are further discussed below. Figures 5 and S2 show each of the 16 complexes, including the minimized crystal structure and lowest-scoring result from AnchoredDesign. For most cases, the prediction is indistinguishable from the correct structure. Note that lowest-scoring is defined purely by Rosetta's standard Score12 scorefunction, plus a chainbreak term used in CCD loop modeling; these weights are listed in Table S1.

Bottom Line: The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space.This protocol was implemented within the Rosetta3 software suite.This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

ABSTRACT

Background: Few existing protein-protein interface design methods allow for extensive backbone rearrangements during the design process. There is also a dichotomy between redesign methods, which take advantage of the native interface, and de novo methods, which produce novel binders.

Methodology: Here, we propose a new method for designing novel protein reagents that combines advantages of redesign and de novo methods and allows for extensive backbone motion. This method requires a bound structure of a target and one of its natural binding partners. A key interaction in this interface, the anchor, is computationally grafted out of the partner and into a surface loop on the design scaffold. The design scaffold's surface is then redesigned with backbone flexibility to create a new binding partner for the target. Careful choice of a scaffold will bring experimentally desirable characteristics into the new complex. The use of an anchor both expedites the design process and ensures that binding proceeds against a known location on the target. The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space.

Conclusions and significance: This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.

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