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Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.

Sevy AM, Jacobs TM, Crowe JE, Meiler J - PLoS Comput. Biol. (2015)

Bottom Line: Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD) paradigm.As a result, RECON can readily be used in simulations with a flexible protein backbone.We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

View Article: PubMed Central - PubMed

Affiliation: Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America.

ABSTRACT
Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

No MeSH data available.


Incorporation of backbone motion into RECON recapitulates evolutionary sequence profiles in un-minimized structures.Multi-specificity design using RECON was repeated on structures that had not been previously energy minimized to evaluate the benefit of incorporating backbone movements. Designs were generated using either a fixed backbone protocol (Fixed BB), alternating rounds of φ, ψ, and χ angle minimization (Minimize), or using backrub motions (Backrub). P values were calculated by a paired two-tailed t test.
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pcbi.1004300.g007: Incorporation of backbone motion into RECON recapitulates evolutionary sequence profiles in un-minimized structures.Multi-specificity design using RECON was repeated on structures that had not been previously energy minimized to evaluate the benefit of incorporating backbone movements. Designs were generated using either a fixed backbone protocol (Fixed BB), alternating rounds of φ, ψ, and χ angle minimization (Minimize), or using backrub motions (Backrub). P values were calculated by a paired two-tailed t test.

Mentions: From our initial benchmark results, we did not observe a difference in evolutionary sequence similarity for designs created with fixed backbone versus backbone minimization protocols (Fig 5D). However, as previous reports have shown the utility of incorporating backbone motion into a design protocol [8,27–29], we hypothesized that the initial minimization of structures before entering them into multi-specificity design reduced the impact of alternating backbone minimization with design. We hypothesize that backbone movement should have a larger impact on design of structures that have not been pre-minimized. To test this hypothesis, we repeated the benchmark with structures that had not been pre-minimized, and performed multi-specificity design with three protocols: 1) fixed backbone design, 2) alternating design with minimization of φ, ψ, and χ angles, and 3) alternating design with backrub movements. The backrub motion involves rotation of a rigid backbone around axes between nearby Cα atoms, and has been shown to recapitulate alternative backbone conformations in high-resolution crystal structures [30] as well as improving prediction of the conformation of point mutant side chains [31]. We predicted that a design protocol including backrub motions between design rounds should result in the highest agreement to evolutionary sequence profiles, given the sampling of more biologically relevant conformational space than simple minimization. We therefore analyzed the similarity to evolutionary sequence profiles for the top ten designs produced by the three methods and compared to evaluate whether backbone motion in this context confers any additional benefit. As expected, incorporating backrub movements results in a statistically significant increase in similarity to evolutionary profiles as compared to a fixed backbone protocol or one involving minimization (Fig 7). This agrees with previous studies indicated that backrub motions are able to sample biologically relevant conformational space, and shows that backrub motions can be incorporated in a multi-specificity context to provide more robust results in terms of evolutionary sequence recovery.


Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.

Sevy AM, Jacobs TM, Crowe JE, Meiler J - PLoS Comput. Biol. (2015)

Incorporation of backbone motion into RECON recapitulates evolutionary sequence profiles in un-minimized structures.Multi-specificity design using RECON was repeated on structures that had not been previously energy minimized to evaluate the benefit of incorporating backbone movements. Designs were generated using either a fixed backbone protocol (Fixed BB), alternating rounds of φ, ψ, and χ angle minimization (Minimize), or using backrub motions (Backrub). P values were calculated by a paired two-tailed t test.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493036&req=5

pcbi.1004300.g007: Incorporation of backbone motion into RECON recapitulates evolutionary sequence profiles in un-minimized structures.Multi-specificity design using RECON was repeated on structures that had not been previously energy minimized to evaluate the benefit of incorporating backbone movements. Designs were generated using either a fixed backbone protocol (Fixed BB), alternating rounds of φ, ψ, and χ angle minimization (Minimize), or using backrub motions (Backrub). P values were calculated by a paired two-tailed t test.
Mentions: From our initial benchmark results, we did not observe a difference in evolutionary sequence similarity for designs created with fixed backbone versus backbone minimization protocols (Fig 5D). However, as previous reports have shown the utility of incorporating backbone motion into a design protocol [8,27–29], we hypothesized that the initial minimization of structures before entering them into multi-specificity design reduced the impact of alternating backbone minimization with design. We hypothesize that backbone movement should have a larger impact on design of structures that have not been pre-minimized. To test this hypothesis, we repeated the benchmark with structures that had not been pre-minimized, and performed multi-specificity design with three protocols: 1) fixed backbone design, 2) alternating design with minimization of φ, ψ, and χ angles, and 3) alternating design with backrub movements. The backrub motion involves rotation of a rigid backbone around axes between nearby Cα atoms, and has been shown to recapitulate alternative backbone conformations in high-resolution crystal structures [30] as well as improving prediction of the conformation of point mutant side chains [31]. We predicted that a design protocol including backrub motions between design rounds should result in the highest agreement to evolutionary sequence profiles, given the sampling of more biologically relevant conformational space than simple minimization. We therefore analyzed the similarity to evolutionary sequence profiles for the top ten designs produced by the three methods and compared to evaluate whether backbone motion in this context confers any additional benefit. As expected, incorporating backrub movements results in a statistically significant increase in similarity to evolutionary profiles as compared to a fixed backbone protocol or one involving minimization (Fig 7). This agrees with previous studies indicated that backrub motions are able to sample biologically relevant conformational space, and shows that backrub motions can be incorporated in a multi-specificity context to provide more robust results in terms of evolutionary sequence recovery.

Bottom Line: Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD) paradigm.As a result, RECON can readily be used in simulations with a flexible protein backbone.We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

View Article: PubMed Central - PubMed

Affiliation: Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America.

ABSTRACT
Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

No MeSH data available.