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A rotamer library to enable modeling and design of peptoid foldamers.

Renfrew PD, Craven TW, Butterfoss GL, Kirshenbaum K, Bonneau R - J. Am. Chem. Soc. (2014)

Bottom Line: We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design.We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces.We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.

View Article: PubMed Central - PubMed

Affiliation: Center for Genomics and Systems Biology, Department of Biology, ‡Department of Chemistry, and §Courant Institute of Mathematical Sciences, Computer Science Department, New York University , New York, New York 10003, United States.

ABSTRACT
Peptoids are a family of synthetic oligomers composed of N-substituted glycine units. Along with other "foldamer" systems, peptoid oligomer sequences can be predictably designed to form a variety of stable secondary structures. It is not yet evident if foldamer design can be extended to reliably create tertiary structure features that mimic more complex biomolecular folds and functions. Computational modeling and prediction of peptoid conformations will likely play a critical role in enabling complex biomimetic designs. We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design. We find that peptoids can be described by a "rotamer" treatment, similar to that established for proteins, in which the peptoid side chains display rotational isomerism to populate discrete regions of the conformational landscape. Because of the insufficient number of solved peptoid structures, we have calculated the relative energies of side-chain conformational states to provide a backbone-dependent (BBD) rotamer library for a set of 54 different peptoid side chains. We evaluated two rotamer library development methods that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify side-chain rotamers. We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces. We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.

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Backbone-Independent (BBI) (left) and Backbone-Dependent(BBD) “dipeptoid”(right) Models Used in the Rotamer Library Creation Protocols
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sch4: Backbone-Independent (BBI) (left) and Backbone-Dependent(BBD) “dipeptoid”(right) Models Used in the Rotamer Library Creation Protocols


A rotamer library to enable modeling and design of peptoid foldamers.

Renfrew PD, Craven TW, Butterfoss GL, Kirshenbaum K, Bonneau R - J. Am. Chem. Soc. (2014)

Backbone-Independent (BBI) (left) and Backbone-Dependent(BBD) “dipeptoid”(right) Models Used in the Rotamer Library Creation Protocols
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4227732&req=5

sch4: Backbone-Independent (BBI) (left) and Backbone-Dependent(BBD) “dipeptoid”(right) Models Used in the Rotamer Library Creation Protocols
Bottom Line: We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design.We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces.We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.

View Article: PubMed Central - PubMed

Affiliation: Center for Genomics and Systems Biology, Department of Biology, ‡Department of Chemistry, and §Courant Institute of Mathematical Sciences, Computer Science Department, New York University , New York, New York 10003, United States.

ABSTRACT
Peptoids are a family of synthetic oligomers composed of N-substituted glycine units. Along with other "foldamer" systems, peptoid oligomer sequences can be predictably designed to form a variety of stable secondary structures. It is not yet evident if foldamer design can be extended to reliably create tertiary structure features that mimic more complex biomolecular folds and functions. Computational modeling and prediction of peptoid conformations will likely play a critical role in enabling complex biomimetic designs. We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design. We find that peptoids can be described by a "rotamer" treatment, similar to that established for proteins, in which the peptoid side chains display rotational isomerism to populate discrete regions of the conformational landscape. Because of the insufficient number of solved peptoid structures, we have calculated the relative energies of side-chain conformational states to provide a backbone-dependent (BBD) rotamer library for a set of 54 different peptoid side chains. We evaluated two rotamer library development methods that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify side-chain rotamers. We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces. We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.

Show MeSH