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Rodríguez CS, Laurents DV. Architectonic principles of polyproline II helix bundle protein domains. Arch Biochem Biophys 2024; 756:109981. [PMID: 38593862 DOI: 10.1016/j.abb.2024.109981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/18/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
Glycine rich polyproline II helix assemblies are an emerging class of natural domains found in several proteins with different functions and diverse origins. The distinct properties of these domains relative to those composed of α-helices and β-sheets could make glycine-rich polyproline II helix assemblies a useful building block for protein design. Whereas the high population of polyproline II conformers in disordered state ensembles could facilitate glycine-rich polyproline II helix folding, the architectonic bases of these structures are not well known. Here, we compare and analyze their structures to uncover common features. These protein domains are found to be highly tolerant of distinct flanking sequences. This speaks to the robustness of this fold and strongly suggests that glycine rich polyproline II assemblies could be grafted with other protein domains to engineer new structures and functions. These domains are also well packed with few or no cavities. Moreover, a significant trend towards antiparallel helix configuration is observed in all these domains and could provide stabilizing interactions among macrodipoles. Finally, extensive networks of Cα-H···OC hydrogen bonds are detected in these domains. Despite their diverse evolutionary origins and activities, glycine-rich polyproline II helix assemblies share architectonic features which could help design novel proteins.
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Affiliation(s)
| | - Douglas V Laurents
- Instituto de Química Física "Blas Cabrera" CSIC, Serrano 119 Madrid, Spain.
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Itagaki T, Ito Y, Ueda M. Peptide flat-rod formation by precise arrangement among enantiomeric hydrophobic helices. J Colloid Interface Sci 2022; 617:129-135. [DOI: 10.1016/j.jcis.2022.02.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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Heinz-Kunert SL, Pandya A, Dang VT, Tran PN, Ghosh S, McElheny D, Santarsiero BD, Ren Z, Nguyen AI. Assembly of π-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework. J Am Chem Soc 2022; 144:7001-7009. [PMID: 35390261 DOI: 10.1021/jacs.2c02146] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The evolution of proteins from simpler, self-assembled peptides provides a powerful blueprint for the design of complex synthetic materials. Previously, peptide-metal frameworks using short sequences (≤3 residues) have shown great promise as proteomimetic materials that exhibit sophisticated capabilities. However, their development has been hindered due to few variable residues and restricted choice of side-chains that are compatible with metal ions. Herein, we developed a noncovalent strategy featuring π-stacking bipyridyl residues to assemble much longer peptides into crystalline frameworks that tolerate even previously incompatible acidic and basic functionalities and allow an unprecedented level of pore variations. Single-crystal X-ray structures are provided for all variants to guide and validate rational design. These materials exhibit hallmark proteomimetic behaviors such as guest-selective induced fit and assembly of multimetallic units. Significantly, we demonstrate facile optimization of the framework design to substantially increase affinity toward a complex organic molecule.
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Affiliation(s)
- Sherrie L Heinz-Kunert
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ashma Pandya
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Viet Thuc Dang
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Phuong Nguyen Tran
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sabari Ghosh
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Bernard D Santarsiero
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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