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Daniecki NJ, Bhatt MR, Yap GPA, Zondlo NJ. Proline C-H Bonds as Loci for Proline Assembly via C-H/O Interactions. Chembiochem 2022; 23:e202200409. [PMID: 36129371 DOI: 10.1002/cbic.202200409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Indexed: 01/25/2023]
Abstract
Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized C-H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. C-H/O interactions, between proline C-H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C-H/O interactions in the crystallographic state, with H⋅⋅⋅O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of C-H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C-H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular C-H/O interactions at proline C-H bonds, suggesting that C-H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C-H bonds, proline residues are uniquely positioned as sites for binding and recognition via C-H/O interactions.
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Affiliation(s)
- Noah J Daniecki
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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Nguyen TQN, Tooh YW, Sugiyama R, Nguyen TPD, Purushothaman M, Leow LC, Hanif K, Yong RHS, Agatha I, Winnerdy FR, Gugger M, Phan AT, Morinaka BI. Post-translational formation of strained cyclophanes in bacteria. Nat Chem 2020; 12:1042-1053. [DOI: 10.1038/s41557-020-0519-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/04/2020] [Indexed: 11/09/2022]
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Toniolo C, Moretto A, Formaggio F, Broxterman QB, Crisma M. From Amherst (Massachusetts, USA) to Padua (Italy) and back again: Louis A. Carpino's scientifically productive journey. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Claudio Toniolo
- Department of ChemistryUniversity of Padua Via Marzolo 1, 35131 Padua Italy
- Institute of Biomolecular Chemistry, Padua UnitCNR Via Marzolo 1, 35131 Padua Italy
| | - Alessandro Moretto
- Department of ChemistryUniversity of Padua Via Marzolo 1, 35131 Padua Italy
- Institute of Biomolecular Chemistry, Padua UnitCNR Via Marzolo 1, 35131 Padua Italy
| | - Fernando Formaggio
- Department of ChemistryUniversity of Padua Via Marzolo 1, 35131 Padua Italy
- Institute of Biomolecular Chemistry, Padua UnitCNR Via Marzolo 1, 35131 Padua Italy
| | | | - Marco Crisma
- Institute of Biomolecular Chemistry, Padua UnitCNR Via Marzolo 1, 35131 Padua Italy
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Ganguly HK, Basu G. Conformational landscape of substituted prolines. Biophys Rev 2020; 12:25-39. [PMID: 31953795 PMCID: PMC7040156 DOI: 10.1007/s12551-020-00621-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The cyclic side chain of the amino acid proline confers unique conformational restraints on its backbone and side chain dihedral angles. This affects two equilibria-one at the backbone (cis/trans) and the other at the side chain (endo/exo). Substitutions on the proline ring impose additional steric and stereoelectronic effects that can further modulate both these equilibria, which in turn can also affect the backbone dihedral angle (ϕ, ψ) preferences. In this review, we have explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. The impact of incorporating these derivatives within model peptides and proteins are also discussed for selected cases. Several of these substituents have been used to introduce bioorthogonal functionality and modulate structure-specific ligand recognition or used as spectroscopic probes. The incorporation of these diversely applicable functional groups, coupled with their ability to define an amino acid conformation via stereoelectronic effects, have a broad appeal among chemical biologists, molecular biophysicists, and medicinal chemists.
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Affiliation(s)
- Himal Kanti Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
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Costantini NV, Ganguly HK, Martin MI, Wenzell NA, Yap GPA, Zondlo NJ. The Distinct Conformational Landscapes of 4S-Substituted Prolines That Promote an endo Ring Pucker. Chemistry 2019; 25:11356-11364. [PMID: 31237705 PMCID: PMC6710147 DOI: 10.1002/chem.201902382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Indexed: 12/28/2022]
Abstract
4-Substitution on proline directly impacts protein main chain conformational preferences. The structural effects of N-acyl substitution and of 4-substitution were examined by NMR spectroscopy and X-ray crystallography on minimal molecules with a proline 4S-nitrobenzoate. The effects of N-acyl substitution on conformation were attenuated in the 4S-nitrobenzoate context, due to the minimal role of the n→π* interaction in stabilizing extended conformations. By X-ray crystallography, an extended conformation was observed for most molecules. The formyl derivative adopted a δ conformation that is observed at the i+2 position of β-turns. Computational analysis indicated that the structures observed crystallographically represent the inherent conformational preferences of 4S-substituted prolines with electron-withdrawing 4-position substituents. The divergent conformational preferences of 4R- and 4S-substituted prolines suggest their wider structure-specific application in molecular design. In particular, the proline endo ring pucker favored by 4S-substituted prolines uniquely promotes the δ conformation [(ϕ, ψ) ≈(-80°, 0°)] found in β-turns. In contrast to other acyl capping groups, the pivaloyl group strongly promoted trans amide bond and polyproline II helix conformation, with a close n→π* interaction in the crystalline state, despite the endo ring pucker, suggesting its special capabilities in promoting compact conformations in ϕ due to its strongly electron-donating character.
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Affiliation(s)
- Nicholas V. Costantini
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Maxwell I. Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Nicole A. Wenzell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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Kubyshkin V, Pridma S, Budisa N. Comparative effects of trifluoromethyl- and methyl-group substitutions in proline. NEW J CHEM 2018. [DOI: 10.1039/c8nj02631a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
| | | | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
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Forbes CR, Sinha SK, Ganguly HK, Bai S, Yap GPA, Patel S, Zondlo NJ. Insights into Thiol-Aromatic Interactions: A Stereoelectronic Basis for S-H/π Interactions. J Am Chem Soc 2017; 139:1842-1855. [PMID: 28080040 PMCID: PMC5890429 DOI: 10.1021/jacs.6b08415] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thiols can engage favorably with aromatic rings in S-H/π interactions, within abiological systems and within proteins. However, the underlying bases for S-H/π interactions are not well understood. The crystal structure of Boc-l-4-thiolphenylalanine tert-butyl ester revealed crystal organization centered on the interaction of the thiol S-H with the aromatic ring of an adjacent molecule, with a through-space Hthiol···Caromatic distance of 2.71 Å, below the 2.90 Å sum of the van der Waals radii of H and C. The nature of this interaction was further examined by DFT calculations, IR spectroscopy, solid-state NMR spectroscopy, and analysis of the Cambridge Structural Database. The S-H/π interaction was found to be driven significantly by favorable molecular orbital interactions, between an aromatic π donor orbital and the S-H σ* acceptor orbital (a π → σ* interaction). For comparison, a structural analysis of O-H/π interactions and of cation/π interactions of alkali metal cations with aromatic rings was conducted. Na+ and K+ exhibit a significant preference for the centroid of the aromatic ring and distances near the sum of the van der Waals and ionic radii, as expected for predominantly electrostatic interactions. Li+ deviates substantially from Na+ and K+. The S-H/π interaction differs from classical cation/π interactions by the preferential alignment of the S-H σ* toward the ring carbons and an aromatic π orbital rather than toward the aromatic centroid. These results describe a potentially broadly applicable approach to understanding the interactions of weakly polar bonds with π systems.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | | | | | - Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
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