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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Guan X, Wang S, Shi G, Zhang J, Wan X. Thermoswitching of Helical Inversion of Dynamic Polyphenylacetylenes through cis-trans Isomerization of Amide Pendants. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00538] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiaoyan Guan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Sheng Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ge Shi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jie Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinhua Wan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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3
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Zhang JH, Pan CL, Zhang HH, Xu PF, Luo YC. Sc(OTf) 3 catalyzed [3 + 2]-annulation reaction of donor–acceptor aziridines with methylene exo-glycals: synthesis of chiral carbohydrate-spiro-heterocycles. Org Chem Front 2021. [DOI: 10.1039/d1qo00228g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A Sc(OTf)3 catalyzed [3 + 2]-annulation reaction between D–A N-tosyl aziridines and methylene exo-glycals was developed for the synthesis of carbohydrate-spiro-heterocycles.
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Affiliation(s)
- Jie-Hui Zhang
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Cheng-Lin Pan
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Huan-Huan Zhang
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Peng-Fei Xu
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Yong-Chun Luo
- State Key Laboratory of Applied Organic Chemistry
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
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4
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Masson MAC, Karpfenstein R, de Oliveira-Silva D, Teuler JM, Archirel P, Maître P, Correra TC. Evaluation of Ca2+ Binding Sites in Tacrolimus by Infrared Multiple Photon Dissociation Spectroscopy. J Phys Chem B 2018; 122:9860-9868. [DOI: 10.1021/acs.jpcb.8b06523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Maria Angélica C. Masson
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo, São Paulo, Brazil
| | - Renan Karpfenstein
- Department of Chemistry, Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, St. Prof. Arthur Riedel 275, 09972-270 Diadema, São Paulo, Brazil
| | - Diogo de Oliveira-Silva
- Department of Chemistry, Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, St. Prof. Arthur Riedel 275, 09972-270 Diadema, São Paulo, Brazil
| | - Jean-Marie Teuler
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Pierre Archirel
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Thiago C. Correra
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo, São Paulo, Brazil
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Kubyshkin V, Budisa N. Construction of a polyproline structure with hydrophobic exterior using octahydroindole-2-carboxylic acid. Org Biomol Chem 2017; 15:619-627. [DOI: 10.1039/c6ob02306a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Oligomeric octahydroindole-2-carboxilic acid (Oic) forms a stable polyproline-II type helix.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis group
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
| | - Nediljko Budisa
- Biocatalysis group
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
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6
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Iwahana S, Iida H, Yashima E, Pescitelli G, Di Bari L, Petrovic AG, Berova N. Absolute Stereochemistry of a 4 a-Hydroxyriboflavin Analogue of the Key Intermediate of the FAD-Monooxygenase Cycle. Chemistry 2014; 20:4386-95. [DOI: 10.1002/chem.201304393] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Indexed: 11/10/2022]
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7
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Newberry RW, VanVeller B, Guzei IA, Raines RT. n→π* interactions of amides and thioamides: implications for protein stability. J Am Chem Soc 2013; 135:7843-6. [PMID: 23663100 PMCID: PMC3742804 DOI: 10.1021/ja4033583] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Indexed: 01/05/2023]
Abstract
Carbonyl-carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n→π* donor-acceptor interaction with an energy of at least 0.27 kcal/mol. The n→π* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor-acceptor orbital interactions rather than dipole-dipole interactions.
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Affiliation(s)
- Robert W. Newberry
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Brett VanVeller
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Ilia A. Guzei
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Ronald T. Raines
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
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Naziga EB, Schweizer F, Wetmore SD. Solvent interactions stabilize the polyproline II conformation of glycosylated oligoprolines. J Phys Chem B 2013; 117:2671-81. [PMID: 23363073 DOI: 10.1021/jp312487v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In nature, proline residues carry several post-translational modifications (PTMs), including 4R hydroxylation and glycosylation. A recent study synthesized contiguously hydroxylated and glycosylated nonaproline peptides and revealed that both PTMs lead to a significant increase in the thermal stability of PPII relative to the unmodified oligoproline. The increased stability of the hydroxylated peptide can be explained by increased stability of the trans isomer due to stereoelectronic effects. However, the effects of glycosylation cannot be completely explained by stereoelectronics since previous experimental results indicate that 4R-glycosylation does not produce observable changes in the trans preference compared to 4R-hydroxylation. We therefore used sophisticated molecular modeling techniques to determine the reason for the further increase in thermal stability upon glycosylation. Free energy estimates obtained from adaptively biased molecular dynamics calculations in implicit (explicit) solvent are -9 kcal mol(-1) (-20 kcal mol(-1)) for the hydroxylated compound and -9 kcal mol(-1) (-46 kcal mol(-1)) for the glycosylated compound, indicating that direct solvent-peptide interactions are vital for explaining the glycosylation effects on PPII stability. Our data reveals for the first time that interactions between the hydroxyl groups in the glycosylated compound and water act in a complementary fashion with stereoelectronic effects to stabilize the PPII conformation in these substituted oligoproline peptides.
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Affiliation(s)
- Emmanuel B Naziga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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Teklebrhan RB, Owens NW, Xidos JD, Schreckenbach G, Wetmore SD, Schweizer F. Conformational Preference of Fused Carbohydrate-Templated Proline Analogues—A Computational Study. J Phys Chem B 2012; 117:199-205. [DOI: 10.1021/jp310690c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robel B. Teklebrhan
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Neil W. Owens
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - James D. Xidos
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Stacey D. Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
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10
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Reddy DN, Thirupathi R, Tumminakatti S, Prabhakaran EN. A method for stabilizing the cis prolyl peptide bond: influence of an unusual n→π∗ interaction in 1,3-oxazine and 1,3-thiazine containing peptidomimetics. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.06.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Naziga EB, Schweizer F, Wetmore SD. Conformational Study of the Hydroxyproline–O–Glycosidic Linkage: Sugar–Peptide Orientation and Prolyl Amide Isomerization in (α/β)–Galactosylated 4(R/S)–Hydroxyproline. J Phys Chem B 2012; 116:860-71. [DOI: 10.1021/jp207479q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuel B. Naziga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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12
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Synthesis and antibacterial properties of carbohydrate-templated lysine surfactants. Carbohydr Res 2011; 346:588-94. [DOI: 10.1016/j.carres.2011.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 01/14/2011] [Accepted: 01/21/2011] [Indexed: 02/08/2023]
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13
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Kuemin M, Nagel YA, Schweizer S, Monnard FW, Ochsenfeld C, Wennemers H. Tuning the cis/trans conformer ratio of Xaa-Pro amide bonds by intramolecular hydrogen bonds: the effect on PPII helix stability. Angew Chem Int Ed Engl 2010; 49:6324-7. [PMID: 20665611 DOI: 10.1002/anie.201001851] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Kuemin
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
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Kuemin M, Nagel Y, Schweizer S, Monnard F, Ochsenfeld C, Wennemers H. Tuning the cis/trans Conformer Ratio of Xaa-Pro Amide Bonds by Intramolecular Hydrogen Bonds: The Effect on PPII Helix Stability. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001851] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Teklebrhan RB, Zhang K, Schreckenbach G, Schweizer F, Wetmore SD. Intramolecular Hydrogen Bond-Controlled Prolyl Amide Isomerization in Glucosyl 3(S)-Hydroxy-5-hydroxymethylproline Hybrids: A Computational Study. J Phys Chem B 2010; 114:11594-602. [DOI: 10.1021/jp1006186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robel B. Teklebrhan
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - Kaidong Zhang
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - G. Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - Stacey D. Wetmore
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
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Synthesis of allose-templated hydroxyornithine and hydroxyarginine analogs. Carbohydr Res 2010; 345:1533-40. [DOI: 10.1016/j.carres.2010.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 04/05/2010] [Accepted: 04/19/2010] [Indexed: 11/19/2022]
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17
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Zhang K, Schweizer F. Influence of glucose-templated proline mimetics on the β-turn conformation of the peptide fragment Ac-Leu-d-Phe-Pro-Val-NMe2 found in Gramicidin S. Carbohydr Res 2010; 345:1114-22. [DOI: 10.1016/j.carres.2010.03.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/23/2010] [Accepted: 03/28/2010] [Indexed: 10/19/2022]
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Owens NW, Lee A, Marat K, Schweizer F. The implications of (2S,4S)-hydroxyproline 4-O-glycosylation for prolyl amide isomerization. Chemistry 2009; 15:10649-57. [PMID: 19739208 DOI: 10.1002/chem.200900844] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The conformations of peptides and proteins are often influenced by glycans O-linked to serine (Ser) or threonine (Thr). (2S,4R)-4-Hydroxyproline (Hyp), together with L-proline (Pro), are interesting targets for O-glycosylation because they have a unique influence on peptide and protein conformation. In previous work we found that glycosylation of Hyp does not affect the N-terminal amide trans/cis ratios (K(trans/cis)) or the rates of amide isomerization in model amides. The stereoisomer of Hyp--(2S,4S)-4-hydroxyproline (hyp)--is rarely found in nature, and has a different influence both on the conformation of the pyrrolidine ring and on K(trans/cis). Glycans attached to hyp would be expected to be projected from the opposite face of the prolyl side chain relative to Hyp; the impact this would have on K(trans/cis) was unknown. Measurements of (3)J coupling constants indicate that the glycan has little impact on the C(gamma)-endo conformation produced by hyp. As a result, it was found that the D-galactose residue extending from a C(gamma)-endo pucker affects both K(trans/cis) and the rate of isomerization, which is not found to occur when it is projected from a C(gamma)-exo pucker; this reflects the different environments delineated by the proline side chain. The enthalpic contributions to the stabilization of the trans amide isomer may be due to disruption of intramolecular interactions present in hyp; the change in enthalpy is balanced by a decrease in entropy incurred upon glycosylation. Because the different stereoisomers--Hyp and hyp--project the O-linked carbohydrates in opposite spatial orientations, these glycosylated amino acids may be useful for understanding of how the projection of a glycan from the peptide or protein backbone exerts its influence.
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Affiliation(s)
- Neil W Owens
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
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