1
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Deka JKR, Borah D, Das P, Sahariah B, Vishnoi P, Sarma BK. Synergistic n → π* and n N → π* Ar interactions in C-terminal modified prolines: effect on Xaa-Pro cis/ trans equilibrium. Chem Commun (Camb) 2023; 59:6080-6083. [PMID: 37128689 DOI: 10.1039/d3cc01494k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Carbonyl-carbonyl (CO⋯CO) n → π* interaction often coexists with a hydrogen bond (HB) or another n → π* interaction. Although the interplay between HB and n → π* interaction was previously studied, there is no systematic investigation that shows a synergistic relationship of n → π* with another noncovalent interaction. Herein, we have studied a set of proline-diacylhydrazine (Pro-DAH) molecules and observed that increase in the strength of the nN → π*Ar interaction on their DAH side strengthened the n → π* interaction on the Pro side, which was experimentally determined by measuring the Ktrans/cis of the Xaa-Pro amide bond. Overall, we describe a simple C-terminal modification strategy to stabilize the trans-Pro geometry that could be useful to stabilize PPII helices and collagen triple helices that require Pro to adopt the trans amide geometry.
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Affiliation(s)
- Jugal Kishore Rai Deka
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Debashree Borah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Paramesh Das
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Pratap Vishnoi
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
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2
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Gupta SK, Banerjee S, Prabhakaran EN. Understanding the anomaly of cis-trans isomerism in Pro-His sequence. Bioorg Med Chem Lett 2022; 76:128985. [PMID: 36165914 DOI: 10.1016/j.bmcl.2022.128985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/05/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022]
Abstract
The anomalous absence of cisPro stabilizing CαHαXaa···πAro interactions at Xaa-Pro-Aro exclusively when Aro is His, is understood by NMR structural analyses of model peptides, as due to i → i backbone-side chain C6 H-bond that forms uniquely when Aro is His, which significantly decreases its χ1-g- population essential for CαHαXaa···πAro formation.
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Affiliation(s)
- Sunil K Gupta
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Erode N Prabhakaran
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.
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3
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Lameiras P, Nuzillard JM. Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 123:1-50. [PMID: 34078536 DOI: 10.1016/j.pnmrs.2020.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/06/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between 1H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).
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Affiliation(s)
- Pedro Lameiras
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
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4
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Prabhakaran EN, Reddy DN, Banerjee S. A kinetic method for detecting intramolecular peptide H-bonds. NEW J CHEM 2021. [DOI: 10.1039/d1nj03544d] [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
The current method for the detection of peptide hydrogen bond (PHB) formation places charge donors/acceptors (D/A) at the N-/C-termini of the peptides involved in the putative PHB.
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Affiliation(s)
- Erode N. Prabhakaran
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Damodara N. Reddy
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Shreya Banerjee
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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5
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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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6
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Čakić Semenčić M, Kodrin I, Barišić L, Nuskol M, Meden A. Synthesis and Conformational Study of Monosubstituted Aminoferrocene‐Based Peptides Bearing Homo‐ and Heterochiral Pro‐Ala Sequences. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mojca Čakić Semenčić
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Ivan Kodrin
- Department of ChemistryFaculty of ScienceUniversity of ZagrebHorvatovac 102A10000ZagrebCroatia
| | - Lidija Barišić
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Marko Nuskol
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Anton Meden
- Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaVecna pot 1131000LjubljanaSlovenia
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7
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Siebler C, Maryasin B, Kuemin M, Erdmann RS, Rigling C, Grünenfelder C, Ochsenfeld C, Wennemers H. Importance of dipole moments and ambient polarity for the conformation of Xaa-Pro moieties - a combined experimental and theoretical study. Chem Sci 2015; 6:6725-6730. [PMID: 30154996 PMCID: PMC6090429 DOI: 10.1039/c5sc02211h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/27/2015] [Indexed: 12/04/2022] Open
Abstract
NMR spectroscopic studies with a series of proline derivatives revealed that the polarity of the environment has a significant effect on the trans : cis isomer ratio of Xaa-Pro bonds. Computational studies showed that this effect is due to differences in the overall dipole moments of trans and cis conformers. Comparisons between the conformational properties of amide and ester derivatives revealed an intricate balance between polarity effects and n → π* interactions of adjacent carbonyl groups. The findings have important implications for protein folding and signaling as well as the performance of proline-based stereoselective catalysts.
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Affiliation(s)
- Christiane Siebler
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Boris Maryasin
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Michael Kuemin
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Roman S Erdmann
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Carla Rigling
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Claudio Grünenfelder
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
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8
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Reddy DN, Prabhakaran EN. Steric and electronic interactions controlling the cis/trans isomer equilibrium at X-pro tertiary amide motifs in solution. Biopolymers 2013; 101:66-77. [DOI: 10.1002/bip.22278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 04/27/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Damodara N. Reddy
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 Karnataka India
| | - Erode N. Prabhakaran
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 Karnataka India
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9
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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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10
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Reddy DN, George G, Prabhakaran EN. Crystal-Structure Analysis of cis-X-Pro-Containing Peptidomimetics: Understanding the Steric Interactions at cisX-Pro Amide Bonds. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Reddy DN, George G, Prabhakaran EN. Crystal-structure analysis of cis-X-Pro-containing peptidomimetics: understanding the steric interactions at cis X-Pro amide bonds. Angew Chem Int Ed Engl 2013; 52:3935-9. [PMID: 23450815 DOI: 10.1002/anie.201209517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/18/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Damodara N Reddy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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12
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Krow GR, Shoulders MD, Edupuganti R, Gandla D, Yu F, Sonnet PE, Sender M, Choudhary A, DeBrosse C, Ross CW, Carroll P, Raines RT. Synthesis of 5-fluoro- and 5-hydroxymethanoprolines via lithiation of N-BOC-methanopyrrolidines. Constrained Cγ-exo and Cγ-endo Flp and Hyp conformer mimics. J Org Chem 2012; 77:5331-44. [PMID: 22607128 PMCID: PMC3381989 DOI: 10.1021/jo300700a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proline derivatives with a C(γ)-exo pucker typically display a high amide bond trans/cis (K(T/C)) ratio. This pucker enhances n→π* overlap of the amide oxygen and ester carbonyl carbon, which favors a trans amide bond. If there were no difference in n→π* interaction between the ring puckers, then the correlation between ring pucker and K(T/C) might be broken. To explore this possibility, proline conformations were constrained using a methylene bridge. We synthesized discrete gauche and anti 5-fluoro- and 5-hydroxy-N-acetylmethanoproline methyl esters from 3-syn and 3-anti fluoro- and hydroxymethanopyrrolidines using directed α-metalation to introduce the α-ester group. NBO calculations reveal minimal n→π* orbital interactions, so contributions from other forces might be of greater importance in determining K(T/C) for the methanoprolines. Consistent with this hypothesis, greater trans amide preferences were found in CDCl(3) for anti isomers en-MetFlp and en-MetHyp (72-78% trans) than for the syn stereoisomers ex-MetFlp and ex-MetHyp (54-67% trans). These, and other, K(T/C) results that we report here indicate how substituents on proline analogues can affect amide preferences by pathways other than ring puckering and n→π* overlap and suggest that caution should be exercised in assigning enhanced pyrrolidine C(γ)-exo ring puckering based solely on enhanced trans amide preference.
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Affiliation(s)
- Grant R Krow
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA.
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13
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Lee KK, Park KH, Joo C, Kwon HJ, Jeon J, Jung HI, Park S, Han H, Cho M. Infrared Probing of 4-Azidoproline Conformations Modulated by Azido Configurations. J Phys Chem B 2012; 116:5097-110. [DOI: 10.1021/jp1085119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Kyung-Koo Lee
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Kwang-Hee Park
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Cheonik Joo
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Jonggu Jeon
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Hyeon-Il Jung
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Sungnam Park
- Department of Chemistry, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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14
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Lee KK, Park KH, Joo C, Kwon HJ, Han H, Ha JH, Park S, Cho M. Ultrafast internal rotational dynamics of the azido group in (4S)-azidoproline: Chemical exchange 2DIR spectroscopic investigations. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.04.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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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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16
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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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17
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Shoulders MD, Kotch FW, Choudhary A, Guzei IA, Raines RT. The aberrance of the 4S diastereomer of 4-hydroxyproline. J Am Chem Soc 2010; 132:10857-65. [PMID: 20681719 PMCID: PMC2931826 DOI: 10.1021/ja103082y] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl 4-hydroxylases install a hydroxyl group in the 4R configuration on the gamma-carbon atom of certain (2S)-proline (Pro) residues in tropocollagen, elastin, and other proteins to form (2S,4R)-4-hydroxyproline (Hyp). The gauche effect arising from this prevalent post-translational modification enforces a C(gamma)-exo ring pucker and stabilizes the collagen triple helix. The Hyp diastereomer (2S,4S)-4-hydroxyproline (hyp) has not been observed in a protein, despite the ability of electronegative 4S substituents to enforce the more common C(gamma)-endo ring pucker of Pro. Here, we use density functional theory, spectroscopy, crystallography, and calorimetry to explore the consequences of hyp incorporation on protein stability using a collagen model system. We find that the 4S-hydroxylation of Pro to form hyp does indeed enforce a C(gamma)-endo ring pucker but a transannular hydrogen bond between the hydroxyl moiety and the carbonyl of hyp distorts the main-chain torsion angles that typically accompany a C(gamma)-endo ring pucker. This same transannular hydrogen bond enhances an n-->pi* interaction that stabilizes the trans conformation of the peptide bond preceding hyp, endowing hyp with the unusual combination of a C(gamma)-endo ring pucker and high trans/cis ratio. O-Methylation of hyp to form (2S,4S)-4-methoxyproline (mop) eliminates the transannular hydrogen bond and restores a prototypical C(gamma)-endo pucker. mop residues endow the collagen triple helix with much more conformational stability than do hyp residues. These findings highlight the critical importance of the configuration of the hydroxyl group installed on C(gamma) of proline residues.
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Affiliation(s)
- Matthew D. Shoulders
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Frank W. Kotch
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Amit Choudhary
- Graduate Program in Biophysics. University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
- Department of Biochemistry. University of Wisconsin–Madison, Madison, Wisconsin 53706
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18
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Jakobsche CE, Choudhary A, Miller SJ, Raines RT. n --> pi* Interaction and n)(pi Pauli repulsion are antagonistic for protein stability. J Am Chem Soc 2010; 132:6651-3. [PMID: 20420451 PMCID: PMC2874455 DOI: 10.1021/ja100931y] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many common protein secondary structures, such as alpha-, 3(10), and polyproline II helices, an n --> pi* interaction places the adjacent backbone amide carbonyl groups in close proximity to each other. This interaction, which is reminiscent of the Burgi-Dunitz trajectory, involves delocalization of the lone pairs (n) of the oxygen (O(i-1)) of a peptide bond over the antibonding orbital (pi*) of C(i)=O(i) of the subsequent peptide bond. Such a proximal arrangement of the amide carbonyl groups should be opposed by the Pauli repulsion between the lone pairs (n) of O(i-1) and the bonding orbital (pi) of C(i)=O(i). We explored the conformational effects of this Pauli repulsion by employing common peptidomimetics, wherein the n --> pi* interaction is attenuated while the Pauli repulsion is retained. Our results indicate that this Pauli repulsion prevents the attainment of such proximal arrangement of the carbonyl groups in the absence of the n --> pi* interaction. This finding indicates that the poor mimicry of the amide bond by many peptidomimetics stems from their inability to partake in the n --> pi* interaction and emphasizes the quantum-mechanical nature of the interaction between adjacent amide carbonyl groups in proteins.
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Affiliation(s)
| | - Amit Choudhary
- Graduate Program in Biophysics, University of Wisconsin, Madison, Wisconsin 53706
| | - Scott J. Miller
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
| | - Ronald T. Raines
- Departments of Biochemistry and Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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19
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Quantum mechanical origin of the conformational preferences of 4-thiaproline and its S-oxides. Amino Acids 2010; 41:181-6. [PMID: 20221839 DOI: 10.1007/s00726-010-0504-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 01/25/2010] [Indexed: 10/19/2022]
Abstract
The saturated ring and secondary amine of proline spawn equilibria between pyrrolidine ring puckers as well as peptide bond isomers. These conformational equilibria can be modulated by alterations to the chemical architecture of proline. For example, C(γ) in the pyrrolidine ring can be replaced with sulfur, which can be oxidized either stereoselectively to yield diastereomeric S-oxides or completely to yield a sulfone. Here, the thiazolidine ring and peptide bond conformations of 4-thiaproline and its S-oxides were analyzed in an Ac-Xaa-OMe system using NMR spectroscopy, X-ray crystallography, and hybrid density functional theory. The results indicate that the ring pucker of the S-oxides is governed by the gauche effect, and the prolyl peptide bond conformation is determined by the strength of the n → π* interaction between the amide oxygen and the ester carbonyl group. These findings, which are consistent with those of isologous 4-hydroxyprolines and 4-fluoroprolines, substantiate the importance of electron delocalization in amino acid conformation.
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Góbi S, Knapp K, Vass E, Majer Z, Magyarfalvi G, Hollósi M, Tarczay G. Is β-homo-proline a pseudo-γ-turn forming element of β-peptides? An IR and VCD spectroscopic study on Ac-β-HPro-NHMe in cryogenic matrices and solutions. Phys Chem Chem Phys 2010; 12:13603-15. [DOI: 10.1039/c0cp00145g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Vass E, Majer Z, Kőhalmy K, Hollósi M. Vibrational and chiroptical spectroscopic characterization of γ-turn model cyclic tetrapeptides containing two β-Ala residues. Chirality 2010; 22:762-71. [DOI: 10.1002/chir.20831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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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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Kuemin M, Schweizer S, Ochsenfeld C, Wennemers H. Effects of Terminal Functional Groups on the Stability of the Polyproline II Structure: A Combined Experimental and Theoretical Study. J Am Chem Soc 2009; 131:15474-82. [DOI: 10.1021/ja906466q] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Michael Kuemin
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
| | - Sabine Schweizer
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
| | - Helma Wennemers
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
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Zhang K, Teklebrhan RB, Schreckenbach G, Wetmore S, Schweizer F. Intramolecular hydrogen bond-controlled prolyl amide isomerization in glucosyl 3'(S)-hydroxy-5'-hydroxymethylproline hybrids: influence of a C-5'-hydroxymethyl substituent on the thermodynamics and kinetics of prolyl amide cis/trans isomerization. J Org Chem 2009; 74:3735-43. [PMID: 19354261 DOI: 10.1021/jo9003458] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide mimics containing spirocyclic glucosyl-(3'-hydroxy-5'-hydroxymethyl)proline hybrids (Glc3'(S)-5'(CH(2)OH)HypHs) with a polar hydroxymethyl substituent at the C-5' position, such as C-terminal ester Ac-Glc3'(S)-5'(CH(2)OH)Hyp-OMe and C-terminal amide Ac-Glc3'(S)-5'(CH(2)OH)Hyp-N'-CH(3), were synthesized. C-Terminal esters exhibit increased cis population (23-53%) relative to Ac-3(S)HyPro-OMe (17%) or Ac-Pro-OMe (14%) in D(2)O. The prolyl amide cis population is further increased to 38-74% in the C-terminal amide form in D(2)O. Our study shows that the stereochemistry of the hydroxymethyl substituent at the C-5' position of proline permits tuning of the prolyl amide cis/trans isomer ratio. Inversion-magnetization transfer NMR experiments indicate that the stereochemistry of the hydroxymethyl substituent has a dramatic effect on the kinetics of prolyl amide cis/trans isomerization. A 200-fold difference in the trans-to-cis (k(tc)) isomerization and a 90-fold rate difference in the cis-to-trans (k(ct)) isomerization is observed between epimeric C-5' 3 and 4. When compared to reference peptide mimics Ac-Pro-OMe and Ac-3(S)Hyp-OMe, our study demonstrates that a (13-16)-fold decrease in k(tc) and k(ct) is observed for the C-5'(S), while a (5-24)-fold acceleration is observed for the C-5'(R) epimer. DFT calculations indicate that the pyrrolidine ring prefers a C(beta) exo pucker in both Ac-Glc3'(S)-5'(CH(2)OH)Hyp-OMe diastereoisomers. Computational calculations and chemical shift temperature coefficient (Delta delta/Delta T) experiments indicate that the hydroxymethyl group at C-5' in Ac-Glc3'(S)-5'(CH(2)OH)Hyp-OMe forms a stabilizing intramolecular hydrogen bond to the carbonyl of the N-acetyl group in both epimeric cis isomers. However, a competing intramolecular hydrogen bond between the hydroxymethyl groups in the pyrrolidine ring and pyran ring stabilizes the trans isomer in the C-5'(S) diastereoisomer. The dramatic differences in the kinetic properties of the diastereoisomeric peptide mimics are rationalized by the presence or absence of an intramolecular hydrogen bond between the hydroxymethyl substituent located at C-5' and the developing lone pair on the nitrogen atom of the N-acetyl group in the transition state.
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Affiliation(s)
- Kaidong Zhang
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Choudhary A, Gandla D, Krow GR, Raines RT. Nature of amide carbonyl--carbonyl interactions in proteins. J Am Chem Soc 2009; 131:7244-6. [PMID: 19469574 PMCID: PMC2811422 DOI: 10.1021/ja901188y] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions define and modulate biomolecular structure, function, and dynamics. In many protein secondary structures, an intimate interaction exists between adjacent carbonyl groups of the main-chain amide bonds. As this short contact contributes to the energetics of protein conformational stability as well as protein-ligand interactions, understanding its nature is crucial. The intimacy of the carbonyl groups could arise from a charge-charge or dipole-dipole interaction, or n-->pi * electronic delocalization. This last putative origin, which is reminiscent of the Burgi-Dunitz trajectory, involves delocalization of the lone pairs (n) of the oxygen (O(i-1)) of a peptide bond over the antibonding orbital (pi*) of the carbonyl group (C(i)=O(i)) of the subsequent peptide bond. By installing isosteric chemical substituents in a peptidic model system and using NMR spectroscopy, X-ray diffraction analysis, and ab initio calculations to analyze the consequences, the intimate interaction between adjacent carbonyl groups is shown to arise primarily from n-->pi* electronic delocalization. This finding has implications for organic, biological, and medicinal chemistry.
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Flores-Ortega A, Casanovas J, Assfeld X, Alemán C. Protonation of the Side Group in β- and γ-Aminated Proline Analogues: Effects on the Conformational Preferences. J Org Chem 2009; 74:3101-8. [DOI: 10.1021/jo900169s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Jordi Casanovas
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Xavier Assfeld
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
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27
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LISOWSKI MAREK, PIETRZYŃSKI GRZEGORZ, RZESZOTARSKA BARBARA. Conformational investigation of α,β-dehydropeptides. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1993.tb00156.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Flores-Ortega A, Casanovas J, Nussinov R, Alemán C. Conformational preferences of beta- and gamma-aminated proline analogues. J Phys Chem B 2008; 112:14045-55. [PMID: 18842022 PMCID: PMC2836598 DOI: 10.1021/jp807638p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical calculations have been used to investigate how the incorporation of an amino group to the Cbeta- or Cgamma-positions of the pyrrolidine ring affects the intrinsic conformational properties of the proline. Specifically, a conformational study of the N-acetyl-N'-methylamide derivatives of four isomers of aminoproline, which differ not only in the beta- or gamma-position of the substituent but also in its cis or trans relative disposition, has been performed. To further understand the role of the intramolecular hydrogen bonds between the backbone carbonyl groups and the amino side group, a conformational study was also performed on the corresponding four analogues of (dimethylamino)proline. In addition, the effects of solvation on aminoproline and (dimethylamino)proline dipeptides have been evaluated using a self-consistent reaction field model, and considering four different solvents (carbon tetrachloride, chloroform, methanol and water). Results indicate that the incorporation of the amino substituent into the pyrrolidine ring affects the conformational properties, with backbone...side chain intramolecular hydrogen bonds detected when it is incorporated in a cis relative disposition. In general, the incorporation of the amino side group tends to stabilize those structures where the peptide bond involving the pyrrolidine nitrogen is arranged in cis. The aminoproline isomer with the substituent attached to the Cgamma-position with a cis relative disposition is the most stable in the gas phase and in chloroform, methanol and water solutions. Replacement of the amino side group by the dimethylamino substituent produces significant changes in the potential energy surfaces of the four investigated (dimethylamino)proline-containing dipeptides. Thus, these changes affect not only the number of minima, which increases considerably, but also the backbone and pseudorotational preferences. In spite of these effects, comparison of the conformational preferences, i.e., the more favored conformers, calculated for different isomers of aminoproline and (dimethylamino)proline dipeptides showed a high degree of consistency for the two families of compounds.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
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29
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Perczel A, Csizmadia IG. Searching for the simplest structural units to describe the three-dimensional structure of proteins. INT REV PHYS CHEM 2008. [DOI: 10.1080/01442359509353307] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Flores-Ortega A, Jiménez AI, Cativiela C, Nussinov R, Alemán C, Casanovas J. Conformational preferences of alpha-substituted proline analogues. J Org Chem 2008; 73:3418-27. [PMID: 18351745 PMCID: PMC2679371 DOI: 10.1021/jo702710x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the alpha hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N'-methylamide derivatives of L-proline, L-alpha-methylproline, and L-alpha-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated by using a Self-Consistent Reaction Field model. As expected, tetrasubstitution at the alpha carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at C (alpha) may play a significant role in modulating the conformational preferences of proline.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
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31
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A matrix isolation study on Ac–l-Pro–NH2: a frequent structural element of β- and γ-turns of peptides and proteins. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.12.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Baeza JL, Gerona-Navarro G, Pérez de Vega J, García-López MT, González-Muñiz R, Martín-Martínez M. Azetidine-Derived Amino Acids versus Proline Derivatives. Alternative Trends in Reverse Turn Induction. J Org Chem 2008; 73:1704-15. [DOI: 10.1021/jo701746w] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José Luis Baeza
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Jesús Pérez de Vega
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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33
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Sul S, Karaiskaj D, Jiang Y, Ge NH. Conformations of N-acetyl-L-prolinamide by two-dimensional infrared spectroscopy. J Phys Chem B 2007; 110:19891-905. [PMID: 17020375 DOI: 10.1021/jp062039h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Femtosecond two-dimensional infrared (2D IR) spectroscopy has been applied to study the conformations of a model dipeptide, N-acetyl-L-prolinamide (AcProNH2) in deuterated chloroform (CDCl3). Spectral features in the amide-I and -II regions are obtained by rephasing (R), nonrephasing (NR), and reverse photon echo (RPE) pulse sequences with two polarization conditions. The 2D spectra obtained by the RPE and NR sequences with (0, 0, 0, 0) polarization reveal new spectral features associated with the multiple conformers of AcProNH2 that are difficult to discern using R sequence and linear-IR spectroscopy. The high resolving power of the RPE sequence comes from destructive interference between the positive and negative peaks of nearby vibrators, similar to the NR sequence. The RPE response functions that are useful for 2D spectral simulations are evaluated, including the effects of vibrational frequency correlations. The 2D spectra obtained with (45, -45, 90, 0) polarization exhibit clear cross-peak patterns in the off-diagonal region for the R and RPE sequences but in the diagonal region for the NR sequence. These patterns, free from strong diagonal contributions, are crucial for structure determination. DFT calculations, normal-mode analysis, Hessian matrix reconstruction, and vibrational exciton Hamiltonian diagonalization yield molecular parameters needed for quantitative simulations of 2D spectra: angles between transition dipoles, coupling constants, and off-diagonal anharmonicities of the amide-I and -II modes are obtained for solvated trans-C7 and cis structures and for gas-phase trans conformers in the region of phi = -120 degrees to 0 degrees and psi = -100 degrees to 180 degrees in the Ramachandran space. Systematic simulations based on a 4:1 population ratio of the solvated trans-C7 and cis structures reproduce well the 2D spectral features obtained at both polarization conditions. However, better agreement between the experimental and simulated cross-peak patterns can be reached if the dihedral angles of the major trans conformer are close to (phi, psi) = (-80 degrees , 100 degrees ). Our results suggest that the major conformer of AcProNH2 in CDCl3 deviates from the gas-phase global minimum, the trans-C7 form, to an extended intermediate between the C7 and polyproline-II structure. These results are discussed in relationship with earlier findings obtained by NMR, transient IR studies, and MD simulations.
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Affiliation(s)
- Soohwan Sul
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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Pohl G, Perczel A, Vass E, Magyarfalvi G, Tarczay G. A matrix isolation study on Ac-Gly–NHMe and Ac-l-Ala–NHMe, the simplest chiral and achiral building blocks of peptides and proteins. Phys Chem Chem Phys 2007; 9:4698-708. [PMID: 17700871 DOI: 10.1039/b705098d] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The infrared absorption (IR) spectra of acetyl-N-methyl-glycine and acetyl-N-methyl-alanine have been recorded in dichloromethane and dimethyl sulfoxide-d(6) solution, as well as in Ar and Kr matrices. The spectra were assigned with the help of quantum chemical calculations. Based on the assignments of the matrix-isolation IR spectra, in line with theoretical predictions, two different hydrogen bonded conformers were identified, furthermore a third conformer is likely to be present, which cannot be unambiguously identified. In dichloromethane two conformers could be observed, while in dimethyl sulfoxide a single conformer could be identified. Vibrational circular dichroism (VCD) spectra of acetyl-N-methyl-l-alanine have also been recorded in solutions and matrices. These matrix-isolation VCD spectra not only support the assignments of the matrix-isolation IR spectra, but also demonstrate that these spectra can be interpreted much easier with the help of quantum chemical calculations than the VCD spectra recorded in solutions. It is also shown that the rotatory strength of some vibrational transitions changes rapidly as a function of the backbone torsional coordinates; hence the appearance of some regions in the VCD spectra is extremely dependent on any perturbations, e.g. weak intermolecular interactions.
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Affiliation(s)
- Gábor Pohl
- Structural Chemistry and Biology Laboratory, Institute of Chemistry, Eötvös University, Budapest, Hungary
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35
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Park J, Hochstrasser RM. Multidimensional infrared spectroscopy of a peptide intramolecular hydrogen bond. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.08.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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de Carvalho IM, de Sousa Moreira Í, Gehlen MH. Luminescence study of Ru(II) bipyridine–acridine spaced by amide and proline bridges. Polyhedron 2005. [DOI: 10.1016/j.poly.2004.09.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Taylor CM, Hardré R, Edwards PJB, Park JH. Factors affecting conformation in proline-containing peptides. Org Lett 2004; 5:4413-6. [PMID: 14602013 DOI: 10.1021/ol035711r] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] NMR was used to study the thermodynamics of the cis --> trans isomerization for prolyl amide bonds in the compounds shown. The magnitude of K(t/c) for C-terminal esters is greater than for the corresponding amides, signifying stronger backbone stereoelectronic effects in esters. Increasing the steric bulk of the N-terminal residue from Ac- to Ac-Gly- favors the trans conformation. Incorporation of a Phe residue N-terminal to Pro, however, shifts the equilibrium in favor of the cis conformation, via a stabilizing aromatic-proline interaction.
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Affiliation(s)
- Carol M Taylor
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
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38
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Jiménez AI, Ballano G, Cativiela C. First Observation of Two Consecutive γ Turns in a Crystalline Linear Dipeptide. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200461230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Jiménez AI, Ballano G, Cativiela C. First Observation of Two Consecutive γ Turns in a Crystalline Linear Dipeptide. Angew Chem Int Ed Engl 2004; 44:396-9. [PMID: 15538708 DOI: 10.1002/anie.200461230] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ana I Jiménez
- Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain.
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40
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Kang YK, Choi HY. Cis–trans isomerization and puckering of proline residue. Biophys Chem 2004; 111:135-42. [PMID: 15381311 DOI: 10.1016/j.bpc.2004.05.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2004] [Revised: 05/16/2004] [Accepted: 05/17/2004] [Indexed: 11/19/2022]
Abstract
We report here the results on N-acetyl-L-proline-N'-methylamide (Ac-Pro-NHMe) calculated at the HF/6-31+G(d) level with the conductor-like polarizable continuum model (CPCM) of self-consistent reaction field methods to investigate the changes of backbone and prolyl ring along the cis-trans isomerization of the prolyl peptide bond. From the potential energy surface, the barrier to ring flip from the down-puckered conformation to the up-puckered one is estimated to be 2.5 and 3.2 kcal/mol for trans and cis conformers of Ac-Pro-NHMe, respectively. In particular, the ring flip seems to be inaccessible in the intermediate regions between trans and cis conformations, because of higher barriers (approximately 13-19 kcal/mol) to rotation of the prolyl peptide bond. The torsion angles for backbone and prolyl ring vary largely around the transition states at omega' approximately 120 degrees and -70 degrees for the prolyl peptide bond. Three kinds of puckering amplitudes show the same trend of puckering along the cis-trans isomerization although their absolute values are different. In particular, trans and cis conformations have the almost same degree of puckering. The cis populations and barriers to rotation of the prolyl peptide bond for Ac-Pro-NHMe are increased with the increase of solvent polarity, which is mainly ascribed to the decreases of relative free energies for cis conformations and the increase of relative free energies for transition states.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea.
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Hanessian S, Papeo G, Fettis K, Therrien E, Viet MTP. Synthesis of 310-Helix-Inducing Constrained Analogues of l-Proline. J Org Chem 2004; 69:4891-9. [PMID: 15255713 DOI: 10.1021/jo0401422] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A bicyclic indolizidinone carboxylic acid and a tricyclic constrained analogue of l-proline were synthesized and evaluated for their ability to induce helix formation as l-Ala tetrapeptides. Variable-temperature NMR, DMSO titration, CD spectra, and X-ray structure analyses, in conjunction with molecular modeling, confirmed the existence of 3(10)-helical motifs with di- and tetrapeptides of l-Ala.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C. P. 6128, Succ. Centre-Ville, Montréal, Quebec, Canada H3C 3J7.
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42
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Dugave C, Demange L. Cis-trans isomerization of organic molecules and biomolecules: implications and applications. Chem Rev 2003; 103:2475-532. [PMID: 12848578 DOI: 10.1021/cr0104375] [Citation(s) in RCA: 753] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christophe Dugave
- CEA/Saclay, Département d'Ingénierie et d'Etudes des Protéines (DIEP), Bâtiment 152, 91191 Gif-sur-Yvette, France.
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Abstract
The well-known preference of the peptide bond for the trans conformation has been attributed to steric effects. Here, we show that a proline residue with an N-formyl group (H(i-1)-C'(i-1)=O(i-1)), in which H(i-1) presents less steric hindrance than does O(i-1), likewise prefers a trans conformation. Thus, the preference of the peptide bond for the trans conformation cannot be explained by steric effects alone. Rather, an n --> pi* interaction between the oxygen of the peptide bond (O(i-1)), and the subsequent carbonyl carbon in the polypeptide chain (C'(i)) also contributes to this preference. The O(i-1) and C'(i) distance and O(i-1).C'(i)=O(i) angle are especially favorable for such an n --> pi* interaction in a polyproline II helix. We propose that this electronic effect provides substantial stabilization to this and other elements of protein structure.
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Affiliation(s)
- Matthew P Hinderaker
- Department of Chemistry and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Vass E, Hollósi M, Besson F, Buchet R. Vibrational spectroscopic detection of beta- and gamma-turns in synthetic and natural peptides and proteins. Chem Rev 2003; 103:1917-54. [PMID: 12744696 DOI: 10.1021/cr000100n] [Citation(s) in RCA: 246] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elemér Vass
- Department of Organic Chemistry, Eötvös Loránd University, H-1518 Budapest 112, P.O. Box 32, Hungary
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46
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Comparative conformational study of N-acetyl-N′-methylprolineamide with different basis sets. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00077-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kang YK. cis – trans Isomerization of N -acetyl- N ′-methylamides of 5-methylproline and 5,5-dimethylproline. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00054-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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48
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Cavelier F, Vivet B, Martinez J, Aubry A, Didierjean C, Vicherat A, Marraud M. Influence of silaproline on peptide conformation and bioactivity. J Am Chem Soc 2002; 124:2917-23. [PMID: 11902882 DOI: 10.1021/ja017440q] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The analogue gamma-(dimethylsila)-proline, denoted silaproline (Sip), was synthesized in both enantiomerically pure forms by diastereoselective alkylation of a chiral glycine equivalent with use of Schöllkopf's bis-lactim ether method. The effect of replacing a proline residue in model peptides by this new proline surrogate has been examined in the crystal state by X-ray diffraction and in solution by IR absorption and NMR techniques. Silaproline and proline-containing sequences exhibit very similar conformational properties. Silaproline was also substituted for proline in a neurotensin (8-13) analogue that retained biological activity and exhibited enhanced resistance to biodegradation.
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Affiliation(s)
- Florine Cavelier
- Laboratoire des Amino acides, Peptides et Protéines, UMR-CNRS 5810, Universités de Montpellier I et II, UM II, CC19-34095 Montpellier Cedex 05, France
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E.T.S.E.I.B, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
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Zanni MT, Gnanakaran S, Stenger J, Hochstrasser RM. Heterodyned Two-Dimensional Infrared Spectroscopy of Solvent-Dependent Conformations of Acetylproline-NH2. J Phys Chem B 2001. [DOI: 10.1021/jp0100093] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin T. Zanni
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - S. Gnanakaran
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - Jens Stenger
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
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