1
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Ploetz EA, Karunaweera S, Bentenitis N, Chen F, Dai S, Gee MB, Jiao Y, Kang M, Kariyawasam NL, Naleem N, Weerasinghe S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20. J Chem Theory Comput 2021; 17:2964-2990. [PMID: 33878263 DOI: 10.1021/acs.jctc.1c00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nikolaos Bentenitis
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Feng Chen
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Shu Dai
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Moon B Gee
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Yuanfang Jiao
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Myungshim Kang
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nilusha L Kariyawasam
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | | | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
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2
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Maschio MC, Fregoni J, Molteni C, Corni S. Proline isomerization effects in the amyloidogenic protein β2-microglobulin. Phys Chem Chem Phys 2021; 23:356-367. [DOI: 10.1039/d0cp04780e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein β2-microglobulin can aggregate in insoluble amyloid fibrils. By relying on extensive sampling simulations, we study the Pro32 isomerization as a possible triggering factor leading to structural modifications in β2-m.
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Affiliation(s)
| | - Jacopo Fregoni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| | - Carla Molteni
- Department of Physics
- King's College London
- Strand
- London WC2R 2LS
- UK
| | - Stefano Corni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
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3
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Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
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4
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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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5
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Dabalos CL, Ohgo K, Kumashiro KK. Detection of Labile Conformations of Elastin’s Prolines by Solid-State Nuclear Magnetic Resonance and Fourier Transform Infrared Techniques. Biochemistry 2019; 58:3848-3860. [DOI: 10.1021/acs.biochem.9b00414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Chester L. Dabalos
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K. Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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6
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Park HS, Kang YK. Which DFT levels of theory are appropriate in predicting the prolyl cis–trans isomerization in solution? NEW J CHEM 2019. [DOI: 10.1039/c9nj02946j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DFTs were assessed for the conformational preferences of the peptides containing Pro and its derivatives in chloroform and water.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry
- Chungbuk National University
- Cheongju
- Republic of Korea
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7
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Sun X, Li M, Sun M, Li X, Xi BJ, Wu Y, Yao J, Zhan Z, Bai X, Xi N. Studies on structural requirements for atropisomerism in N -phenyl γ-lactams. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.04.090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Krüger K, Lüdke V, Pettinger J, Ashton L, Bonnet L, Motti CA, Lex J, Oelgemöller M. Photochemical synthesis of cyclic peptide models from phthalimido acetamides and phthaloyl dipeptide esters. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.02.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Chaume G, Simon J, Lensen N, Pytkowicz J, Brigaud T, Miclet E. Homochiral versus Heterochiral Trifluoromethylated Pseudoproline Containing Dipeptides: A Powerful Tool to Switch the Prolyl-Amide Bond Conformation. J Org Chem 2017; 82:13602-13608. [DOI: 10.1021/acs.joc.7b01944] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Grégory Chaume
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France
| | - Julien Simon
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Nathalie Lensen
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Julien Pytkowicz
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Thierry Brigaud
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Emeric Miclet
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France
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10
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Bröhl A, Albrecht B, Zhang Y, Maginn E, Giernoth R. Influence of Hofmeister Ions on the Structure of Proline-Based Peptide Models: A Combined Experimental and Molecular Modeling Study. J Phys Chem B 2017; 121:2062-2072. [PMID: 28191953 DOI: 10.1021/acs.jpcb.6b12465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are also able to stabilize the conformers over wide temperature ranges.
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Affiliation(s)
- Andreas Bröhl
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstrasse 4, 50939 Cologne, Germany
| | - Benjamin Albrecht
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstrasse 4, 50939 Cologne, Germany
| | - Yong Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Edward Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Ralf Giernoth
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstrasse 4, 50939 Cologne, Germany
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11
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Conformational studies of new pseudotripeptide with pyrazine amidoxime motif and simplified analogs using IR, NMR spectroscopy, and molecular dynamic simulations. Struct Chem 2016. [DOI: 10.1007/s11224-016-0870-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Ovdiichuk OV, Hordiyenko OV, Arrault A. Synthesis and conformational study of novel pyrazine-based pseudopeptides bearing amidoxime, amidoxime ester and 1,2,4-oxadiazole units. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.04.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Kubyshkin V, Durkin P, Budisa N. Energetic contribution to both acidity and conformational stability in peptide models. NEW J CHEM 2016. [DOI: 10.1039/c5nj03611a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The acidity difference of the amide rotamers has been revised for a large set ofN-acetyl amino acids.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
| | - Patrick Durkin
- 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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14
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Toniolo C, Crisma M, Moretto A, Peggion C, Formaggio F, Alemán C, Cativiela C, Ramakrishnan C, Balaram P. Peptide δ-Turn: Literature Survey and Recent Progress. Chemistry 2015; 21:13866-77. [PMID: 26243713 DOI: 10.1002/chem.201501467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Among the various types of α-peptide folding motifs, δ-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the δ-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.
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Affiliation(s)
- Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy).
| | - Marco Crisma
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Alessandro Moretto
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Fernando Formaggio
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Carlos Alemán
- Departament d'Enginyeria Quimica, ETSEIB, Universitat Politècnica de Catalunya, 08028 Barcelona (Spain)
| | - Carlos Cativiela
- Department of Organic Chemistry, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC - Universidad de Zaragoza, 50009 Zaragoza (Spain)
| | | | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, 0091 Bangalore (India)
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15
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Karunaratne C, Weldeghiorghis TK, West CM, Taylor CM. Conformational changes associated with post-translational modifications of Pro(143) in Skp1 of Dictyostelium--a dipeptide model system. J Am Chem Soc 2014; 136:15170-5. [PMID: 25250945 PMCID: PMC4227711 DOI: 10.1021/ja5033277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 01/16/2023]
Abstract
Prolyl hydroxylation and subsequent glycosylation of the E3(SCF) ubiquitin ligase subunit Skp1 affects its conformation and its interaction with F-box proteins and, ultimately, O2-sensing in the organism. Taking a reductionist approach to understand the molecular basis for these effects, a series of end-capped Thr-Pro dipeptides was synthesized, tracking the sequential post-translational modifications that occur in the protein. The conformation of the pyrrolidine ring in each compound was gauged via coupling constants ((3)JHα,Hβ) and the electronegativity of the Cγ-substituents by chemical shifts ((13)C). The equilibrium between the cis-trans conformations about the central prolyl peptide bond was investigated by integration of signals corresponding to the two species in the (1)H NMR spectra over a range of temperatures. These studies revealed an increasing preference for the trans-conformation in the order Pro < Hyp < [α-(1,4)GlcNAc]Hyp. Rates for the forward and reverse reactions, determined by magnetization transfer experiments, demonstrated a reduced rate for the trans-to-cis conversion and a significant increase in the cis-to-trans conversion upon hydroxylation of the proline residue in the dipeptide. NOE experiments suggest that the Thr side chain pushes the sugar away from the pyrrolidine ring. These effects, which depended on the presence of the N-terminal Thr residue, offer a mechanism to explain altered properties of the corresponding full-length proteins.
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Affiliation(s)
- Chamini
V. Karunaratne
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Thomas K. Weldeghiorghis
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Christopher M. West
- Department
of Biochemistry & Molecular Biology, Oklahoma Center for Medical
Glycobiology, University of Oklahoma Health
Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Carol M. Taylor
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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16
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Native peptide folding dominates over stereoelectronic effects of prolyl hydroxylation in loop 5 of the macrocyclic peptide kalata B1. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Pandey AK, Thomas KM, Forbes C, Zondlo NJ. Tunable control of polyproline helix (PPII) structure via aromatic electronic effects: an electronic switch of polyproline helix. Biochemistry 2014; 53:5307-14. [PMID: 25075447 PMCID: PMC4139158 DOI: 10.1021/bi500696k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Indexed: 01/10/2023]
Abstract
Aromatic rings exhibit defined interactions via the unique aromatic π face. Aromatic amino acids interact favorably with proline residues via both the hydrophobic effect and aromatic-proline interactions, C-H/π interactions between the aromatic π face and proline ring C-H bonds. The canonical aromatic amino acids Trp, Tyr, and Phe strongly disfavor a polyproline helix (PPII) when they are present in proline-rich sequences because of the large populations of cis amide bonds induced by favorable aromatic-proline interactions (aromatic-cis-proline and proline-cis-proline-aromatic interactions). We demonstrate the ability to tune polyproline helix conformation and cis-trans isomerism in proline-rich sequences using aromatic electronic effects. Electron-rich aromatic residues strongly disfavor polyproline helix and exhibit large populations of cis amide bonds, while electron-poor aromatic residues exhibit small populations of cis amide bonds and favor polyproline helix. 4-Aminophenylalanine is a pH-dependent electronic switch of polyproline helix, with cis amide bonds favored as the electron-donating amine, but trans amide bonds and polyproline helix preferred as the electron-withdrawing ammonium. Peptides with block proline-aromatic PPXPPXPPXPP sequences exhibited electronically switchable pH-dependent structures. Electron-poor aromatic amino acids provide special capabilities to integrate aromatic residues into polyproline helices and to serve as the basis of aromatic electronic switches to change structure.
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Affiliation(s)
- Anil K. Pandey
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Krista M. Thomas
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christina
R. Forbes
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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18
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Sonti R, Rao KNS, Chidanand S, Gowd KH, Raghothama S, Balaram P. Conformational Analysis of a 20-Membered Cyclic Peptide Disulfide fromConus virgowith a WPW Segment: Evidence for an Aromatic-Proline Sandwich. Chemistry 2014; 20:5075-86. [DOI: 10.1002/chem.201303687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Indexed: 11/06/2022]
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19
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Chang CW, Wu CC, Chang YY, Lin CC, Chien TC. Synthesis and Unexpected Oxidization of the Tricyclic Core of Ugibohlin, Isophakellin, and Styloguanidine. J Org Chem 2013; 78:10459-68. [DOI: 10.1021/jo401911a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Chia-Wei Chang
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Chi-Cheng Wu
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yung-Yu Chang
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Chia-Chi Lin
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Tun-Cheng Chien
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
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20
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Sonti R, Gowd KH, Rao KNS, Ragothama S, Rodriguez A, Perez JJ, Balaram P. Conformational Diversity in Contryphans fromConusVenom:cis-transIsomerisation and Aromatic/Proline Interactions in the 23-Membered Ring of a 7-Residue Peptide Disulfide Loop. Chemistry 2013; 19:15175-89. [DOI: 10.1002/chem.201301722] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Indexed: 11/05/2022]
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21
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Wernisch S, Trapp O, Lindner W. Application of cinchona-sulfonate-based chiral zwitterionic ion exchangers for the separation of proline-containing dipeptide rotamers and determination of on-column isomerization parameters from dynamic elution profiles. Anal Chim Acta 2013; 795:88-98. [DOI: 10.1016/j.aca.2013.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 01/28/2023]
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22
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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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23
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Abstract
Proline residues have unique roles in protein folding, structure, and function. Proline and the aromatic amino acids comprise the encoded cyclic protein residues. Aromatic protein side chains are defined by their negatively charged π faces, while the faces of the proline ring are partially positively charged. This polarity results from their two-point connection of the side chain to the electron-withdrawing protein backbone, and the lower electronegativity of hydrogen compared to carbon, nitrogen, and oxygen. The hydrogens adjacent to the carbonyl and amide nitrogen, Hα and Hδ, respectively, are the most partially positive. Proline's side chain is also conformationally restricted, allowing for interaction with aromatic residues with minimal entropic or steric penalty. Proline and aromatic residues can interact favorably with each other, due to both the hydrophobic effect and the interaction between the π aromatic face and the polarized C-H bonds, called a CH/π interaction. Aromatic-proline interactions can occur locally, for example, to stabilize cis-amide bonds, and over larger distances, in the tertiary structures of proteins, and intermolecularly in protein-protein interactions. In peptides and proteins, aromatic-proline sequences more readily adopt cis-prolyl amide bonds, where the aromatic ring interacts with the proline ring in the cis conformation. In aromatic-proline sequences, Trp and Tyr are more likely to induce cis-amide bonds than Phe, suggesting an aromatic electronic effect. This result would be expected for a CH/π interaction, in which a more electron-rich aromatic would have a stronger (more cis-stabilizing) interaction with partial positive charges on prolyl hydrogens. In this Account, we describe our investigations into the nature of local aromatic-proline interactions, using peptide models. We synthesized a series of 26 peptides, TXPN, varying X from electron-rich to electron poor aromatic amino acids, and found that the population of cis-amide bond (Ktrans/cis) is tunable by aromatic electronics. With 4-substituted phenylalanines, we observed a Hammett correlation between aromatic electronics and Ktrans/cis, with cis-trans isomerism electronically controllable by 1.0 kcal/mol. All aromatic residues exhibit a higher cis population than Ala or cyclohexylalanine, with Trp showing the strongest aromatic-proline interaction. In addition, proline stereoelectronic effects can modulate cis-trans isomerism by an additional 1.0 kcal/mol. The aromatic-proline interaction is enthalpic, consistent with its description as a CH/π interaction. Proline-aromatic sequences can also promote cis-prolyl bonds, either through interactions of the aromatic ring with the preceding cis-proline or with the Hα prior to cis-proline. Within proline-rich peptides, sequences commonly found in natively disordered proteins, aromatic residues promote multiple cis-amide bonds due to multiple favorable aromatic-proline interactions. Collectively, we found aromatic-proline interactions to be significantly CH/π in nature, tunable by aromatic electronics. We discuss these data in the context of aromatic-proline and aromatic-glycine interactions in local structure, in tertiary structure, in protein-protein interactions, and in protein assemblies.
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Affiliation(s)
- Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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Pandey AK, Naduthambi D, Thomas KM, Zondlo NJ. Proline editing: a general and practical approach to the synthesis of functionally and structurally diverse peptides. Analysis of steric versus stereoelectronic effects of 4-substituted prolines on conformation within peptides. J Am Chem Soc 2013; 135:4333-63. [PMID: 23402492 PMCID: PMC4209921 DOI: 10.1021/ja3109664] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.
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Affiliation(s)
- Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Devan Naduthambi
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Krista M. Thomas
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
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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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26
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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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Hsu SF, Ko CW, Wu YT. Cobalt-Catalyzed Carbon-Carbon Bond Formation: Synthesis and Applications of Enantiopure Pyrrolidine Derivatives[1]. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100220] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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van der Wel H, Johnson JM, Xu Y, Karunaratne CV, Wilson KD, Vohra Y, Boons GJ, Taylor CM, Bendiak B, West CM. Requirements for Skp1 processing by cytosolic prolyl 4(trans)-hydroxylase and α-N-acetylglucosaminyltransferase enzymes involved in O₂ signaling in dictyostelium. Biochemistry 2011; 50:1700-13. [PMID: 21247092 PMCID: PMC3192012 DOI: 10.1021/bi101977w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The social amoeba Dictyostelium expresses a hypoxia inducible factor-α (HIFα) type prolyl 4-hydroxylase (P4H1) and an α-N-acetylglucosaminyltransferase (Gnt1) that sequentially modify proline-143 of Skp1, a subunit of the SCF (Skp1/Cullin/F-box protein) class of E3 ubiquitin ligases. Prior genetic studies have implicated Skp1 and its modification by these enzymes in O(2) regulation of development, suggesting the existence of an ancient O(2)-sensing mechanism related to modification of the transcription factor HIFα by animal prolyl 4-hydroxylases (PHDs). To better understand the role of Skp1 in P4H1-dependent O(2) signaling, biochemical and biophysical studies were conducted to characterize the reaction product and the basis of Skp1 substrate selection by P4H1 and Gnt1. (1)H NMR demonstrated formation of 4(trans)-hydroxyproline as previously found for HIFα, and highly purified P4H1 was inhibited by Krebs cycle intermediates and other compounds that affect animal P4Hs. However, in contrast to hydroxylation of HIFα by PHDs, P4H1 depended on features of full-length Skp1, based on truncation, mutagenesis, and competitive inhibition studies. These features are conserved during animal evolution, as even mammalian Skp1, which lacks the target proline, became a good substrate upon its restoration. P4H1 recognition may depend on features conserved for SCF complex formation as heterodimerization with an F-box protein blocked Skp1 hydroxylation. The hydroxyproline-capping enzyme Gnt1 exhibited similar requirements for Skp1 as a substrate. These and other findings support a model in which the protist P4H1 conditionally hydroxylates Skp1 of E3(SCF)ubiquitin ligases to control half-lives of multiple targets, rather than the mechanism of animal PHDs where individual proteins are hydroxylated leading to ubiquitination by the evolutionarily related E3(VBC)ubiquitin ligases.
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Affiliation(s)
- Hanke van der Wel
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
| | - Jennifer M. Johnson
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
| | - Yuechi Xu
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
| | - Chamini V. Karunaratne
- Department of Chemistry, 742 Choppin Hall, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Kyle D. Wilson
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
| | - Yusuf Vohra
- Dept. of Chemistry and Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602 USA
| | - Geert-Jan Boons
- Dept. of Chemistry and Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602 USA
| | - Carol M. Taylor
- Department of Chemistry, 742 Choppin Hall, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Brad Bendiak
- Department of Cell and Developmental Biology and Structural Biology and Biophysics Program, University of Colorado Denver, Anschutz Medical Campus, Mail Stop 8108, RC-1 South Bldg., L18-12120, 12801 East 17th Avenue, Aurora, CO 80045 USA
| | - Christopher M. West
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
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Cipolla L, Airoldi C, Bini D, Gregori M, Marcelo F, Jiménez-Barbero J, Nicotra F. Fructose-Based Proline Analogues: Exploring the Prolyl trans/cis-Amide Rotamer Population in Model Peptides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000983] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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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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31
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Kang YK, Park HS. Conformational preferences and cis-trans isomerization of L-3,4-dehydroproline residue. Biopolymers 2009; 92:387-98. [PMID: 19373924 DOI: 10.1002/bip.21203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conformational study of N-acetyl-N'-methylamide of L-3,4-dehydroproline (Ac-Dhp-NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self-consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between C(beta) and C(gamma) into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis-trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the C(beta)-C(gamma) bonds become shorter by approximately 0.2 A and the bond angles C(alpha)-C(beta)-C(gamma) and C(beta)-C(gamma)-C(delta) are widened by approximately 8 degrees than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01-0.07 A, indicating that the 3,4-dehydroprolyl ring is quite less puckered. However, polyproline-like conformations become preferred and the relative stability of the conformation tC with a C(7) intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis-trans isomerization of the Ac-Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide N-H group seems to contribute in stabilizing the transition state structures.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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32
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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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Melis C, Bussi G, Lummis SCR, Molteni C. Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor. J Phys Chem B 2009; 113:12148-53. [PMID: 19663504 PMCID: PMC2733763 DOI: 10.1021/jp9046962] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Indexed: 12/17/2022]
Abstract
Trans-cis isomerization of a proline peptide bond is a potential mechanism to open the channel of the 5-HT(3) receptor. Here, we have used the metadynamics method to theoretically explore such a mechanism. We have determined the free energy surfaces in aqueous solution of a series of dipeptides of proline analogues and evaluated the free energy difference between the cis and trans isomers. These theoretical results were then compared with data from mutagenesis experiments, in which the response of the 5-HT(3) receptor was measured when the proline at the apex of the M2-M3 transmembrane domain loop was mutated. The strong correlation between the experimental and the theoretical data supports the existence of a trans-cis proline switch for opening the 5-HT(3) receptor ion channel.
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Affiliation(s)
| | | | | | - Carla Molteni
- Corresponding author. Phone: +44 20 78482170. Fax: +44 20 7848 2420. E-mail:
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34
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Cheng YQ, Bian Z, He YB, Han FS, Kang CQ, Ning ZL, Gao LX. Asymmetric Michael addition of aldehydes to nitroolefins catalyzed by l-prolinamide derivatives using phenols as co-catalysts. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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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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36
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Kang YK, Kang NS. Conformational preferences ofN-methoxycarbonyl proline dipeptide. J Comput Chem 2009; 30:1116-27. [DOI: 10.1002/jcc.21136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Yonezawa Y, Nakata K, Sakakura K, Takada T, Nakamura H. Intra- and Intermolecular Interaction Inducing Pyramidalization on Both Sides of a Proline Dipeptide during Isomerization: An Ab Initio QM/MM Molecular Dynamics Simulation Study in Explicit Water. J Am Chem Soc 2009; 131:4535-40. [DOI: 10.1021/ja807814x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasushige Yonezawa
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Kazuto Nakata
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Kota Sakakura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Toshikazu Takada
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
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38
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Zhang K, Schweizer F. Design and synthesis of glucose-templated proline–lysine chimera: polyfunctional amino acid chimera with high prolyl cis amide rotamer population. Carbohydr Res 2009; 344:576-85. [DOI: 10.1016/j.carres.2008.12.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 12/17/2008] [Accepted: 12/28/2008] [Indexed: 11/16/2022]
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39
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Anbanandam A, Albarado DC, Tirziu DC, Simons M, Veeraraghavan S. Molecular basis for proline- and arginine-rich peptide inhibition of proteasome. J Mol Biol 2008; 384:219-27. [PMID: 18823992 DOI: 10.1016/j.jmb.2008.09.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 09/05/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
Abstract
PR39, a naturally occurring and cell-permeable proline- and arginine-rich peptide, blocks the degradation of inhibitor of nuclear factor kappaB (IkappaBalpha), thereby attenuating inflammation. It is a noncompetitive and reversible inhibitor of 20S proteasome. To identify its basis of action, we used solution NMR spectroscopy and mutational analyses of the active fragment, PR11, which identified amino acids required for human 20S proteasome inhibiting activity. We then examined PR11-mediated changes in the expression of nuclear factor kappaB-dependent genes in situ. The results provide prerequisites for proteasome inhibition by proline- and arginine-rich peptides, providing a powerful new tool to investigate inflammatory processes. These findings offer new leads in developing drugs to treat heart diseases or stroke.
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Affiliation(s)
- Asokan Anbanandam
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Medical School, 6431 Fannin St., Houston, TX 77030, USA
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Chatterjee B, Saha I, Raghothama S, Aravinda S, Rai R, Shamala N, Balaram P. Designed peptides with homochiral and heterochiral diproline templates as conformational constraints. Chemistry 2008; 14:6192-204. [PMID: 18491347 DOI: 10.1002/chem.200702029] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).
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Affiliation(s)
- Bhaswati Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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41
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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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42
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Kang YK, Park HS. Conformational Preferences of Pseudoproline Residues. J Phys Chem B 2007; 111:12551-62. [DOI: 10.1021/jp074128f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
| | - Hae Sook Park
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
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Flores-Ortega A, Casanovas J, Zanuy D, Nussinov R, Alemán C. Conformations of proline analogues having double bonds in the ring. J Phys Chem B 2007; 111:5475-82. [PMID: 17458993 DOI: 10.1021/jp0712001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The intrinsic conformational preferences of proline analogues having double bonds between carbon atoms in their rings have been investigated using quantum mechanical calculations at the B3LYP/6-31+G(d,p) level. For this purpose, the potential energy surface of the N-acety-N'-methylamide derivatives of three dehydroprolines (proline analogues unsaturated at alpha,beta; beta,gamma; and gamma,delta) and pyrrole (proline analogue with unsaturations at both alpha,beta and gamma,delta) have been explored, and the results are compared with those obtained for the derivative of the nonmodified proline. We found that the double bonds affect the ring puckering and the geometric internal parameters, even though the backbone conformation was influenced the most. Results indicate that the formation of double bonds between carbon atoms in the pyrrolidine ring should be considered as an effective procedure to restrict the conformational flexibility of prolines. Interestingly, we also found that the N-acetyl-N'-methylamide derivative of pyrrole shows a high probability of having a cis peptide bond preceding the proline analogue.
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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, Diagonal 647, Barcelona E-08028, Spain
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Kang YK, Byun BJ. Conformational Preferences and cis−trans Isomerization of Azaproline Residue. J Phys Chem B 2007; 111:5377-85. [PMID: 17439267 DOI: 10.1021/jp067826t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational study of N-acetyl-N'-methylamide of azaproline (Ac-azPro-NHMe, the azPro dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the effects of the replacement of the backbone CHalpha group by the nitrogen atom on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). The incorporation of the Nalpha atom into the prolyl ring results in the different puckering, backbone population, and barriers to prolyl cis-trans isomerization from those of Ac-Pro-NHMe (the Pro dipeptide). In particular, the azPro dipeptide has a dominant backbone conformation D (beta2) with the cis peptide bond preceding the azPro residue in both the gas phase and solution. This may be ascribed to the favorable electrostatic interaction or intramolecular hydrogen bond between the prolyl nitrogen and the amide hydrogen following the azPro residue and to the absence of the unfavorable interactions between electron lone pairs of the acetyl carbonyl oxygen and the prolyl Nalpha. This calculated higher population of the cis peptide bond is consistent with the results from X-ray and NMR experiments. As the solvent polarity increases, the conformations B and B* with the trans peptide bond become more populated and the cis population decreases more, which is opposite to the results for the Pro dipeptide. The conformation B lies between conformations D and A (alpha) and conformation B* is a mirror image of the conformation B on the phi-psi map. The barriers to prolyl cis-trans isomerization for the azPro dipeptide increase with the increase of solvent polarity, and the cis-trans isomerization proceeds through only the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond for the azPro dipeptide in the gas phase and in solution, as seen for the Pro dipeptide. The pertinent distance d(N...H-NNHMe) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure and the lower rotational barriers for the azPro dipeptide than those for the Pro dipeptide in the gas phase and in solution.
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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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Jhon JS, Kang YK. Conformational Preferences of Proline Analogues with Different Ring Size. J Phys Chem B 2007; 111:3496-507. [PMID: 17388495 DOI: 10.1021/jp066835z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational study on L-azetidine-2-carboxylic acid (Ac-Aze-NHMe, the Aze dipeptide) and (S)-piperidine-2-carboxylic acid (Ac-Pip-NHMe, the Pip dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in conformational preferences and cis-trans isomerization for proline residue and its analogues with different ring size in the gas phase and in solution (chloroform and water). The change of ring size by deleting a CH2 group from or adding a CH2 group to the prolyl ring results the remarkable changes in backbone and ring structures compared with those of the Pro dipeptide, especially in the C'-N imide bond length and the bond angles around the N-C(alpha) bond. The four-membered azetidine ring can have either puckered structure depending on the backbone structure because of the less puckered structure. The six-membered piperidine ring can adopt chair and boat conformations, but the chair conformation is more preferred than the boat conformation. These calculated preferences for puckering are consistent with experimental results from analysis of X-ray structures of Aze- and Pip-containing peptides. On going from Pro to Aze to Pip, the axiality (i.e., a tendency to adopt the axial orientation) of the NHMe group becomes stronger, which can be ascribed to reduce the steric hindrances between 1,2-substituted Ac and NHMe groups. As the solvent polarity increases, the polyproline II-like conformation becomes more populated and the relative stability of conformation tC with a C7 hydrogen bond between C'=O of the amino group and N-H of the carboxyl group decreases for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. The cis population and rotational barriers for the imide bond increase with the increase of solvent polarity for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. In particular, the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about azetyl and piperidyl peptide bonds in the gas phase and in solution, as seen for alanyl and prolyl peptide bonds. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure, but the lower rotational barriers for the Aze and Pip dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized.
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Affiliation(s)
- Jong Suk Jhon
- Department of Chemistry and Basic Science Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea
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Dörr A, Lubell WD. Synthesis of a new π-deficient phenylalanine derivative from a common 1,4-diketone intermediate and study of the influence of aromatic density on prolyl amide isomer population. Biopolymers 2007; 88:290-9. [PMID: 17143857 DOI: 10.1002/bip.20643] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Enantiopure (2S)-N-(Boc)-3-(6-methylpyridazinyl)alanine (14) has been synthesized to serve as a phenylalanine analog lacking significant pi-donor capability. Two approaches were developed to furnish the target compound from L-aspartic acid as chiral educt in respectively six and nine steps and 13% and 12% yields. In both routes, a key homoallylic ketone intermediate was synthesized by a copper-catalyzed cascade addition of vinylmagnesium bromide to a carboxylic ester. Dipeptide models Ac-Xaa-Pro-NHMe (21a-c) were prepared and the relative populations of prolyl cis- and trans-amide isomers were measured in chloroform, dimethylsulfoxide, and water by proton NMR spectroscopy in order to assess the significance of the electron density of the neighboring aromatic residue on the prolyl amide geometry.
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Affiliation(s)
- Aurélie Dörr
- Département de Chimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC, Canada
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Tzakos AG, Naqvi N, Comporozos K, Pierattelli R, Theodorou V, Husain A, Gerothanassis IP. The molecular basis for the selection of captopril cis and trans conformations by angiotensin I converting enzyme. Bioorg Med Chem Lett 2006; 16:5084-7. [PMID: 16889963 DOI: 10.1016/j.bmcl.2006.07.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2006] [Revised: 07/11/2006] [Accepted: 07/12/2006] [Indexed: 11/20/2022]
Abstract
Enzyme-inhibitor recognition is considered one of the most fundamental aspects in the area of drug discovery. However, the molecular mechanism of this recognition process (induced fit or prebinding and adaptive selection among multiple conformers) in several cases remains unexplored. In order to shed light toward this step of the recognition process in the case of human angiotensin I converting enzyme (hACE) and its inhibitor captopril, we have established a novel combinatorial approach exploiting solution NMR, flexible docking calculations, mutagenesis, and enzymatic studies. We provide evidence that an equimolar ratio of the cis and trans states of captopril exists in solution and that the enzyme selects only the trans state of the inhibitor that presents architectural and stereoelectronic complementarity with its substrate binding groove.
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Affiliation(s)
- Andreas G Tzakos
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
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Abstract
The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and Basic Science Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea.
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Meng HY, Thomas KM, Lee AE, Zondlo NJ. Effects of i and i+3 residue identity on cis-trans isomerism of the aromatic(i+1)-prolyl(i+2) amide bond: implications for type VI beta-turn formation. Biopolymers 2006; 84:192-204. [PMID: 16208767 DOI: 10.1002/bip.20382] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cis-trans isomerization of amide bonds plays critical roles in protein molecular recognition, protein folding, protein misfolding, and disease. Aromatic-proline sequences are particularly prone to exhibit cis amide bonds. The roles of residues adjacent to a tyrosine-proline residue pair on cis-trans isomerism were examined. A short series of peptides XYPZ was synthesized and cis-trans isomerism was analyzed. Based on these initial studies, a series of peptides XYPN, X = all 20 canonical amino acids, was synthesized and analyzed by NMR for i residue effects on cis-trans isomerization. The following effects were observed: (a) aromatic residues immediately preceding Tyr-Pro disfavor cis amide bonds, with K(trans/cis)= 5.7-8.0, W > Y > F; (b) proline residues preceding Tyr-Pro lead to multiple species, exhibiting cis-trans isomerization of either or both X-Pro amide bonds; and (c) other residues exhibit similar values of K(trans/cis) (= 2.9-4.2), with Thr and protonated His exhibiting the highest fraction cis. beta-Branched and short polar residues were somewhat more favorable in stabilizing the cis conformation. Phosphorylation of serine at the i position modestly increases the stability of the cis conformer. In addition, the effect of the i+3 residue was examined in a limited series of peptides TYPZ. NMR data indicated that aromatic residues, Pro, Asn, Ala, and Val at the i+3 residue all favor cis amide bonds, with aromatic residues and Asn favoring more compact phi at Tyr(cis) and Ala and Pro favoring more extended phi at Tyr(cis). D-Alanine at the i+3 position particularly disfavors cis amide bonds.
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Affiliation(s)
- Hai Yun Meng
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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