1
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Waly SMA, Benniston AC, Harriman A. Deducing the conformational space for an octa-proline helix. Chem Sci 2024; 15:1657-1671. [PMID: 38303943 PMCID: PMC10829019 DOI: 10.1039/d3sc05287g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024] Open
Abstract
A molecular dyad, PY-P8-PER, comprising a proline octamer sandwiched between pyrene and perylene terminals has been synthesized in order to address the dynamics of electronic energy transfer (EET) along the oligo-proline chain. A simple pyrene-based control compound equipped with a bis-proline attachment serves as a reference for spectroscopic studies. The N-H NMR signal at the terminal pyrene allows distinction between cis and trans amides and, although the crystal structure for the control has the trans conformation, temperature-dependent NMR studies provide clear evidence for trans/cis isomerisation in D6-DMSO. Polar solvents tend to stabilise the trans structure for the pyrene amide group, even for longer oligo-proline units. Circular dichroism shows that the proline spacer for PY-P8-PER exists mainly in the all-trans geometry in methanol. Preferential excitation of the pyrene chromophore is possible at wavelengths in the 320-350 nm range and, for the dyad, is followed by efficacious EET to the perylene emitter. The probability for intramolecular EET, obtained from analysis of steady-state spectroscopic data, is ca. 80-90% in solvents of disparate polarity. Comparison with the Förster critical distance suggests the terminals are ca. 18 Å apart. Time-resolved fluorescence spectroscopy, in conjunction with DFT calculations, indicates the dyad exists as a handful of conformers displaying a narrow range of EET rates. Optimisation of a distributive model allows accurate simulation of the EET dynamics in terms of reasonable structures based on isomerisation of certain amide groups.
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Affiliation(s)
- Sara M A Waly
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Andrew C Benniston
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
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2
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Philippova AN, Vorobyeva DV, Gribanov PS, Dolgushin FM, Osipov SN. Diastereoselective Synthesis of Highly Functionalized Proline Derivatives. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206898. [PMID: 36296490 PMCID: PMC9609175 DOI: 10.3390/molecules27206898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/08/2022]
Abstract
An efficient way to access highly functionalized proline derivatives was developed based on a Cu(I)-catalyzed reaction between CF3-substituted allenynes and tosylazide, which involved a cascade of [3 + 2]-cycloaddition/ketenimine and a rearrangement/Alder-ene cyclization to afford the new proline framework with a high diastereoselectivity.
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Affiliation(s)
- Anna N. Philippova
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov str. 28/1, 119334 Moscow, Russia
| | - Daria V. Vorobyeva
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov str. 28/1, 119334 Moscow, Russia
| | - Pavel S. Gribanov
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov str. 28/1, 119334 Moscow, Russia
| | - Fedor M. Dolgushin
- N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119071 Moscow, Russia
- Plekhanov Russian University of Economics, 36 Stremyanny per., 117997 Moscow, Russia
| | - Sergey N. Osipov
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov str. 28/1, 119334 Moscow, Russia
- Correspondence: ; Tel.: +7-499-135-1873
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3
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Catalyst‐ and Base‐Free Asymmetric Synthesis of Functionalized Prolines via One‐Pot Cascade Reactions. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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4
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Tiwari VS, Singh G, Gurudayal, Ampapathi RS, Haq W. Pyrrolidine ring puckering and prolyl amide bond configurations of 2-methyl-allo-hydroxyproline-based dipeptides. Org Biomol Chem 2019; 17:4460-4464. [PMID: 30994683 DOI: 10.1039/c9ob00150f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An expeditious method for the synthesis of homo and heterochiral dipeptides containing l-alanine and d/l 2-methyl allo-hydroxyl prolines was developed using direct aminolysis of bicyclic lactones derived from d/l alanine. The impact of C-2 methylation and its spatial orientation on the pyrrolidine ring puckering and prolyl amide bond configuration was ascertained by solution NMR studies. The present studies reveal that C-2 methylation causes the prolyl amide bond to exist exclusively in the trans geometry in both homo- and heterochiral dipeptides. However, the spatial orientation of the C-2 methyl group and its i + 2 position in appropriately capped model dipeptides may nucleate into a turn like structure.
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Affiliation(s)
- Vinay Shankar Tiwari
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
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5
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Drouillat B, Peggion C, Biondi B, Wright K, Couty F, Crisma M, Formaggio F, Toniolo C. Heterochiral Ala/(
αMe)Aze
sequential oligopeptides:
S
ynthesis and conformational study. J Pept Sci 2019; 25:e3165. [DOI: 10.1002/psc.3165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Bruno Drouillat
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | | | - Barbara Biondi
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Karen Wright
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | - François Couty
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | - Marco Crisma
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Fernando Formaggio
- Department of ChemistryUniversity of Padova Padova 35131 Italy
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Claudio Toniolo
- Department of ChemistryUniversity of Padova Padova 35131 Italy
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
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6
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Cho H, Jeon H, Shin JE, Lee S, Park S, Kim S. Asymmetric Synthesis of Cα-Substituted Prolines through Curtin-Hammett-Controlled Diastereoselective N-Alkylation. Chemistry 2019; 25:2447-2451. [PMID: 30569571 DOI: 10.1002/chem.201804965] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Indexed: 11/09/2022]
Abstract
Asymmetric synthesis of α-substituted proline derivatives has been accomplished by an efficient chirality-transfer method. High diastereoselectivity of the N-alkylation of the proline ester (C→N chirality transfer) was achieved when a 2,3-disubstituted benzyl group was used as the N-substituent. DFT calculations provided a mechanistic rationale for the high degree of stereoselectivity. The generated N-chirality of the quaternary ammonium salt was transferred back to the α-carbon through a stereoselective [2,3]-Stevens rearrangement (N→C chirality transfer) to give α-substituted proline ester.
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Affiliation(s)
- Hyunkyung Cho
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Hongjun Jeon
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae Eui Shin
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Seokwoo Lee
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Soojun Park
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Sanghee Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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7
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Drouillat B, Peggion C, Biondi B, Wright K, Couty F, Crisma M, Formaggio F, Toniolo C. A novel peptide conformation: the γ-bend ribbon. Org Biomol Chem 2018; 16:7947-7958. [PMID: 30318540 DOI: 10.1039/c8ob02279h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unlike the extensively investigated relationship between the peptide β-bend ribbon and its prototypical 310-helix conformation, the corresponding relationship between the narrower γ-bend ribbon and its regular γ-helix counterpart still remains to be studied, as the latter 3D-structures have not yet been experimentally authenticated. In this paper, we describe the results of the first characterization, both in the crystal state and in solution, of the γ-bend ribbon conformation using X-ray diffraction and FT-IR absorption, electronic CD and 2D-NMR spectroscopies applied to an appropriate set of synthetic, homo-chiral, sequential dipeptide oligomers based on (S)-Ala and the known γ-bend inducer, Cα-tetrasubstituted, N-alkylated α-amino acid residue (S)-Cα-methyl-azetidine-carboxylic acid.
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Affiliation(s)
- Bruno Drouillat
- Institut Lavoisier de Versailles, UMR CNRS 8180, University of Versailles St-Quentin en Yvelines, 78035 Versailles, France.
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8
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Kubyshkin V, Pridma S, Budisa N. Comparative effects of trifluoromethyl- and methyl-group substitutions in proline. NEW J CHEM 2018. [DOI: 10.1039/c8nj02631a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
| | | | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
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9
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LeNouen D, Defoin A, Behr JB. Determination of the Relative Configuration and Conformational Analysis of Five-memberedN-Acyl-Iminosugars by Relevant3JCoupling Constants. ChemistrySelect 2016. [DOI: 10.1002/slct.201600287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Didier LeNouen
- Université de Haute-Alsace; Institut J. B. Donnet; 3 bis rue Alfred Werner F-68093 Mulhouse Cedex France
| | - Albert Defoin
- Université de Haute-Alsace; Institut J. B. Donnet; 3 bis rue Alfred Werner F-68093 Mulhouse Cedex France
| | - Jean-Bernard Behr
- Université de Reims-Champagne-Ardenne; ICMR-UMR 7312, BP 1039 F-51687 Reims Cedex 2 France
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10
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Gutiérrez A, Cativiela C, Laguna A, Gimeno MC. Bioactive gold(i) complexes with 4-mercaptoproline derivatives. Dalton Trans 2016; 45:13483-90. [DOI: 10.1039/c6dt02000c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Unprecedented gold(i) bioconjugates bearing non-proteinogenic amino acid 4-mercaptoproline species as bioorganic ligands have been prepared. The complexes displayed excellent cytotoxic activity with IC50 values in the low μM range and even in the nM range.
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Affiliation(s)
- Alejandro Gutiérrez
- Departamento de Química Inorgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC-Universidad de Zaragoza
- E-50009 Zaragoza
- Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC-Universidad de Zaragoza
- E-50009 Zaragoza
- Spain
| | - Antonio Laguna
- Departamento de Química Inorgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC-Universidad de Zaragoza
- E-50009 Zaragoza
- Spain
| | - M. Concepción Gimeno
- Departamento de Química Inorgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC-Universidad de Zaragoza
- E-50009 Zaragoza
- Spain
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11
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Duttagupta I, Misra D, Bhunya S, Paul A, Sinha S. Cis–Trans Conformational Analysis of δ-Azaproline in Peptides. J Org Chem 2015; 80:10585-604. [DOI: 10.1021/acs.joc.5b01668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Indranil Duttagupta
- Department of Organic
Chemistry and ‡Raman Centre for Atomic, Optical
and Molecular Physics, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Debojyoti Misra
- Department of Organic
Chemistry and ‡Raman Centre for Atomic, Optical
and Molecular Physics, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Sourav Bhunya
- Department of Organic
Chemistry and ‡Raman Centre for Atomic, Optical
and Molecular Physics, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Ankan Paul
- Department of Organic
Chemistry and ‡Raman Centre for Atomic, Optical
and Molecular Physics, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Surajit Sinha
- Department of Organic
Chemistry and ‡Raman Centre for Atomic, Optical
and Molecular Physics, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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12
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Kubyshkin V, Afonin S, Kara S, Budisa N, Mykhailiuk PK, Ulrich AS. γ-(S)-Trifluoromethyl proline: evaluation as a structural substitute of proline for solid state (19)F-NMR peptide studies. Org Biomol Chem 2015; 13:3171-3181. [PMID: 25703116 DOI: 10.1039/c5ob00034c] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
γ-(4S)-Trifluoromethyl proline was synthesised according to a modified literature protocol with improved yield on a multigram scale. Conformational properties of the amide bond formed by the amino acid were characterised using N-acetyl methyl ester model. The amide populations (s-trans vs. s-cis) and thermodynamic parameters of the isomerization were found to be similar to the corresponding values for intact proline. Therefore, the γ-trifluoromethyl proline was suggested as a structurally low-disturbing proline substitution in peptides for their structural studies by (19)F-NMR. Indeed, the exchange of native proline for γ-trifluoromethyl proline in the peptide antibiotic gramicidin S was shown to preserve the overall amphipathic peptide structure. The utility of the amino acid as a selective (19)F-NMR label was demonstrated by observing the re-alignment of the labelled gramicidin S in oriented lipid bilayers.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. and Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), KIT, POB 3640, 76021 Karlsruhe, Germany
| | - Sezgin Kara
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Pavel K Mykhailiuk
- Faculty of Chemistry, Taras Shevchenko National University of Kyiv, vul. Volodymyrska 62a, 01601 Kyiv, Ukraine. and Enamine Ltd., vyl. Chervonotkatska 78, 02660 Kyiv, Ukraine
| | - Anne S Ulrich
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. and Institute of Biological Interfaces (IBG-2), KIT, POB 3640, 76021 Karlsruhe, Germany
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13
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Torbeev V, Ebert MO, Dolenc J, Hilvert D. Substitution of proline32 by α-methylproline preorganizes β2-microglobulin for oligomerization but not for aggregation into amyloids. J Am Chem Soc 2015; 137:2524-35. [PMID: 25633201 DOI: 10.1021/ja510109p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Conversion of soluble folded proteins into insoluble amyloids generally proceeds in three distinct mechanistic stages: (1) initial protein misfolding into aggregation-competent conformers, (2) subsequent formation of oligomeric species and, finally, (3) self-assembly into extended amyloid fibrils. In the work reported herein, we interrogated the amyloidogenesis mechanism of human β2-microglobulin (β2m), which is thought to be triggered by a pivotal cis-trans isomerization of a proline residue at position 32 in the polypeptide, with nonstandard amino acids. Using chemical protein synthesis we prepared a β2m analogue in which Pro32 was replaced by the conformationally constrained amino acid α-methylproline (MePro). The strong propensity of MePro to adopt a trans prolyl bond led to enhanced population of a non-native [trans-MePro32]β2m protein conformer, which readily formed oligomers at neutral pH. In the presence of the antibiotic rifamycin SV, which inhibits amyloid growth of wild-type β2m, [MePro32]β2m was nearly quantitatively converted into different spherical oligomeric species. Self-assembly into amyloid fibrils was not observed in the absence of seeding, however, even at low pH (<3), where wild-type β2m spontaneously forms amyloids. Nevertheless, we found that aggregation-preorganized [MePro32]β2m can act in a prion-like fashion, templating misfolded conformations in a natively folded protein. Overall, these results provide detailed insight into the role of cis-trans isomerization of Pro32 and ensuing structural rearrangements that lead to initial β2m misfolding and aggregation. They corroborate the view that conformational protein dynamics enabled by reversible Pro32 cis-trans interconversion rather than simple population of the trans conformer is critical for both nucleation and subsequent growth of β2m amyloid structures.
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Affiliation(s)
- Vladimir Torbeev
- Laboratory of Organic Chemistry and ‡Laboratory of Physical Chemistry, ETH Zurich , Zurich CH-8093, Switzerland
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14
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Soto-Delgado J, Torras J, del Valle LJ, Estrany F, Alemán C. Examining the compatibility of collagen and a polythiophene derivative for the preparation of bioactive platforms. RSC Adv 2015. [DOI: 10.1039/c4ra13812k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Poly(3,4-ethylenedioxythiophene) and collagen interact specifically forming biocomposites that mimic the growing of biological tissues.
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Affiliation(s)
- Jorge Soto-Delgado
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andrés Bello
- Viña del Mar
- Chile
| | - Juan Torras
- Departament d'Enginyeria Química
- Escola d'Enginyeria d'Igualada
- Universitat Politècnica de Catalunya
- Igualada 08700
- Spain
| | - Luis J. del Valle
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- Barcelona E-08028
- Spain
| | - Francesc Estrany
- Departament d'Enginyeria Química
- Escola Universitària d'Enginyeria Tècnica Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08036 Barcelona
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- Barcelona E-08028
- Spain
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15
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Hayashi Y, Okamura D, Yamazaki T, Ameda Y, Gotoh H, Tsuzuki S, Uchimaru T, Seebach D. A Theoretical and Experimental Study of the Effects of Silyl Substituents in Enantioselective Reactions Catalyzed by Diphenylprolinol Silyl Ether. Chemistry 2014; 20:17077-88. [DOI: 10.1002/chem.201403514] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 11/09/2022]
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16
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Knapp K, Górecki M, Frelek J, Luboradzki R, Hollósi M, Majer Z, Vass E. Comprehensive Chiroptical Study of Proline-Containing Diamide Compounds. Chirality 2014; 26:228-42. [DOI: 10.1002/chir.22305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/13/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Krisztina Knapp
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Marcin Górecki
- Institute of Organic Chemistry; Polish Academy of Sciences; Warsaw Poland
| | - Jadwiga Frelek
- Institute of Organic Chemistry; Polish Academy of Sciences; Warsaw Poland
| | - Roman Luboradzki
- Institute of Physical Chemistry; Polish Academy of Sciences; Warsaw Poland
| | - Miklós Hollósi
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Zsuzsa Majer
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Elemér Vass
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
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17
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Torras J, Warren JG, Revilla-López G, Jiménez AI, Cativiela C, Alemán C. Solvent-induced conformational flexibility of a bicyclic proline analogue: Octahydroindole-2-carboxylic acid. Biopolymers 2014; 102:176-90. [PMID: 24458264 DOI: 10.1002/bip.22465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/07/2014] [Accepted: 01/16/2014] [Indexed: 11/08/2022]
Abstract
The conformational preferences of the N-acetyl-N'-methylamide derivatives of the four octahydroindole-2-carboxylic acid (Oic) stereoisomers have been investigated in the gas-phase and in aqueous solution using quantum mechanical calculations. In addition to the conformational effects provoked by the stereochemical diversity of Oic, which presents three chiral centers, results provide evidence of interesting and rather unusual features. The conformational preferences of the Oic stereoisomers in solution are only well described by applying a complete and systematic search process, results achieved by simple re-optimization of the gas-phase minima being very imprecise. This is because the conformational rigidity detected in the gas-phase, which is imposed by the chemical restrictions of the fused bicyclic skeleton, disappears in aqueous solution, the four stereoisomers behaving as flexible molecules in this environment. Thus, in general, the γ-turn is the only minimum energy conformation in the gas-phase while in aqueous solution the helical, polyproline-II and γ-turn motifs are energetically favored. Molecular dynamics simulations indicate that the conformational flexibility predicted by quantum mechanical calculations for the four Oic stereoisomers in solution is satisfactorily reproduced by classical force-fields.
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Affiliation(s)
- Juan Torras
- Departament d'Enginyeria Química, EEI, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada, 08700, Spain
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18
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19
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Kang YK, Park HS. Conformational preferences of the 2-methylproline residue and its role in stabilizing β-turn and polyproline II structures of peptides. NEW J CHEM 2014. [DOI: 10.1039/c4nj00072b] [Citation(s) in RCA: 8] [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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20
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Teklebrhan RB, Owens NW, Xidos JD, Schreckenbach G, Wetmore SD, Schweizer F. Conformational Preference of Fused Carbohydrate-Templated Proline Analogues—A Computational Study. J Phys Chem B 2012; 117:199-205. [DOI: 10.1021/jp310690c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robel B. Teklebrhan
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Neil W. Owens
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - James D. Xidos
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Stacey D. Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
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21
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Curcó D, Michaux C, Roussel G, Tinti E, Perpète EA, Alemán C. Stochastic simulation of structural properties of natively unfolded and denatured proteins. J Mol Model 2012; 18:4503-16. [DOI: 10.1007/s00894-012-1456-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 05/02/2012] [Indexed: 01/05/2023]
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22
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Revilla-López G, Warren JG, Torras J, Jiménez AI, Cativiela C, Alemán C. Effects of ring contraction on the conformational preferences of α-substituted proline analogs. Biopolymers 2011; 98:98-110. [DOI: 10.1002/bip.21716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 08/22/2011] [Accepted: 08/29/2011] [Indexed: 11/09/2022]
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23
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Vandormael B, De Wachter R, Martins JC, Hendrickx PMS, Keresztes A, Ballet S, Mallareddy JR, Tóth F, Tóth G, Tourwé D. Asymmetric Synthesis and Conformational Analysis by NMR Spectroscopy and MD of Aba- and α-MeAba-Containing Dermorphin Analogues. ChemMedChem 2011; 6:2035-47. [DOI: 10.1002/cmdc.201100314] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Indexed: 11/10/2022]
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24
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Parasuk W, Parasuk V. Proline- and thioproline-derived enamines: The theoretical study of torsional and ring-puckering conformations. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Qiu S, Li G, Wang P, Zhou J, Feng Z, Li C. pH-Dependent Chirality of l-Proline Studied by Raman Optical Activity and Density Functional Theory Calculation. J Phys Chem A 2011; 115:1340-9. [DOI: 10.1021/jp111631a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shi Qiu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanna Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaochi Feng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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26
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Warren JG, Revilla-López G, Alemán C, Jiménez AI, Cativiela C, Torras J. Conformational preferences of proline analogues with a fused benzene ring. J Phys Chem B 2011; 114:11761-70. [PMID: 20722365 DOI: 10.1021/jp105456r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of indoline-2-carboxylic acid (Inc) and its α-methylated derivative (αMeInc) have been investigated using quantum mechanical calculations. Specifically, the behavior of their N-acetyl-N'-methylamide derivatives, Ac-L-Inc-NHMe and Ac-L-αMeInc-NHMe, has been explored at the B3LYP/6-31+G(d,p) level. Such amino acids are analogues of proline and (α-methyl)proline, respectively, bearing a benzene ring fused to the C(γ)-C(δ) bond of the five-membered pyrrolidine ring. The additional aromatic group has been shown to significantly restrict the conformational space available to these residues by reducing the flexibility of both the five-membered cycle and the peptide backbone. The fused benzene ring also plays a critical role in determining the cis-trans arrangement of the amide bond involving the pyrrolidine nitrogen, which is also modulated by the presence of the α-methyl group in the αMeInc derivative. Furthermore, the influence of the environment on the conformational propensities of these compounds has been evaluated by using both a self-consistent reaction field model and a recently developed interface in a hybrid QM/MM scheme, in which the solvent molecules are treated explicitly with classical mechanics while the solute is described by quantum mechanics at the density functional theory level.
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Affiliation(s)
- Javier G Warren
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
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27
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Revilla-López G, Jiménez AI, Cativiela C, Nussinov R, Alemán C, Zanuy D. Conformational profile of a proline-arginine hybrid. J Chem Inf Model 2010; 50:1781-9. [PMID: 20886854 PMCID: PMC2997958 DOI: 10.1021/ci100135f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The intrinsic conformational preferences of a new nonproteinogenic amino acid have been explored by computational methods. This tailored molecule, named ((β)Pro)Arg, is conceived as a replacement for arginine in bioactive peptides when the stabilization of folded turn-like conformations is required. The new residue features a proline skeleton that bears the guanidilated side chain of arginine at the C(β) position of the five-membered pyrrolidine ring, in either a cis or a trans orientation with respect to the carboxylic acid. The conformational profiles of the N-acetyl-N'-methylamide derivatives of the cis and trans isomers of ((β)Pro)Arg have been examined in the gas phase and in solution by B3LYP/6-31+G(d,p) calculations and molecular dynamics simulations. The main conformational features of both isomers represent a balance between geometric restrictions imposed by the five-membered pyrrolidine ring and the ability of the guanidilated side chain to interact with the backbone through hydrogen bonds. Thus, both cis- and trans-((β)Pro)Arg exhibit a preference for the α(L) conformation as a consequence of the interactions established between the guanidinium moiety and the main-chain amide groups.
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Affiliation(s)
- Guillermo Revilla-López
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, 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 Science 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, Diagonal 647, Barcelona E-08028, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - David Zanuy
- 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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28
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Teklebrhan RB, Zhang K, Schreckenbach G, Schweizer F, Wetmore SD. Intramolecular Hydrogen Bond-Controlled Prolyl Amide Isomerization in Glucosyl 3(S)-Hydroxy-5-hydroxymethylproline Hybrids: A Computational Study. J Phys Chem B 2010; 114:11594-602. [DOI: 10.1021/jp1006186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robel B. Teklebrhan
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - Kaidong Zhang
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - G. Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
| | - Stacey D. Wetmore
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9 Canada, and Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4 Canada
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29
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Revilla-López G, Torras J, Curcó D, Casanovas J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Grodzinski P, Alemán C. NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. J Phys Chem B 2010; 114:7413-22. [PMID: 20455555 PMCID: PMC2896893 DOI: 10.1021/jp102092m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids--also called non-coded, non-canonical, or non-standard--is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, alpha-tetrasubstituted alpha-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - David Curcó
- Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/ Jaume II n°69, Lleida E-25001, Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 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 Science 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
| | - Piotr Grodzinski
- Alliance for Nanotechnology in Cancer, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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30
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Computational investigations of the stereoselectivities of proline-related catalysts for aldol reactions. ACTA ACUST UNITED AC 2010; 324:31-38. [PMID: 20634993 DOI: 10.1016/j.molcata.2010.03.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Computational investigation of the aldol reaction of benzaldehyde with acetone catalyzed by various proline derivatives and 2-azetidine carboxylic acid reveal the origins of stereoselectivities of these reactions. Structural differences between catalysts and transition states were analyzed with density functional theory geometries in order to establish the key factors that will help in the design of new catalysts.
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31
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Baeza JL, Gerona-Navarro G, Thompson K, Pérez de Vega MJ, Infantes L, García-López MT, González-Muñiz R, Martín-Martínez M. Further Evidence for 2-Alkyl-2-carboxyazetidines as γ-Turn Inducers. J Org Chem 2009; 74:8203-11. [DOI: 10.1021/jo901712x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- José Luis Baeza
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Kevin Thompson
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Lourdes Infantes
- Instituto de Química Física Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain
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32
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De Poli M, Moretto A, Crisma M, Peggion C, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Is the backbone conformation of C(alpha)-methyl proline restricted to a single region? Chemistry 2009; 15:8015-8025. [PMID: 19579242 DOI: 10.1002/chem.200900688] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
C(alpha)-methyl-L-proline, or L-(alphaMe)Pro, is probably the most conformationally constrained alpha-amino acid. In particular, its omega and phi torsion angles are restricted to about 180 and -60 degrees, respectively, and only three ranges of values are theoretically available for psi in mono- or longer peptides, namely, about -30 degrees (cis', 3(10)/alpha-helical structure), 60 degrees (inverse gamma turn), or 140 degrees (trans', poly(L-Pro)(n) II structure). In this work, we examined the tendency of a number of N(alpha)-acyl dipeptide N'-alkylamides of the type RCO-(alphaMe)Pro-Xxx-NHR' or RCO-Xxx-(alphaMe)Pro-NHR', in which Xxx is L (or D)-Ala, Aib (alpha-aminoisoburyric acid), or L (or D)-(alphaMe)Pro, long enough to fold into intramolecularly hydrogen-bonded gamma or beta turns. The results are compared with those obtained for the corresponding dipeptides based on Pro, a well-known turn-forming residue. For the crystal-state 3D-structural analysis we used X-ray diffraction, whereas our solution conformational analysis was heavily based on the FTIR absorption and (1)H and (13)C NMR spectroscopy techniques. We conclude that (alphaMe)Pro is able to explore both trans' and cis' psi areas of the conformational space, but in (alphaMe)Pro the latter is overwhelmingly more populated, in marked contrast to the Pro preference. This finding is a clear indication that in (alphaMe)Pro the major 3D-structural determinant is the C(alpha)-methyl group. The circular dichroism (CD) signature of a peptide type III' beta-turn conformation is also proposed.
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Affiliation(s)
- Matteo De Poli
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova via Marzolo 1, 35131 Padova, Italy
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33
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Ahmad S, Rao NM. Thermally denatured state determines refolding in lipase: mutational analysis. Protein Sci 2009; 18:1183-96. [PMID: 19472328 DOI: 10.1002/pro.126] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Irreversibility of thermally denatured proteins due to aggregation limits thermodynamic characterization of proteins and also confounds the identification of thermostable mutants in protein populations. Identification of mutations that prevent the aggregation of unfolded proteins provides insights into folding pathways. In a lipase from Bacillus subtilis, evolved by directed evolution procedures, the irreversibility due to temperature-mediated aggregation was completely prevented by a single mutation, M137P. Though the parent and the mutants unfold completely on heating, mutants having substitutions M137P, along with M134E and S163P, completely or partially prevent the formation of aggregation-prone intermediate(s) at 75 degrees C. The three mutants show only a marginal increase in free energy of unfolding (DeltaG(H(2)O)), however, the profiles of the residual activity with temperature shows remarkable shift to higher temperature compared to parent. The intermediate(s) were characterized by enhanced binding of bis-ANS, a probe to titrate surface hydrophobicity, aggregation profiles and by estimation of soluble protein. Inclusion of salt in the refolding conditions prevents the reversibility of mutant having charge substitution, while the reversibility of mutant with the introduction of proline was unaffected, indicating the role of charge mediated interaction in M134E in preventing aggregation. Partial prevention of thermal aggregation in wild-type lipase with single substitution, M137P, incorporated by site-directed mutagenesis, suggests that the affect of M137P is independent of the intrinsic thermostability of lipase. Various effects of the mutations suggest their role is in prevention of the formation of aggregation prone intermediate(s). These mutations, describe yet another strategy to enhance the thermotolerance of proteins, where their influence is observed only on the denatured ensemble.
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Affiliation(s)
- Shoeb Ahmad
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, India
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34
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Choi JH, May BC, Govaerts C, Cohen FE. Site-Directed Mutagenesis Demonstrates the Plasticity of the β Helix: Implications for the Structure of the Misfolded Prion Protein. Structure 2009; 17:1014-23. [DOI: 10.1016/j.str.2009.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 04/20/2009] [Accepted: 05/16/2009] [Indexed: 10/20/2022]
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35
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Zanuy D, Flores-Ortega A, Jiménez AI, Calaza MI, Cativiela C, Nussinov R, Ruoslahti E, Alemán C. In silico molecular engineering for a targeted replacement in a tumor-homing peptide. J Phys Chem B 2009; 113:7879-89. [PMID: 19432404 PMCID: PMC2734192 DOI: 10.1021/jp9006119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A new amino acid has been designed as a replacement for arginine (Arg, R) to protect the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) from proteases. This amino acid, denoted (Pro)hArg, is characterized by a proline skeleton bearing a specifically oriented guanidinium side chain. This residue combines the ability of Pro to induce turn-like conformations with the Arg side-chain functionality. The conformational profile of the CREKA analogue incorporating this Arg substitute has been investigated by a combination of simulated annealing and molecular dynamics. Comparison of the results with those previously obtained for the natural CREKA shows that (Pro)hArg significantly reduces the conformational flexibility of the peptide. Although some changes are observed in the backbone...backbone and side-chain...side-chain interactions, the modified peptide exhibits a strong tendency to accommodate turn conformations centered at the (Pro)hArg residue and the overall shape of the molecule in the lowest energy conformations characterized for the natural and the modified peptides exhibit a high degree of similarity. In particular, the turn orients the backbone such that the Arg, Glu, and Lys side chains face the same side of the molecule, which is considered important for bioactivity. These results suggest that replacement of Arg by (Pro)hArg in CREKA may be useful in providing resistance against proteolytic enzymes while retaining conformational features which are essential for tumor-homing activity.
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Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
| | - 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
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza - CSIC, 50009 Zaragoza, Spain
| | - M. Isabel Calaza
- 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
| | - Erkki Ruoslahti
- Vascular Mapping Center, The Burnham Institute for Medical Research at UCSB, Santa Barbara, California 93106, USA
- Cancer Research Center, The Burnham Institute for Medical Research, La Jolla, California 92037, USA
| | - Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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36
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Carreras J, Avenoza A, Busto JH, Peregrina JM. A highly regioselective ring-opening metathesis-cross metathesis process modulated by the electronic effects of the cross metathesis partner: an entry to quaternary prolines. J Org Chem 2009; 74:1736-9. [PMID: 19133729 DOI: 10.1021/jo802399k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A modulation of the regioselectivity in the ring-opening metathesis-cross metathesis (ROCM) process, originated by the electronic features of the acyclic olefin, is described. Electron-poor and electron-rich olefins showed opposing behavior giving different regioisomers. The reaction opens the way to the synthesis of interesting proline analogues incorporating a quaternary stereocenter.
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Affiliation(s)
- Javier Carreras
- Departamento de Química, Universidad de La Rioja, Grupo de Sííntesis Química de La Rioja, UA-CSIC, 26006 Logrono, Spain
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37
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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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De Wachter R, Brans L, Ballet S, Van den Eynde I, Feytens D, Keresztes A, Toth G, Urbanczyk-Lipkowska Z, Tourwé D. Influence of ring substitution on the conformation and β-turn mimicry of 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one peptide mimetics. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.01.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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Concise access to enantiopure (S)- and (R)-α-trifluoromethyl pyroglutamic acids from ethyl trifluoropyruvate-based chiral CF3-oxazolidines (Fox). J Fluor Chem 2008. [DOI: 10.1016/j.jfluchem.2008.07.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chandan N, Moloney MG. Rapid diastereocontrolled synthesis of 2,2,5-trisubstituted pyrrolidines. Org Biomol Chem 2008; 6:3664-6. [DOI: 10.1039/b811642c] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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