1
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Zhou X, Kato M, McKnight SL. How do disordered head domains assist in the assembly of intermediate filaments? Curr Opin Cell Biol 2023; 85:102262. [PMID: 37871501 PMCID: PMC11009871 DOI: 10.1016/j.ceb.2023.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/23/2023] [Accepted: 09/24/2023] [Indexed: 10/25/2023]
Abstract
The dominant structural feature of intermediate filament (IF) proteins is a centrally located α-helix. These long α-helical segments become paired in a parallel orientation to form coiled-coil dimers. Pairs of dimers further coalesce in an anti-parallel orientation to form tetramers. These early stages of intermediate filament assembly can be accomplished solely by the central α-helices. By contrast, the assembly of tetramers into mature intermediate filaments is reliant upon an N-terminal head domain. IF head domains measure roughly 100 amino acids in length and have long been understood to exist in a state of structural disorder. Here, we describe experiments favoring the unexpected idea that head domains self-associate to form transient structural order in the form of labile cross-β interactions. We propose that this weak form of protein structure allows for dynamic regulation of IF assembly and disassembly. We further offer that what we have learned from studies of IF head domains may represent a simple, unifying template for understanding how thousands of other intrinsically disordered proteins help to establish dynamic morphological order within eukaryotic cells.
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Affiliation(s)
- Xiaoming Zhou
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, Texas 75390-9152, USA
| | - Masato Kato
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, Texas 75390-9152, USA; Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Steven L McKnight
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, Texas 75390-9152, USA.
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2
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Zhou X, Sumrow L, Tashiro K, Sutherland L, Liu D, Qin T, Kato M, Liszczak G, McKnight SL. Mutations linked to neurological disease enhance self-association of low-complexity protein sequences. Science 2022; 377:eabn5582. [PMID: 35771920 PMCID: PMC9610444 DOI: 10.1126/science.abn5582] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein domains of low sequence complexity do not fold into stable, three-dimensional structures. Nevertheless, proteins with these sequences assist in many aspects of cell organization, including assembly of nuclear and cytoplasmic structures not surrounded by membranes. The dynamic nature of these cellular assemblies is caused by the ability of low-complexity domains (LCDs) to transiently self-associate through labile, cross-β structures. Mechanistic studies useful for the study of LCD self-association have evolved over the past decade in the form of simple assays of phase separation. Here, we have used such assays to demonstrate that the interactions responsible for LCD self-association can be dictated by labile protein structures poised close to equilibrium between the folded and unfolded states. Furthermore, missense mutations causing Charcot-Marie-Tooth disease, frontotemporal dementia, and Alzheimer's disease manifest their pathophysiology in vitro and in cultured cell systems by enhancing the stability of otherwise labile molecular structures formed upon LCD self-association.
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3
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de la Sierra-Gallay IL, Belnou M, Chambraud B, Genet M, van Tilbeurgh H, Aumont-Nicaise M, Desmadril M, Baulieu EE, Jacquot Y, Byrne C. Bioinspired Hybrid Fluorescent Ligands for the FK1 Domain of FKBP52. J Med Chem 2020; 63:10330-10338. [PMID: 32866001 DOI: 10.1021/acs.jmedchem.0c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The protein FKBP52 is a steroid hormone receptor coactivator likely involved in neurodegenerative disease. A series of small, water-soluble, bioinspired, pseudopeptidic fluorescent ligands for the FK1 domain of this protein are described. The design is such that engulfing of the ligand in the pocket of this domain is accompanied by hydrogen-bonding of the dansyl chromophore which functions as both an integral part of the ligand and a fluorescent reporter. Binding is concomitant with a significant wavelength shift and an enhancement of the ligand fluorescence signal. Excitation of FK1 domain native tryptophan residues in the presence of bound ligand results in Förster resonance energy transfer. Variation of key ligand residues within the short sequence was undertaken, and the interaction of the resulting library with the protein was measured by techniques including isothermal calorimetry analysis, fluorescence, and FRET quenching, and a range of Kd values were determined. Cocrystallization of a protein ligand complex at 2.30 Å resolution provided detailed information at the atomic scale, while also providing insight into native substrate binding.
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Affiliation(s)
- Inès Li de la Sierra-Gallay
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Mathilde Belnou
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | | | - Melanie Genet
- Institut Baulieu, INSERM UMR 1195, Neuroprotection et Neurorégénération, Université Paris-Saclay, 94270Le Kremlin Bicêtre, France
| | - Herman van Tilbeurgh
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Magali Aumont-Nicaise
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Michel Desmadril
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Etienne-Emile Baulieu
- Institut Baulieu, INSERM UMR 1195, Neuroprotection et Neurorégénération, Université Paris-Saclay, 94270Le Kremlin Bicêtre, France
| | - Yves Jacquot
- Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR 8038, INSERM U1268, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 75270 Paris Cedex 06, France
| | - Cillian Byrne
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France.,Institut Baulieu, INSERM UMR 1195, Neuroprotection et Neurorégénération, Université Paris-Saclay, 94270Le Kremlin Bicêtre, France
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4
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Fuster C, Varese M, García J, Giralt E, Sánchez‐Navarro M, Teixidó M. Expanding the MiniAp‐4 BBB‐shuttle family: Evaluation of proline
cis
‐
trans
ratio as tool to fine‐tune transport. J Pept Sci 2019; 25:e3172. [DOI: 10.1002/psc.3172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 01/12/2023]
Affiliation(s)
- Cristina Fuster
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Barcelona Spain
- Department of Inorganic and Organic ChemistryUniversity of Barcelona Barcelona Spain
| | - Macarena Sánchez‐Navarro
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Meritxell Teixidó
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Barcelona Spain
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5
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Chingle R, Mulumba M, Chung NN, Nguyen TMD, Ong H, Ballet S, Schiller PW, Lubell WD. Solid-Phase Azopeptide Diels–Alder Chemistry for Aza-pipecolyl Residue Synthesis To Study Peptide Conformation. J Org Chem 2019; 84:6006-6016. [DOI: 10.1021/acs.joc.8b03283] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Nga N. Chung
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montréal, Québec H2W 1R7, Canada
| | - Thi M.-D. Nguyen
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montréal, Québec H2W 1R7, Canada
| | | | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Peter W. Schiller
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montréal, Québec H2W 1R7, Canada
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6
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Byrne C, Belnou M, Baulieu E, Lequin O, Jacquot Y. Electronic circular dichroism and nuclear magnetic resonance studies of peptides derived from the FKBP52‐interacting β‐turn of the hERα ligand‐binding domain. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Cillian Byrne
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
- Institut Baulieu, Université Paris‐SaclayINSERM UMR 1195, Neuroprotection and Neuroregeneration Le Kremlin Bicêtre France
| | - Mathilde Belnou
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
| | - Etienne‐Emile Baulieu
- Institut Baulieu, Université Paris‐SaclayINSERM UMR 1195, Neuroprotection and Neuroregeneration Le Kremlin Bicêtre France
| | - Olivier Lequin
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
| | - Yves Jacquot
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
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7
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Verhoork SJM, Killoran PM, Coxon CR. Fluorinated Prolines as Conformational Tools and Reporters for Peptide and Protein Chemistry. Biochemistry 2018; 57:6132-6143. [DOI: 10.1021/acs.biochem.8b00787] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sanne J. M. Verhoork
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
| | - Patrick M. Killoran
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
| | - Christopher R. Coxon
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
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8
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Dai P, Williams JK, Zhang C, Welborn M, Shepherd JJ, Zhu T, Van Voorhis T, Hong M, Pentelute BL. A structural and mechanistic study of π-clamp-mediated cysteine perfluoroarylation. Sci Rep 2017; 7:7954. [PMID: 28801573 PMCID: PMC5554146 DOI: 10.1038/s41598-017-08402-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/07/2017] [Indexed: 01/27/2023] Open
Abstract
Natural enzymes use local environments to tune the reactivity of amino acid side chains. In searching for small peptides with similar properties, we discovered a four-residue π-clamp motif (Phe-Cys-Pro-Phe) for regio- and chemoselective arylation of cysteine in ribosomally produced proteins. Here we report mutational, computational, and structural findings directed toward elucidating the molecular factors that drive π-clamp-mediated arylation. We show the significance of a trans conformation prolyl amide bond for the π-clamp reactivity. The π-clamp cysteine arylation reaction enthalpy of activation (ΔH‡) is significantly lower than a non-π-clamp cysteine. Solid-state NMR chemical shifts indicate the prolyl amide bond in the π-clamp motif adopts a 1:1 ratio of the cis and trans conformation, while in the reaction product Pro3 was exclusively in trans. In two structural models of the perfluoroarylated product, distinct interactions at 4.7 Å between Phe1 side chain and perfluoroaryl electrophile moiety are observed. Further, solution 19F NMR and isothermal titration calorimetry measurements suggest interactions between hydrophobic side chains in a π-clamp mutant and the perfluoroaryl probe. These studies led us to design a π-clamp mutant with an 85-fold rate enhancement. These findings will guide us toward the discovery of small reactive peptides to facilitate abiotic chemistry in water.
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Affiliation(s)
- Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Jonathan K Williams
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Matthew Welborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - James J Shepherd
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Tianyu Zhu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States.
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9
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Byrne C, Henen MA, Belnou M, Cantrelle FX, Kamah A, Qi H, Giustiniani J, Chambraud B, Baulieu EE, Lippens G, Landrieu I, Jacquot Y. A β-Turn Motif in the Steroid Hormone Receptor’s Ligand-Binding Domains Interacts with the Peptidyl-prolyl Isomerase (PPIase) Catalytic Site of the Immunophilin FKBP52. Biochemistry 2016; 55:5366-76. [DOI: 10.1021/acs.biochem.6b00506] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Cillian Byrne
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure,
PSL Research University, CNRS UMR 7203, Laboratoire des Biomolécules, 4, place Jussieu, 75252 Paris Cedex 05, France
- Institut Baulieu, INSERM UMR 1195, Neuroprotection
and Neuroregeneration,
Université Paris-Saclay, Bât. Gregory Pincus, 80, rue du Général Leclerc, 94276 Le Kremlin Bicêtre Cedex, France
| | - Morkos A. Henen
- CNRS, UMR 8576,
Glycobiologie Structurale et Fonctionnelle, Université des
Sciences et Technologies de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Mathilde Belnou
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure,
PSL Research University, CNRS UMR 7203, Laboratoire des Biomolécules, 4, place Jussieu, 75252 Paris Cedex 05, France
| | - François-Xavier Cantrelle
- CNRS, UMR 8576,
Glycobiologie Structurale et Fonctionnelle, Université des
Sciences et Technologies de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Amina Kamah
- CNRS, UMR 8576,
Glycobiologie Structurale et Fonctionnelle, Université des
Sciences et Technologies de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Haoling Qi
- CNRS, UMR 8576,
Glycobiologie Structurale et Fonctionnelle, Université des
Sciences et Technologies de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Julien Giustiniani
- Institut Baulieu, INSERM UMR 1195, Neuroprotection
and Neuroregeneration,
Université Paris-Saclay, Bât. Gregory Pincus, 80, rue du Général Leclerc, 94276 Le Kremlin Bicêtre Cedex, France
| | - Béatrice Chambraud
- Institut Baulieu, INSERM UMR 1195, Neuroprotection
and Neuroregeneration,
Université Paris-Saclay, Bât. Gregory Pincus, 80, rue du Général Leclerc, 94276 Le Kremlin Bicêtre Cedex, France
| | - Etienne-Emile Baulieu
- Institut Baulieu, INSERM UMR 1195, Neuroprotection
and Neuroregeneration,
Université Paris-Saclay, Bât. Gregory Pincus, 80, rue du Général Leclerc, 94276 Le Kremlin Bicêtre Cedex, France
| | - Guy Lippens
- CNRS, UMR 8576,
Glycobiologie Structurale et Fonctionnelle, Université des
Sciences et Technologies de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
- LISBP,
Université
de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Isabelle Landrieu
- CNRS, UMR 8576,
Glycobiologie Structurale et Fonctionnelle, Université des
Sciences et Technologies de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Yves Jacquot
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure,
PSL Research University, CNRS UMR 7203, Laboratoire des Biomolécules, 4, place Jussieu, 75252 Paris Cedex 05, France
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10
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Ali R, Singh G, Singh S, Ampapathi RS, Haq W. Diastereoselective Synthesis of 5-Heteroaryl-Substituted Prolines Useful for Controlling Peptide-Bond Geometry. Org Lett 2016; 18:2848-51. [DOI: 10.1021/acs.orglett.6b00863] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Gajendra Singh
- Academy of Scientific and Innovative Research, New Delhi 11000, India
| | | | | | - Wahajul Haq
- Academy of Scientific and Innovative Research, New Delhi 11000, India
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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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Follis AV, Llambi F, Merritt P, Chipuk JE, Green DR, Kriwacki RW. Pin1-Induced Proline Isomerization in Cytosolic p53 Mediates BAX Activation and Apoptosis. Mol Cell 2015; 59:677-84. [PMID: 26236013 PMCID: PMC4546541 DOI: 10.1016/j.molcel.2015.06.029] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/15/2015] [Accepted: 06/22/2015] [Indexed: 12/31/2022]
Abstract
The cytosolic fraction of the tumor suppressor p53 activates the apoptotic effector protein BAX to trigger apoptosis. Here we report that p53 activates BAX through a mechanism different from that associated with activation by BH3 only proteins (BIM and BID). We observed that cis-trans isomerization of proline 47 (Pro47) within p53, an inherently rare molecular event, was required for BAX activation. The prolyl isomerase Pin1 enhanced p53-dependent BAX activation by catalyzing cis-trans interconversion of p53 Pro47. Our results reveal a signaling mechanism whereby proline cis-trans isomerization in one protein triggers conformational and functional changes in a downstream signaling partner. Activation of BAX through the concerted action of cytosolic p53 and Pin1 may integrate cell stress signals to induce a direct apoptotic response.
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Affiliation(s)
- Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabien Llambi
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Parker Merritt
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jerry E Chipuk
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Department of Dermatology, The Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, 920 Court Avenue, Memphis, TN 38163, USA.
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13
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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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14
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Bartuschat AL, Wicht K, Heinrich MR. Switching and Conformational Fixation of Amides Through Proximate Positive Charges. Angew Chem Int Ed Engl 2015; 54:10294-8. [DOI: 10.1002/anie.201502474] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 01/03/2023]
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15
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Bartuschat AL, Wicht K, Heinrich MR. Schaltung und Fixierung der Konformation von Amiden durch nahegelegene positive Ladungen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Rodríguez I, Calaza MI, Jiménez AI, Cativiela C. Synthesis of enantiomerically pure δ-benzylproline derivatives. NEW J CHEM 2015. [DOI: 10.1039/c4nj01894j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The methodology allows for the preparation of enantiopure δ-substituted l-proline analogues bearing the side chain of proteinogenic residues.
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Affiliation(s)
- Isabel Rodríguez
- Departamento de Química Orgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC–Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC–Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC–Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- CSIC–Universidad de Zaragoza
- 50009 Zaragoza
- Spain
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17
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Prabhu G, Narendra N, Basavaprabhu B, Panduranga V, Sureshbabu VV. Amino acid fluorides: viable tools for synthesis of peptides, peptidomimetics and enantiopure heterocycles. RSC Adv 2015. [DOI: 10.1039/c4ra16142d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review provides a broad perspective of the uses of amino acid fluorides in the synthesis of peptides and a wide range of other molecules including peptidomimetics, heterocycles and biologically active molecules.
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Affiliation(s)
- Girish Prabhu
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
| | - N. Narendra
- Department of Chemistry
- University College of Science
- Tumkur University
- Tumkur-572 103
- India
| | - Basavaprabhu Basavaprabhu
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
| | - V. Panduranga
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
| | - Vommina V. Sureshbabu
- Room No. 109, Peptide Research Laboratory
- Department of Studies in Chemistry
- Central College Campus
- Dr B. R. Ambedkar Veedhi
- Bangalore University
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18
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Rémond E, Martin C, Martinez J, Cavelier F. Silaproline, a Silicon-Containing Proline Surrogate. TOPICS IN HETEROCYCLIC CHEMISTRY 2015. [DOI: 10.1007/7081_2015_177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Arnold U. Stability and folding of amphibian ribonuclease A superfamily members in comparison with mammalian homologues. FEBS J 2014; 281:3559-75. [PMID: 24966023 DOI: 10.1111/febs.12891] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/18/2014] [Indexed: 01/05/2023]
Abstract
Comparative studies on homologous proteins can provide knowledge on how limited changes in the primary structure find their expression in large effects on catalytic activity, stability or the folding behavior. For more than half a century, members of the ribonuclease A superfamily have been the subject of a myriad of studies on protein folding and stability. Both the unfolding and refolding kinetics as well as the structure of several folding intermediates of ribonuclease A have been characterized in detail. Moreover, the RNA-degrading activity of these enzymes provides a basis for their cytotoxicity, which renders them potential tumor therapeutics. Because amphibian ribonuclease A homologues evade the human ribonuclease inhibitor, they emerged as particularly promising candidates. Interestingly, the amphibian ribonuclease A homologues investigated to date are more stable than the mammalian homologues. Nevertheless, despite the generation of numerous genetically engineered variants, knowledge of the folding of amphibian ribonuclease A homologues remains rather limited. An exception is onconase, a ribonuclease A homologue from Rana pipiens, which has been characterized in detail. This review summarizes the data on the unfolding and refolding kinetics and pathways, as well on the stability of amphibian ribonuclease A homologues compared with those of ribonuclease A, the best known member of this superfamily.
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Affiliation(s)
- Ulrich Arnold
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Germany
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20
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Efficient synthesis of trypsin inhibitor SFTI-1 via intramolecular ligation of peptide hydrazide. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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21
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Suresh Kumar NV, Singh H. Density functional theory based study on cis-trans isomerism of the amide bond in homodimers of β(2,3)- and β(3)-substituted homoproline. J Phys Chem A 2014; 118:2120-37. [PMID: 24559065 DOI: 10.1021/jp500187z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Preference for a cis/trans peptide bond between residues of dipeptides formed by substituted β(2,3) (I) and β(3) (II) homoproline is investigated using density functional theory (DFT). Potential energy surfaces for monomer and linear dimers are explored at the B3LYP/6-31G(d,p) level of theory. Minimum energy conformations of the dipeptides are optimized using B3LYP, PBE1PBE, B97D, and M06-2X functionals at the 6-31G(d,p) level of basis set in both the gas phase and solvent phase. The relative free energy difference between the selected conformations is marginal. Results obtained using the functionals M06-2X and B97D on dimers of I and II, respectively, agree with experimental results. The lowest energy conformations predicted by B97D/6-31G(d,p) and M06-2X/6-31G(d,p) levels of theory show greater relative MP2 correlation energy. Dipeptides of I with hydrophilic substituents show preference for a trans peptide bond. Support for cis/trans isomerism in dimers of I with hydrophobic substituents comes from potential energy surfaces and free energy data. Although dipeptides of II with hydrophilic substituents show preference for cis peptide bond, the dipeptides with hydrophobic substituent prefer trans bond.
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Affiliation(s)
- N V Suresh Kumar
- Department of Physics, K L University , Greenfields, Vaddeswaram, Guntur 522502, Andhra Pradesh, India
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22
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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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23
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Nash A, Soheili A, Tambar UK. Stereoselective Synthesis of Functionalized Cyclic Amino Acid Derivatives via a [2,3]-Stevens Rearrangement and Ring-Closing Metathesis. Org Lett 2013; 15:4770-3. [DOI: 10.1021/ol402129h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Aaron Nash
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Arash Soheili
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Uttam K. Tambar
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
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24
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Kondratov IS, Dolovanyuk VG, Tolmachova NA, Gerus II, Bergander K, Fröhlich R, Haufe G. Reactions of β-alkoxyvinyl polyfluoroalkyl ketones with ethyl isocyanoacetate and its use for the synthesis of new polyfluoroalkyl pyrroles and pyrrolidines. Org Biomol Chem 2013; 10:8778-85. [PMID: 22948733 DOI: 10.1039/c2ob26176f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hitherto unreported reactions of β-alkoxyvinyl polyfluoroalkyl ketones with ethyl isocyanoacetate and equimolar amounts of potassium-tert-butoxide proceeded mainly in the β-position of the α,β-unsaturated ketones in cases of α-nonsubstituted 1a–e and α-methyl substituted ketones 1g–j. Other α- or β-substituted ketones 1f,k–o gave mainly products 4 of initial attack at the carbonyl carbon. Depending on the solvent, the major products of β-attack do exist in different tautomeric forms. Generally the openchain enol tautomers 5 predominate in the polar DMSO-d(6), while the cyclic γ-hemiaminals 8 are the major tautomers in the less polar CDCl(3). Acid treatment of the latter compounds 8 led to the hitherto unknown ethyl 5-polyfluoroalkyl-pyrrole-2-carboxylates 11 by elimination of formic acid. Catalytic hydrogenation of pyrrole 11a was used for the synthesis of earlier unknown 5-trifluoromethyl proline 16.
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Affiliation(s)
- Ivan S Kondratov
- Institute of Bioorganic Chemistry and Petrochemistry, National Ukrainian Academy of Sciences, Murmanska 1, Kiev-94, 02660, Ukraine
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25
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Rodríguez I, Calaza MI, Cativiela C. Synthesis of Racemic δ,δ-Dimethylproline Derivatives. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201420] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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26
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Torbeev VY, Fumi E, Ebert MO, Schweizer WB, Hilvert D. cis-transPeptide-Bond Isomerization inα-Methylproline Derivatives. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200483] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Mohite AR, Bhat RG. Enantiopure Synthesis of Side Chain-Modified α-Amino Acids and 5-cis-Alkylprolines. J Org Chem 2012; 77:5423-8. [DOI: 10.1021/jo300653u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amar R. Mohite
- Department of Chemistry, Mendeleev Block, Indian Institute of Science Education and Research (IISER),
Pune, Maharashtra, 411008, India
| | - Ramakrishna G. Bhat
- Department of Chemistry, Mendeleev Block, Indian Institute of Science Education and Research (IISER),
Pune, Maharashtra, 411008, India
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28
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Nakamura K, Greenwood A, Binder L, Bigio EH, Denial S, Nicholson L, Zhou XZ, Lu KP. Proline isomer-specific antibodies reveal the early pathogenic tau conformation in Alzheimer's disease. Cell 2012; 149:232-44. [PMID: 22464332 PMCID: PMC3601591 DOI: 10.1016/j.cell.2012.02.016] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 08/29/2011] [Accepted: 02/08/2012] [Indexed: 11/22/2022]
Abstract
cis-trans isomerization of proteins phosphorylated by proline-directed kinases is proposed to control numerous signaling molecules and is implicated in the pathogenesis of Alzheimer's and other diseases. However, there is no direct evidence for the existence of cis-trans protein isomers in vivo or for their conformation-specific function or regulation. Here we develop peptide chemistries that allow the generation of cis- and trans-specific antibodies and use them to raise antibodies specific for isomers of phosphorylated tau. cis, but not trans, p-tau appears early in the brains of humans with mild cognitive impairment, accumulates exclusively in degenerated neurons, and localizes to dystrophic neurites during Alzheimer's progression. Unlike trans p-tau, the cis isomer cannot promote microtubule assembly, is more resistant to dephosphorylation and degradation, and is more prone to aggregation. Pin1 converts cis to trans p-tau to prevent Alzheimer's tau pathology. Isomer-specific antibodies and vaccines may therefore have value for the early diagnosis and treatment of Alzheimer's disease.
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Affiliation(s)
- Kazuhiro Nakamura
- Department of Medicine Beth Israel Deaconess Medical Center Harvard Medical School, Boston, MA 02215, USA
| | - Alex Greenwood
- Department of Molecular Biology and Genetics Cornell University, Ithaca, NY 14853, USA
| | - Lester Binder
- Department of Pathology Northwestern University Feinberg School of Medicine Chicago, IL 60611, USA
| | - Eileen H. Bigio
- Department of Cell and Molecular Biology Northwestern University Feinberg School of Medicine Chicago, IL 60611, USA
| | - Sarah Denial
- Department of Molecular Biology and Genetics Cornell University, Ithaca, NY 14853, USA
| | - Linda Nicholson
- Department of Molecular Biology and Genetics Cornell University, Ithaca, NY 14853, USA
| | - Xiao Zhen Zhou
- Department of Medicine Beth Israel Deaconess Medical Center Harvard Medical School, Boston, MA 02215, USA
| | - Kun Ping Lu
- Department of Medicine Beth Israel Deaconess Medical Center Harvard Medical School, Boston, MA 02215, USA
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29
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Katarzyńska J, Mazur A, Wolf WM, Teat SJ, Jankowski S, Leplawy MT, Zabrocki J. 4-Methylpseudoproline derived from α-methylserine – synthesis and conformational studies. Org Biomol Chem 2012; 10:6705-16. [DOI: 10.1039/c2ob25732g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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McGrath N, Raines RT. Chemoselectivity in chemical biology: acyl transfer reactions with sulfur and selenium. Acc Chem Res 2011; 44:752-61. [PMID: 21639109 PMCID: PMC3242736 DOI: 10.1021/ar200081s] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Indexed: 11/28/2022]
Abstract
A critical source of insight into biological function is derived from the chemist's ability to create new covalent bonds between molecules, whether they are endogenous or exogenous to a biological system. A daunting impediment to selective bond formation, however, is the myriad of reactive functionalities present in biological milieu. The high reactivity of the most abundant molecule in biology, water, makes the challenges all the more difficult. We have met these challenges by exploiting the reactivity of sulfur and selenium in acyl transfer reactions. The reactivity of both sulfur and selenium is high compared with that of their chalcogen congener, oxygen. In this Account, we highlight recent developments in this arena, emphasizing contributions from our laboratory. One focus of our research is furthering the chemistry of native chemical ligation (NCL) and expressed protein ligation (EPL), two related processes that enable the synthesis and semisynthesis of proteins. These techniques exploit the lower pK(a) of thiols and selenols relative to alcohols. Although a deprotonated hydroxyl group in the side chain of a serine residue is exceedingly rare in a biological context, the pK(a) values of the thiol in cysteine (8.5) and of the selenol in selenocysteine (5.7) often render these side chains anionic under physiological conditions. NCL and EPL take advantage of the high nucleophilicity of the thiolate as well as its utility as a leaving group, and we have expanded the scope of these methods to include selenocysteine. Although the genetic code limits the components of natural proteins to 20 or so α-amino acids, NCL and EPL enable the semisynthetic incorporation of a limitless variety of nonnatural modules into proteins. These modules are enabling chemical biologists to interrogate protein structure and function with unprecedented precision. We are also pursuing the further development of the traceless Staudinger ligation, through which a phosphinothioester and azide form an amide. We first reported this chemical ligation method, which leaves no residual atoms in the product, in 2000. Our progress in effecting the reaction in water, without an organic cosolvent, was an important step in the expansion of its utility. Moreover, we have developed the traceless Staudinger reaction as a means for immobilizing proteins on a solid support, providing a general method of fabricating microarrays that display proteins in a uniform orientation. Along with NCL and EPL, the traceless Staudinger ligation has made proteins more readily accessible targets for chemical synthesis and semisynthesis. The underlying acyl transfer reactions with sulfur and selenium provide an efficient means to synthesize, remodel, and immobilize proteins, and they have enabled us to interrogate biological systems.
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Affiliation(s)
- Nicholas
A. McGrath
- Departments of Chemistry and Biochemistry, University of Wisconsin, Madison, Wisconsin 53706,
United States
| | - Ronald T. Raines
- Departments of Chemistry and Biochemistry, University of Wisconsin, Madison, Wisconsin 53706,
United States
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31
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Konuma T, Kimura T, Matsumoto S, Goto Y, Fujisawa T, Fersht AR, Takahashi S. Time-Resolved Small-Angle X-ray Scattering Study of the Folding Dynamics of Barnase. J Mol Biol 2011; 405:1284-94. [DOI: 10.1016/j.jmb.2010.11.052] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 11/24/2010] [Accepted: 11/25/2010] [Indexed: 12/01/2022]
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32
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Hu Q, Nie A, Welsh K, Pinacho Crisóstomo FR, Zhu X, Li Z, An J, Reed JC, Zhang L, Huang Z. Novel X-linked inhibitor of apoptosis protein inhibitors as probes of apoptosis in biology and medicine. Exp Biol Med (Maywood) 2011; 236:247-51. [DOI: 10.1258/ebm.2010.010284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report here a series of new inhibitors of the X-linked inhibitor of apoptosis protein (XIAP protein) based on the SMAC-tetrapeptide AVPI. The structural novelty of these molecules is the presence of the proline mimetic exo-2-azabicyclo[2.2.1]heptane-3-carboxylic acid, leading to analogs with similar activity to the natural ligand peptide. The structure–activity relationship and computational docking studies support the convenience of this unnatural amino acid as a building block to develop new peptides or small molecules targeting the XIAP-BIR3 domain.
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Affiliation(s)
- Qi Hu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191
| | - Aihua Nie
- Department of Medicinal Chemistry, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Kate Welsh
- The Burnham Institute for Medical Research
| | | | - Xuejun Zhu
- The Burnham Institute for Medical Research
| | - Zhengxiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191
| | - Jing An
- The Burnham Institute for Medical Research
- Current address: Department of Pharmacology, SUNY Upstate Cancer Research Institute, State University of New York, Syracuse, NY 13210, USA
| | | | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191
| | - Ziwei Huang
- The Burnham Institute for Medical Research
- Department of Pathology, University of California at San Diego, La Jolla, CA 92037, USA
- Current address: Department of Pharmacology, SUNY Upstate Cancer Research Institute, State University of New York, Syracuse, NY 13210, USA
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Hosoya M, Otani Y, Kawahata M, Yamaguchi K, Ohwada T. Water-Stable Helical Structure of Tertiary Amides of Bicyclic β-Amino Acid Bearing 7-Azabicyclo[2.2.1]heptane. Full Control of Amide Cis−Trans Equilibrium by Bridgehead Substitution. J Am Chem Soc 2010; 132:14780-9. [DOI: 10.1021/ja1017877] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masahiro Hosoya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Yuko Otani
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Masatoshi Kawahata
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Kentaro Yamaguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, and Department of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
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34
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Synthesis of allose-templated hydroxyornithine and hydroxyarginine analogs. Carbohydr Res 2010; 345:1533-40. [DOI: 10.1016/j.carres.2010.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 04/05/2010] [Accepted: 04/19/2010] [Indexed: 11/19/2022]
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35
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36
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Zhang K, Schweizer F. Influence of glucose-templated proline mimetics on the β-turn conformation of the peptide fragment Ac-Leu-d-Phe-Pro-Val-NMe2 found in Gramicidin S. Carbohydr Res 2010; 345:1114-22. [DOI: 10.1016/j.carres.2010.03.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/23/2010] [Accepted: 03/28/2010] [Indexed: 10/19/2022]
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37
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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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38
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Paul A, Einsiedel J, Waibel R, Heinemann FW, Meyer K, Gmeiner P. Novel triazolopeptides: chirospecific synthesis and conformational studies of proline derived analogs. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.05.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Incorporation of non-natural modules into proteins: structural features beyond the genetic code. Biotechnol Lett 2009; 31:1129-39. [DOI: 10.1007/s10529-009-0002-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 04/02/2009] [Accepted: 04/06/2009] [Indexed: 11/25/2022]
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40
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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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41
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Alladoum J, Roland S, Vrancken E, Mangeney P, Kadouri-Puchot C. Short Enantioselective Syntheses of trans-5-Alkylprolines from New Functionalized Amino Alcohols. J Org Chem 2008; 73:9771-4. [DOI: 10.1021/jo8014243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeanne Alladoum
- Université Pierre et Marie Curie-Paris 6, Laboratoire de Chimie Organique UMR 7611, Institut de Chimie Moléculaire FR 2769, 4 place Jussieu, case courrier 47, 75005 Paris, France
| | - Sylvain Roland
- Université Pierre et Marie Curie-Paris 6, Laboratoire de Chimie Organique UMR 7611, Institut de Chimie Moléculaire FR 2769, 4 place Jussieu, case courrier 47, 75005 Paris, France
| | - Emmanuel Vrancken
- Université Pierre et Marie Curie-Paris 6, Laboratoire de Chimie Organique UMR 7611, Institut de Chimie Moléculaire FR 2769, 4 place Jussieu, case courrier 47, 75005 Paris, France
| | - Pierre Mangeney
- Université Pierre et Marie Curie-Paris 6, Laboratoire de Chimie Organique UMR 7611, Institut de Chimie Moléculaire FR 2769, 4 place Jussieu, case courrier 47, 75005 Paris, France
| | - Catherine Kadouri-Puchot
- Université Pierre et Marie Curie-Paris 6, Laboratoire de Chimie Organique UMR 7611, Institut de Chimie Moléculaire FR 2769, 4 place Jussieu, case courrier 47, 75005 Paris, France
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42
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Medina JR, Blackledge CW, Erhard KF, Axten JM, Miller WH. Benzyl 2-Cyano-3,3-Dimethyl-1-pyrrolidinecarboxylate, a Versatile Intermediate for the Synthesis of 3,3-Dimethylproline Derivatives. J Org Chem 2008; 73:3946-9. [DOI: 10.1021/jo7027163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesus R. Medina
- Oncology Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania 19426
| | - Charles W. Blackledge
- Oncology Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania 19426
| | - Karl F. Erhard
- Oncology Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania 19426
| | - Jeffrey M. Axten
- Oncology Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania 19426
| | - William H. Miller
- Oncology Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania 19426
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Cadamuro S, Reichold R, Kusebauch U, Musiol HJ, Renner C, Tavan P, Moroder L. Conformational Properties of 4-Mercaptoproline and Related Derivatives. Angew Chem Int Ed Engl 2008; 47:2143-6. [DOI: 10.1002/anie.200704310] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Cadamuro S, Reichold R, Kusebauch U, Musiol HJ, Renner C, Tavan P, Moroder L. Konformationseigenschaften des 4-Mercaptoprolins und verwandter Derivate. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704310] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Liang C, Collet F, Robert-Peillard F, Müller P, Dodd RH, Dauban P. Toward a synthetically useful stereoselective C-H amination of hydrocarbons. J Am Chem Soc 2007; 130:343-50. [PMID: 18072775 DOI: 10.1021/ja076519d] [Citation(s) in RCA: 301] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reaction between a sulfur(VI) compound and an iodine(III) oxidant in the presence of a catalytic quantity (<=3 mol %) of a rhodium(II) catalyst leads to the formation of a chiral metallanitrene of unprecedented reactivity. The latter allows intermolecular C-H amination to proceed in very high yields up to 92% and excellent diastereoselectivities up to 99% with C-H bond containing starting materials as the limiting component. The scope of this C-H functionalization includes benzylic and allylic substrates as well as alkanes. Secondary positions react preferentially, but insertion into activated primary C-H bonds or sterically accessible tertiary sites is also possible. Cooperative effects between the nitrene precursor and the chiral catalyst at the origin of these good results have also been applied to kinetic resolution of racemic sulfonimidamide. This methodology paves the way to the use of Csp3-H bonds as synthetic precursors for the introduction of a nitrogen functionality into selected positions.
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Affiliation(s)
- Chungen Liang
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
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Suaifan GA, Mahon MF, Arafat T, Threadgill MD. Effects of steric bulk and stereochemistry on the rates of diketopiperazine formation from N-aminoacyl-2,2-dimethylthiazolidine-4-carboxamides (Dmt dipeptide amides)—a model for a new prodrug linker system. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Peters MV, Goddard R, Hecht S. Synthesis and Characterization of Azobenzene-Confined Porphyrins. J Org Chem 2006; 71:7846-9. [PMID: 16995695 DOI: 10.1021/jo0612877] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A versatile synthetic method has been developed to incorporate photochromic azobenzene moieties into tetraphenylporphyrin frameworks in an orthogonal fashion, positioning the phenylazo substituents above and below the plane of the macrocycle. Surprisingly, photoisomerization is completely suppressed in the resulting azobenzene-confined porphyrins.
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Affiliation(s)
- Maike V Peters
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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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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Alonso De Diego SA, Gutiérrez-Rodríguez M, Pérez de Vega MJ, González-Muñiz R, Herranz R, Martín-Martínez M, Cenarruzabeitia E, Frechilla D, Del Río J, Jimeno ML, García-López MT. The neuroprotective activity of GPE tripeptide analogues does not correlate with glutamate receptor binding affinity. Bioorg Med Chem Lett 2006; 16:3396-400. [PMID: 16650992 DOI: 10.1016/j.bmcl.2006.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 04/05/2006] [Accepted: 04/05/2006] [Indexed: 11/21/2022]
Abstract
The influence of several modifications on the GPE tripeptide structure upon the binding to GluRs and on their neuroprotective effects has been studied. The results indicated that the prevention of neuronal death showed by GPE and some analogues is not directly related to their affinity at glutamate receptors.
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