1
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Hernández D, Porras M, Boto A. Conversion of Hydroxyproline "Doubly Customizable Units" to Hexahydropyrimidines: Access to Conformationally Constrained Peptides. J Org Chem 2023. [PMID: 37429014 PMCID: PMC10367070 DOI: 10.1021/acs.joc.3c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The efficient transformation of hydroxyproline "doubly customizable units" into rigid hexahydropyrimidine units takes place in good global yields and generates compounds of pharmaceutical interest. In particular, the process can readily provide access to peptidomimetics and peptides with reversed sequences or with valuable turns.
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Affiliation(s)
- Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Fco. Sánchez, 3, La Laguna, Tenerife 38206, Spain
| | - Marina Porras
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Fco. Sánchez, 3, La Laguna, Tenerife 38206, Spain
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Fco. Sánchez, 3, La Laguna, Tenerife 38206, Spain
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2
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Sun Q, He X, Fu Y. The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water. Molecules 2023; 28:5164. [PMID: 37446826 DOI: 10.3390/molecules28135164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular hydrogen bondings. During folding, hydrophobic interactions are regarded to be the driving forces, especially in the initial structural collapse of a protein. Additionally, folding is guided by the strong interactions within proteins, such as intramolecular hydrogen bondings related to the α-helices and β-sheets of proteins. Therefore, a protein is divided into the folding key (FK) regions related to intramolecular hydrogen bondings and the non-folding key (non-FK) regions. Various conformations are expected for FK and non-FK regions. Different from non-FK regions, it is necessary for FK regions to form the specific conformations in folding, which are regarded as the necessary folding pathways (or "beacons"). Additionally, sequential folding is expected for the FK regions, and the intermediate state is found during folding. They are reflected on the local basins in the free energy landscape (FEL) of folding. To demonstrate the structural model, molecular dynamics (MD) simulations are conducted on the folding pathway of the TRP-cage in water.
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Affiliation(s)
- Qiang Sun
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Xian He
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Yanfang Fu
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
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3
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Bollu A, Giri P, Dalabehera NR, Asmi AR, Sharma NK. Unnatural Amino Acid: 4-Aminopyrazolonyl Amino Acid Comprising Tri-Peptides Forms Organogel With Co-Solvent (EtOAc:Hexane). Front Chem 2022; 10:821971. [PMID: 35601543 PMCID: PMC9117720 DOI: 10.3389/fchem.2022.821971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/29/2022] [Indexed: 11/26/2022] Open
Abstract
Ampyrone is an amino-functionalized heterocyclic pyrazolone derivative that possesses therapeutic values such as analgesic, anti-inflammatory, and antipyretics. The chemical structure of ampyrone exhibits excellent hydrogen bonding sites and is considered as the potential scaffold of supramolecular self-assembly. Recently, this molecule has been derived into unnatural amino acids such as aminopyrazolone amino acid and its peptides. This report describes that one of its amino acids, O-alkylated ampyrone, containing hybrid (α/β) peptides forms organogel after sonication at 50–55°C with 0.7–0.9% (w/v) in ethyl acetate: hexane (1:3). The formation/morphology of such organogels is studied by nuclear magnetic resonance Fourier-transform infrared (FT-IR), circular dichroism (CD), scanning electron microscope (SEM), transmission electron microscopy (TEM), powder X-ray diffraction (Powder-XRD), and thermogravimetric analysis (TGA). Energy-minimized conformation of APA-peptides reveals the possibility of intermolecular hydrogen bonding. Hence, APA-peptides are promising peptidomimetics for the organogel-peptides.
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Affiliation(s)
- Amarnath Bollu
- National Institute of Science Education and Research (NISER), Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Prajnanandan Giri
- National Institute of Science Education and Research (NISER), Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Nihar Ranjan Dalabehera
- National Institute of Science Education and Research (NISER), Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Asmita Rani Asmi
- National Institute of Science Education and Research (NISER), Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Nagendra K Sharma
- National Institute of Science Education and Research (NISER), Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), Mumbai, India
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4
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5
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Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. Int J Mol Sci 2021; 22:9653. [PMID: 34502559 PMCID: PMC8431812 DOI: 10.3390/ijms22179653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/16/2022] Open
Abstract
Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.
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Affiliation(s)
- Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Hongchi Zhang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education), School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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6
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Debnath S, Ghosh S, Pandit G, Satpati P, Chatterjee S. Effect of Differential Geminal Substitution of γ Amino Acid Residues at the ( i + 2) Position of αγ Turn Segments on the Conformation of Template β-Hairpin Peptides. J Org Chem 2021; 86:11310-11323. [PMID: 34479402 DOI: 10.1021/acs.joc.1c00351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The effect of insertion of three geminally dimethyl substituted γ amino acid residues [γ2,2 (4-amino-2,2-dimethylbutanoic acid), γ3,3 (4-amino-3,3-dimethylbutanoic acid), and γ4,4 (4-amino-4,4-dimethylbutanoic acid)] at the (i + 2) position of a two-residue αγ C12 turn segment in a model octapeptide sequence Leu-Phe-Val-Aib-Xxx-Leu-Phe-Val (where Xxx = γ amino acid residues) has been investigated in this study. Solution conformational studies (NMR, CD, and IR) and ab initio calculations indicated that γ3,3 and γ4,4 residues were well accommodated in the β-hairpin nucleating αγ C12 turns, which gave rise to well-registered hairpins, in contrast to γ2,2, which was unable to form a tight C12 β-hairpin nucleating turn and promote a well-registered β-hairpin. Geminal disubstitution at the Cα carbon in γ2,2 led to unfavorable steric contacts, disabling its accommodation in the αγ C12 hairpin nucleating turn unlike the γ3,3 and γ4,4 residues. Geminal substitutions at different carbons along the backbone constrained backbone torsion angles for the three γ amino acid residues differently, generating diverse conformational preferences in them. Folded hairpins were energetically more stable (∼8 to 9 kcal/mol) than the unfolded peptides. Conformational preference of the peptides was independent of the N-terminal protecting group. Such fundamental understanding will instrumentalize the future directed design of foldamers.
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Affiliation(s)
- Swapna Debnath
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Suvankar Ghosh
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Gopal Pandit
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Priyadarshi Satpati
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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7
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Zhang T, Hansen K, Politis A, Müller MM. An Unusually Rapid Protein Backbone Modification Stabilizes the Essential Bacterial Enzyme MurA. Biochemistry 2020; 59:3683-3695. [PMID: 32930597 DOI: 10.1021/acs.biochem.0c00502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins are subject to spontaneous rearrangements of their backbones. Most prominently, asparagine and aspartate residues isomerize to their β-linked isomer, isoaspartate (isoAsp), on time scales ranging from days to centuries. Such modifications are typically considered "molecular wear-and-tear", destroying protein function. However, the observation that some proteins, including the essential bacterial enzyme MurA, harbor stoichiometric amounts of isoAsp suggests that this modification can confer advantageous properties. Here, we demonstrate that nature exploits an isoAsp residue within a hairpin to stabilize MurA. We found that isoAsp formation in MurA is unusually rapid and critically dependent on folding status. Moreover, perturbation of the isoAsp-containing hairpin via site-directed mutagenesis causes aggregation of MurA variants. Structural mass spectrometry revealed that this effect is caused by local protein unfolding in MurA mutants. Our findings demonstrate that MurA evolved to "mature" via a spontaneous post-translational incorporation of a β-amino acid, which raises the possibility that isoAsp-containing hairpins may serve as a structural motif of biological importance.
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Affiliation(s)
- Tianze Zhang
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Manuel M Müller
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
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8
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Tang Q, Zhong Y, Miller DP, Liu R, Zurek E, Lu ZL, Gong B. Reverse Turn Foldamers: An Expanded β-Turn Motif Reinforced by Double Hydrogen Bonds. Org Lett 2020; 22:1003-1007. [DOI: 10.1021/acs.orglett.9b04547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quan Tang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department of Chemistry, Hofstra University, Hempstead, New York 11549, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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9
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Zhang Y, Zhong Y, Connor AL, Miller DP, Cao R, Shen J, Song B, Baker ES, Tang Q, Pulavarti SVSRK, Liu R, Wang Q, Lu ZL, Szyperski T, Zeng H, Li X, Smith RD, Zurek E, Zhu J, Gong B. Folding and Assembly of Short α, β, γ-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures. J Am Chem Soc 2019; 141:14239-14248. [DOI: 10.1021/jacs.9b06094] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yukun Zhang
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Alan L. Connor
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Ruikai Cao
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jie Shen
- The NanoBio Lab, 31 Biopolis Way, The Nanos 138669, Singapore
| | - Bo Song
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Erin S. Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Quan Tang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Surya V. S. R. K. Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiwei Wang
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhong-lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Huaqiang Zeng
- The NanoBio Lab, 31 Biopolis Way, The Nanos 138669, Singapore
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jin Zhu
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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10
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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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11
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Bonnel C, Legrand B, Simon M, Martinez J, Bantignies JL, Kang YK, Wenger E, Hoh F, Masurier N, Maillard LT. C9/12
Ribbon-Like Structures in Hybrid Peptides Alternating α- and Thiazole-Based γ-Amino Acids. Chemistry 2017; 23:17584-17591. [DOI: 10.1002/chem.201704001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Clément Bonnel
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | | | - Young Kee Kang
- Department of Chemistry; Chungbuk National University, Cheongju; Chungbuk 28644 Republic of Korea
| | - Emmanuel Wenger
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisation; Université de Lorraine, CNRS, UMR 7036; Nancy France
| | - Francois Hoh
- Centre de Biochimie Structurale, CNRS UMR 5048-INSERM 1054; University of Montpellier; Montpellier France
| | - Nicolas Masurier
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Ludovic T. Maillard
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
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12
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Mathieu L, Bonnel C, Masurier N, Maillard LT, Martinez J, Lisowski V. Cross-Claisen Condensation ofN-Fmoc-Amino Acids - A Short Route to Heterocyclic γ-Amino Acids. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Ganesh Kumar M, Benke SN, Poopathi Raja KM, Gopi HN. Engineering polypeptide folding through trans double bonds: transformation of miniature β-meanders to hybrid helices. Chem Commun (Camb) 2015. [DOI: 10.1039/c5cc04523a] [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]
Abstract
Utilization of conjugated double bonds to engineer the novel folded miniature β-meander type structures, transformation of miniature β-meanders into 10/12-helices using catalytic hydrogenation, their solution and single crystal conformations are reported.
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Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research
- Pune-411 008
- India
| | - Sushil N. Benke
- Department of Chemistry
- Indian Institute of Science Education and Research
- Pune-411 008
- India
| | - K. Muruga Poopathi Raja
- Department of Physical Chemistry
- School of Chemistry
- Madurai Kamaraj University
- Madurai-625 021
- India
| | - Hosahudya N. Gopi
- Department of Chemistry
- Indian Institute of Science Education and Research
- Pune-411 008
- India
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14
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Kheria S, Nair RV, Kotmale AS, Rajamohanan PR, Sanjayan GJ. The role of N-terminal proline in stabilizing the Ant–Pro zipper motif. NEW J CHEM 2015. [DOI: 10.1039/c4nj02151g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper deals with the role of N-terminal proline in stabilizing the Ant–Pro zipper structure by the co-operative contribution of competing forces viz. hydrogen bonding, aromatic stacking and backbone chirality.
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Affiliation(s)
- Sanjeev Kheria
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Roshna V. Nair
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Amol S. Kotmale
- Central NMR Facility
- National Chemical Laboratory
- Pune 411 008
- India
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15
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Legrand B, Mathieu L, Lebrun A, Andriamanarivo S, Lisowski V, Masurier N, Zirah S, Kang YK, Martinez J, Maillard LT. Thiazole-Based γ-Building Blocks as Reverse-Turn Mimetic to Design a Gramicidin S Analogue: Conformational and Biological Evaluation. Chemistry 2014; 20:6713-20. [DOI: 10.1002/chem.201402190] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 01/09/2023]
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16
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Sonti R, Dinesh B, Basuroy K, Raghothama S, Shamala N, Balaram P. C12 helices in long hybrid (αγ)n peptides composed entirely of unconstrained residues with proteinogenic side chains. Org Lett 2014; 16:1656-9. [PMID: 24588077 DOI: 10.1021/ol500307p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Unconstrained γ(4) amino acid residues derived by homologation of proteinogenic amino acids facilitate helical folding in hybrid (αγ)n sequences. The C12 helical conformation for the decapeptide, Boc-[Leu-γ(4)(R)Val]5-OMe, is established in crystals by X-ray diffraction. A regular C12 helix is demonstrated by NMR studies of the 18 residue peptide, Boc-[Leu-γ(4)(R)Val]9-OMe, and a designed 16 residue (αγ)n peptide, incorporating variable side chains. Unconstrained (αγ)n peptides show an unexpectedly high propensity for helical folding in long polypeptide sequences.
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Affiliation(s)
- Rajesh Sonti
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, India, 560012
- NMR
Research Centre, Indian Institute of Science, Bangalore, India, 560012
| | - Bhimareddy Dinesh
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, India, 560012
| | - Krishnayan Basuroy
- Department
of Physics, Indian Institute of Science, Bangalore, India, 560012
| | | | | | - Padmanabhan Balaram
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, India, 560012
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Roy A, Kotmale AS, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. Probing the folding induction ability of orthanilic acid in peptides: some observations. RSC Adv 2014. [DOI: 10.1039/c3ra47039c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Dinesh B, Vinaya V, Raghothama S, Balaram P. C12-Helix Development in (αγ)nSequences - Spectroscopic Characterization of Boc-[Aib-γ4(R)Val]-OMe Oligomers. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Thorat VH, Ingole TS, Vijayadas KN, Nair RV, Kale SS, Ramesh VVE, Davis HC, Prabhakaran P, Gonnade RG, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. The Ant-Pro Reverse-Turn Motif. Structural Features and Conformational Characteristics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201739] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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20
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Kale SS, Priya G, Kotmale AS, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. Orthanilic acid-promoted reverse turn formation in peptides. Chem Commun (Camb) 2013; 49:2222-4. [DOI: 10.1039/c3cc40522b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Basuroy K, Karuppiah V, Shamala N, Balaram P. The Structural Characterization of Folded Peptides Containing the Conformationally Constrainedβ-Amino Acid Residueβ2,2Ac6c. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200537] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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22
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Baldauf C, Hofmann HJ. Ab initioMO Theory - An Important Tool in Foldamer Research: Prediction of Helices in Oligomers ofω-Amino Acids. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200436] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Basuroy K, Dinesh B, Shamala N, Balaram P. Structural Characterization of Backbone-Expanded Helices in Hybrid Peptides: (αγ)n and (αβ)n Sequences with Unconstrained β and γ Homologues of L-Val. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204436] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Basuroy K, Dinesh B, Shamala N, Balaram P. Structural Characterization of Backbone-Expanded Helices in Hybrid Peptides: (αγ)n and (αβ)n Sequences with Unconstrained β and γ Homologues of L-Val. Angew Chem Int Ed Engl 2012; 51:8736-9. [DOI: 10.1002/anie.201204436] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Indexed: 12/26/2022]
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25
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Ramesh VV, Priya G, Rajamohanan P, Hofmann HJ, Sanjayan GJ. Expanding the structural repertoire of β/α Ant-Pro (anthranilic acid-proline) oligomers into γ/α 2-Amb-Pro (2-aminomethyl benzoic acid-proline) oligomers. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Dinesh B, Basuroy K, Shamala N, Balaram P. Structural characterization of folded pentapeptides containing centrally positioned β(R)Val, γ(R)Val and γ(S)Val residues. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.02.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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27
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Basuroy K, Rajagopal A, Raghothama S, Shamala N, Balaram P. β-Turn analogues in model αβ-hybrid peptides: structural characterization of peptides containing β(2,2)Ac6c and β(3,3)Ac6c residues. Chem Asian J 2012; 7:1671-8. [PMID: 22555984 DOI: 10.1002/asia.201200052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 01/04/2023]
Abstract
The effect of gem-dialkyl substituents on the backbone conformations of β-amino acid residues in peptides has been investigated by using four model peptides: Boc-Xxx-β(2,2)Ac(6)c(1-aminomethylcyclohexanecarboxylic acid)-NHMe (Xxx = Leu (1), Phe (2); Boc = tert-butyloxycarbonyl) and Boc-Xxx-β(3,3)Ac(6)c(1-aminocyclohexaneacetic acid)-NHMe (Xxx = Leu (3), Phe (4)). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc-Leu-β(2,2)Ac(6)c-NHMe (1) established a C(11) hydrogen-bonded turn in the αβ-hybrid sequence. The observed torsion angles (α(ϕ≈-60°, ψ≈-30°), β(ϕ≈-90°, θ≈60°, ψ≈-90°)) corresponded to a C(11) helical turn, which was a backbone-expanded analogue of the type III β turn in αα sequences. The crystal structure of the peptide Boc-Phe-β(3,3)Ac(6)c-NHMe (4) established a C(11) hydrogen-bonded turn with distinctly different backbone torsion angles (α(ϕ≈-60°, ψ≈120°), β(ϕ≈60°, θ≈60°, ψ≈-60°)), which corresponded to a backbone-expanded analogue of the type II β turn observed in αα sequences. In peptide 4, the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these αβ-hybrid sequences.
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Affiliation(s)
- Krishnayan Basuroy
- Department of Physics, Indian Institute of Science, Bangalore-560 012, India
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van der Knaap M, Otero JM, Llamas-Saiz A, van Raaij MJ, Lageveen LI, Busscher HJ, Grotenbreg GM, van der Marel GA, Overkleeft HS, Overhand M. Design, synthesis and structural analysis of mixed α/β-peptides that adopt stable cyclic hairpin-like conformations. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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29
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Tirado M, Rutters J, Chen X, Yeung A, van Maarseveen J, Eyler JR, Berden G, Oomens J, Polfer NC. Disfavoring macrocycle b fragments by constraining torsional freedom: the "twisted" case of QWFGLM b6. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:475-482. [PMID: 22219043 DOI: 10.1007/s13361-011-0315-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/02/2011] [Accepted: 12/04/2011] [Indexed: 05/31/2023]
Abstract
While recent studies have shown that for some peptides, such as oligoglycines and Leu-enkephalin, mid-sized b fragment ions exist as a mixture of oxazolone and macrocycle structures, other primary structure motifs, such as QWFGLM, are shown to exclusively give rise to macrocycle structures. The aim of this study was to determine if certain amino acid residues are capable of suppressing macrocycle formation in the corresponding b fragment. The residues proline and 4-aminomethylbenzoic acid (4AMBz) were chosen because of their intrinsic rigidity, in the expectation that limited torsional flexibility may impede "head-to-tail" macrocycle formation. The presence of oxazolone versus macrocycle b(6) fragment structures was validated by infrared multiple photon dissociation (IRMPD) spectroscopy, using the free electron laser FELIX. It is confirmed that proline disfavors macrocycle formation in the cases of QPWFGLM b(7) and in QPFGLM b(6). The 4AMBz substitution experiments show that merely QWFG(4AMBz)M b(6), with 4AMBz in the fifth position, exhibits a weak oxazolone band. This effect is likely ascribed to a stabilization of the oxazolone structure, due to an extended oxazolone ring-phenyl π-electron system, not due to the rigidity of the 4AMBz residue. These results show that some primary structures have an intrinsic propensity to form macrocycle structures, which is difficult to disrupt, even using residues with limited torsional flexibility.
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Affiliation(s)
- Marcus Tirado
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
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Martínez L, Sampedro A, Sanna E, Costa A, Rotger C. Synthesis and conformational studies of peptido-squaramide foldable modules: a new class of turn-mimetic compounds. Org Biomol Chem 2012; 10:1914-21. [DOI: 10.1039/c2ob06715c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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Pilsl LKA, Reiser O. α/β-Peptide foldamers: state of the art. Amino Acids 2011; 41:709-18. [DOI: 10.1007/s00726-011-0894-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 03/18/2011] [Indexed: 11/24/2022]
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33
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Cozzi PG, Emer E, Gualandi A. Atroposelective Organocatalysis. Angew Chem Int Ed Engl 2011; 50:3847-9. [DOI: 10.1002/anie.201008031] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Indexed: 11/08/2022]
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34
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Roy A, Prabhakaran P, Baruah PK, Sanjayan GJ. Diversifying the structural architecture of synthetic oligomers: the hetero foldamer approach. Chem Commun (Camb) 2011; 47:11593-611. [DOI: 10.1039/c1cc13313f] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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35
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Balaram P. Hybrid polypeptides: Gabapentin as a stereochemically constrained γ-amino acid residue. Biopolymers 2010; 94:733-41. [DOI: 10.1002/bip.21468] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Structural Chemistry of Peptides Containing Backbone Expanded Amino Acid Residues: Conformational Features of β, γ, and Hybrid Peptides. Chem Rev 2010; 111:657-87. [DOI: 10.1021/cr100100x] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Prema. G. Vasudev
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Choi SH, Guzei IA, Spencer LC, Gellman SH. Crystallographic characterization of helical secondary structures in 2:1 and 1:2 alpha/beta-peptides. J Am Chem Soc 2010; 131:2917-24. [PMID: 19203269 DOI: 10.1021/ja808168y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligomers containing both alpha- and beta-amino acid residues ("alpha/beta-peptides") are intriguing as potential foldamers. A large set of alpha/beta-peptide backbones can be generated by combining alpha- and beta-amino acid residues in different patterns; however, most research to date has focused on the simplest pattern, 1:1 alpha:beta. We have begun to explore the range of variation that can be achieved with alpha-residue/beta-residue combinations by examining the folding behavior of oligomers that contain 2:1 and 1:2 alpha:beta patterns. The beta-residues in our systems have a five-membered-ring constraint (trans-2-aminocyclopentanecarboxylic acid (ACPC) residues), because these preorganized subunits strongly promote helical folding for 1:1 alpha:beta backbones and pure beta backbones. Previously we concluded that two helical conformations are available to 2:1 and 1:2 alpha/beta-peptides containing ACPC or analogously constrained beta-residues, one helix defined by i,i+3 CO...H-N backbone hydrogen bonds and the other defined by i,i+4 CO...H-N hydrogen bonds. These deductions were based on 2D NMR analysis of a 2:1 heptamer and a 1:2 hexamer in methanol. Crystallographic analysis of a pair of analogous nonpolar alpha/beta-peptides showed only the i,i+3 hydrogen-bonded helical conformations. We now report four new crystal structures of 2:1 alpha/beta-peptides, ranging in length from 5 to 11 residues, and six new crystal structures of 1:2 alpha/beta-peptides, ranging in length from 6 to 10 residues. All 10 of these new structures are fully helical, and all helices display the i,i+3 CO...H-N hydrogen bonding pattern. These crystallographic data sets, collectively, provide high structural definition for the i,i+3 hydrogen-bonded helical secondary structures available to these foldamer backbones.
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Affiliation(s)
- Soo Hyuk Choi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Shandler SJ, Shapovalov MV, Dunbrack RL, DeGrado WF. Development of a rotamer library for use in beta-peptide foldamer computational design. J Am Chem Soc 2010; 132:7312-20. [PMID: 20446685 PMCID: PMC3079439 DOI: 10.1021/ja906700x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Foldamers present a particularly difficult challenge for accurate computational design compared to the case for conventional peptide and protein design due to the lack of a large body of structural data to allow parametrization of rotamer libraries and energies. We therefore explored the use of molecular mechanics for constructing rotamer libraries for non-natural foldamer backbones. We first evaluated the accuracy of molecular mechanics (MM) for the prediction of rotamer probability distributions in the crystal structures of proteins is explored. The van der Waals radius, dielectric constant and effective Boltzmann temperature were systematically varied to maximize agreement with experimental data. Boltzmann-weighted probabilities from these molecular mechanics energies compare well with database-derived probabilities for both an idealized alpha-helix (R = 0.95) as well as beta-strand conformations (R = 0.92). Based on these parameters, de novo rotamer probabilities for secondary structures of peptides built from beta-amino acids were determined. To limit computational complexity, it is useful to establish a residue-specific criterion for excluding rare, high-energy rotamers from the library. This is accomplished by including only those rotamers with probability greater than a given threshold (e.g., 10%) of the random value, defined as 1/n where n is the number of potential rotamers for each residue type.
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Affiliation(s)
- Scott J. Shandler
- Department of Biochemistry and Molecular Biology, University of Pennsylvania School of Medicine
| | - Maxim V. Shapovalov
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia PA 19111
| | - Roland L. Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia PA 19111
| | - William F. DeGrado
- Department of Biochemistry and Molecular Biology, University of Pennsylvania School of Medicine
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Chandrasekhar S, Kiranmai N, Kiran MU, Devi AS, Reddy GPK, Idris M, Jagadeesh B. Novel helical foldamers: organized heterogeneous backbone folding in 1 : 1 α/nucleoside-derived-β-amino acid sequences. Chem Commun (Camb) 2010; 46:6962-4. [DOI: 10.1039/c0cc01724h] [Citation(s) in RCA: 11] [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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40
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Gabapentin: a stereochemically constrained gamma amino acid residue in hybrid peptide design. Acc Chem Res 2009; 42:1628-39. [PMID: 19572698 DOI: 10.1021/ar9001153] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nature has used the all-alpha-polypeptide backbone of proteins to create a remarkable diversity of folded structures. Sequential patterns of 20 distinct amino acids, which differ only in their side chains, determine the shape and form of proteins. Our understanding of these specific secondary structures is over half a century old and is based primarily on the fundamental elements: the Pauling alpha-helix and beta-sheet. Researchers can also generate structural diversity through the synthesis of polypeptide chains containing homologated (omega) amino acid residues, which contain a variable number of backbone atoms. However, incorporating amino acids with more atoms within the backbone introduces additional torsional freedom into the structure, which can complicate the structural analysis. Fortunately, gabapentin (Gpn), a readily available bulk drug, is an achiral beta,beta-disubstituted gamma amino acid residue that contains a cyclohexyl ring at the C(beta) carbon atom, which dramatically limits the range of torsion angles that can be obtained about the flanking C-C bonds. Limiting conformational flexibility also has the desirable effect of increasing peptide crystallinity, which permits unambiguous structural characterization by X-ray diffraction methods. This Account describes studies carried out in our laboratory that establish Gpn as a valuable residue in the design of specifically folded hybrid peptide structures. The insertion of additional atoms into polypeptide backbones facilitates the formation of intramolecular hydrogen bonds whose directionality is opposite to that observed in canonical alpha-peptide helices. If hybrid structures mimic proteins and biologically active peptides, the proteolytic stability conferred by unusual backbones can be a major advantage in the area of medicinal chemistry. We have demonstrated a variety of internally hydrogen-bonded structures in the solid state for Gpn-containing peptides, including the characterization of the C(7) and C(9) hydrogen bonds, which can lead to ribbons in homo-oligomeric sequences. In hybrid alphagamma sequences, distinct C(12) hydrogen-bonded turn structures support formation of peptide helices and hairpins in longer sequences. Some peptides that include the Gpn residue have hydrogen-bond directionality that matches alpha-peptide helices, while others have the opposite directionality. We expect that expansion of the polypeptide backbone will lead to new classes of foldamer structures, which are thus far unknown to the world of alpha-polypeptides. The diversity of internally hydrogen-bonded structures observed in hybrid sequences containing Gpn shows promise for the rational design of novel peptide structures incorporating hybrid backbones.
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Affiliation(s)
- Prema G. Vasudev
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
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41
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Synthesis of chemically modified bioactive peptides: recent advances, challenges and developments for medicinal chemistry. Future Med Chem 2009; 1:1289-310. [DOI: 10.4155/fmc.09.97] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although not complying with Lipinski’s rule, peptides are to an increasing extent being developed into new active pharmaceutical ingredients. This is mainly due to novel application routes, formulations and chemical modifications, which confer on the peptides improved uptake and increased metabolic stability. A brief survey of currently approved peptide drugs and the present scope of the application of peptides as drugs is provided. Cyclic peptides are emerging as an interesting class of peptides with conformational rigidity and homogeneity, high receptor affinity and selectivity, increased metabolic stability and – in special cases – even oral availability. Challenges and new methodology for the synthesis of cyclic peptides are outlined and an overview of approaches toward the design of peptide conformation and peptide modification by nonproteinogenic building blocks is given.
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Angelici G, Falini G, Hofmann HJ, Huster D, Monari M, Tomasini C. Nanofibers from oxazolidi-2-one containing hybrid foldamers: what is the right molecular size? Chemistry 2009; 15:8037-8048. [PMID: 19360839 DOI: 10.1002/chem.200900185] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A series of oligomers of the type Boc-(L-Phe-D-Oxd)(n)-OBn (Boc = tert-butoxycarbonyl; Oxd = 4-methyl-5-carboxy oxazolidin-2-one; Bn = benzyl) were prepared for n = 2-5. The shortest oligomer, Boc-(L-Phe-D-Oxd)(2)-OBn, aggregates and forms a fiber-like material with an anti-parallel beta-sheet structure in which the oligopeptide units are connected to each other by only one intermolecular hydrogen bond. The longer oligomers exhibit structural heterogeneity. They start to organize into secondary structures by the formation of intramolecular hydrogen bonds at the pentamer level. Microscopy and diffraction of the oligomers indicated a crystalline character for only the shorter ones.
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Affiliation(s)
- Gaetano Angelici
- Dipartimento di Chimica G. Ciamician, Alma Mater Studiorum Università di Bologna, Via Selmi 21, 40126 Bologna, Italy
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Lee HK, Smith MD, Smith BJ, Grussendorf J, Xu L, Gillies RJ, White HS, Bulaj G. Anticonvulsant Met-enkephalin analogues containing backbone spacers reveal alternative non-opioid signaling in the brain. ACS Chem Biol 2009; 4:659-71. [PMID: 19634861 DOI: 10.1021/cb900045c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Prosthesis of non-critical parts of a polypeptide backbone is an attractive strategy to simplify bioactive peptides. This approach was applied to an opioid neuropeptide, Met-enkephalin, in which two adjacent Gly2-Gly3 residues were replaced with a series of non-peptidic backbone spacers varying in length and/or physicochemical properties. The backbone spacers did not affect the overall structural properties of the analogues, but they did dramatically reduce their affinities and agonist activities toward delta- and mu-opioid receptors. Molecular modeling suggested that the decrease of the affinity of Met-enkephalin to delta-opioid receptor could be accounted for by the loss of a single hydrogen bond. Remarkably, the analogues containing the most isostere spacers retained potent antinociceptive and anticonvulsant properties that were comparable to that of the endogenous peptide. This unexpected high in vivo potency could not be accounted for by an increase in metabolic stability. Moreover, the antiepileptic activity could not be reversed by opioid receptor antagonists. In summary, the results obtained with the analogues containing backbone spacers suggest a novel mechanism for seizure control in the brain that involves alternative non-opioid signaling.
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Affiliation(s)
| | - Misty D. Smith
- Department of Pharmacology and Toxicology, The University of Utah, 421 Wakara Way, Suite 360, Salt Lake City, Utah 84108
| | - Brian J. Smith
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Joel Grussendorf
- Department of Pharmacology and Toxicology, The University of Utah, 421 Wakara Way, Suite 360, Salt Lake City, Utah 84108
| | - Liping Xu
- Department of Radiology
- Department of Biochemistry and Molecular Biophysics, Arizona Health Sciences Center, University of Arizona, Tucson, Arizona 85724
| | - Robert J. Gillies
- Department of Radiology
- Department of Biochemistry and Molecular Biophysics, Arizona Health Sciences Center, University of Arizona, Tucson, Arizona 85724
| | - H. Steve White
- Department of Pharmacology and Toxicology, The University of Utah, 421 Wakara Way, Suite 360, Salt Lake City, Utah 84108
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Sharma GVM, Babu BS, Chatterjee D, Ramakrishna KVS, Kunwar AC, Schramm P, Hofmann HJ. Theoretical and Experimental Studies on α/ε-Hybrid Peptides: Design of a 14/12-Helix from Peptides with Alternating (S)-C-Linked Carbo-ε-amino Acid [(S)-ε-Caa(x)] and l-Ala. J Org Chem 2009; 74:6703-13. [DOI: 10.1021/jo901277a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gangavaram V. M. Sharma
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | - Bommagani Shoban Babu
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | - Deepak Chatterjee
- Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | | | - Ajit C. Kunwar
- Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | - Peter Schramm
- Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Hans-Jörg Hofmann
- Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
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Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Nat Struct Mol Biol 2009; 16:684-90. [PMID: 19525973 PMCID: PMC2754385 DOI: 10.1038/nsmb.1610] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 04/23/2009] [Indexed: 11/08/2022]
Abstract
The energetic contributions of hydrogen bonding to protein folding are still unclear, despite more than 70 years of study. This is due partly to the difficulty of extracting thermodynamic information about specific interactions from protein mutagenesis data and partly to the context dependence of hydrogen bond strengths. Herein, we test the hypothesis that hydrogen bond strengths depend on the polarity of their microenvironment, with stronger hydrogen bonds forming in nonpolar surroundings. Double-mutant cycle analysis using a combination of amide-to-ester backbone mutagenesis and traditional side chain mutagenesis revealed that hydrogen bonds can be stronger by up to 1.2 kcal mol(-1) when they are sequestered in hydrophobic surroundings than when they are solvent exposed. Such large coupling energies between hydrogen bond strengths and local polarity suggest that the context dependence of hydrogen bond strengths must be accounted for in any comprehensive account of the forces responsible for protein folding.
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Sharma GV, Babu BS, Ramakrishna KV, Nagendar P, Kunwar AC, Schramm P, Baldauf C, Hofmann HJ. Synthesis and Structure of α/δ-Hybrid Peptides-Access to Novel Helix Patterns in Foldamers. Chemistry 2009; 15:5552-66. [DOI: 10.1002/chem.200802078] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Chatterjee S, Vasudev PG, Raghothama S, Ramakrishnan C, Shamala N, Balaram P. Expanding the Peptide β-Turn in αγ Hybrid Sequences: 12 Atom Hydrogen Bonded Helical and Hairpin Turns. J Am Chem Soc 2009; 131:5956-65. [DOI: 10.1021/ja900618h] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunanda Chatterjee
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Prema G. Vasudev
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Srinivasarao Raghothama
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Chandrasekharan Ramakrishnan
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Narayanaswamy Shamala
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
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Nagaraj R. Peptides: Isolation, production, and use in India. Biotechnol J 2009; 4:329-34. [DOI: 10.1002/biot.200800257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Chatterjee S, Vasudev PG, Raghothama S, Shamala N, Balaram P. Solid state and solution conformations of a hybrid alphagammaalphaalphagammaalpha hexapeptide. Characterization of a backbone expanded analog of the alpha-polypeptide 3(10)-helix. Biopolymers 2009; 90:759-71. [PMID: 18767124 DOI: 10.1002/bip.21076] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The stereochemically constrained gamma amino acid residue gabapentin (1-(aminomethyl)cyclohexaneacetic acid, Gpn) has been incorporated into a host alpha-peptide sequence. The structure of a hybrid alphagammaalphaalphagammaalpha peptide, Boc-Leu-Gpn-Aib-Leu-Gpn-Aib-OMe in crystals reveals a continuous helical conformation stabilized by three intramolecular 4 --> 1 C(12) hydrogen bonds across the alphagamma/alphagamma segments and one C(10) hydrogen bond across the central alphaalpha segment. This conformation corresponds to an expanded analog of the canonical all-alpha polypeptide 3(10)-helix, with insertion of two additional backbone atoms at each gamma residue. Solvent dependence of NH chemical shifts in CDCl(3) solution are consistent with conformation in which the NH groups of Aib (3), Leu (4), Gpn (5), and Aib (6) are hydrogen bonded, a feature observed in the solid state. The nonsequential NOEs between Gpn (2) NH <--> Leu (4) NH and Gpn (2) NH <--> Gpn (5) NH support the presence of additional conformations in solution. Temperature-dependent line broadening of NH resonances confirms the occurrence of rapid exchange between multiple conformations at room temperature. Two conformational models which rationalize the observed nonsequential NOEs are presented, both of which contain three hydrogen bonds and are consistent with the known stereochemical preferences of the Gpn residue.
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Affiliation(s)
- Sunanda Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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