1
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Bucci R, Vaghi F, Di Lorenzo D, Anastasi F, Broggini G, Lo Presti L, Contini A, Gelmi ML. A Non‐coded β2,2‐Amino Acid with Isoxazoline Core Able to Stabilize Peptides Folding Through an Unprecedented Hydrogen Bond. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200601] [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]
Affiliation(s)
- Raffaella Bucci
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Francesco Vaghi
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Davide Di Lorenzo
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Francesco Anastasi
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Gianluigi Broggini
- Università degli Studi dell'Insubria Dipartimento di Scienza e Alta Tecnologia ITALY
| | - Leonardo Lo Presti
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Chimica ITALY
| | - Alessandro Contini
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Maria Luisa Gelmi
- Universita degli Studi di Milano DISFARM, Sezione di Chimica Generale e Organica “A. Marchesini” Via Venezian 21 20133 Milano ITALY
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3
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DuPai CD, Davies BW, Wilke CO. A systematic analysis of the beta hairpin motif in the Protein Data Bank. Protein Sci 2021; 30:613-623. [PMID: 33389765 DOI: 10.1002/pro.4020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022]
Abstract
The beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here, we systematically probe all 49,000 unique beta hairpin substructures contained within the Protein Data Bank (PDB) to uncover key characteristics correlated with stable beta hairpin structure, including amino acid biases and enriched interstrand contacts. We find that position specific amino acid preferences, while seen throughout the beta hairpin structure, are most evident within the turn region, where they depend on subtle turn dynamics associated with turn length and secondary structure. We also establish a set of broad design principles, such as the inclusion of aspartic acid residues at a specific position and the careful consideration of desired secondary structure when selecting residues for the turn region, that can be applied to the generation of libraries encoding proteins or peptides containing beta hairpin structures.
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Affiliation(s)
- Cory D DuPai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, John Ring LaMontagne Center for Infectious Diseases, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Claus O Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
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4
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Marafon G, Moretto A, Zanuy D, Alemán C, Crisma M, Toniolo C. Effect on the Conformation of a Terminally Blocked, ( E) β,γ-Unsaturated δ-Amino Acid Residue Induced by Carbon Methylation. J Org Chem 2020; 85:1513-1524. [PMID: 31769989 DOI: 10.1021/acs.joc.9b02544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptides are well-known to play a fundamental therapeutic role and to represent building blocks for numerous useful biomaterials. Stabilizing their active 3D-structure by appropriate modifications remains, however, a challenge. In this study, we have expanded the available literature information on the conformational propensities of a promising backbone change of a terminally blocked δ-amino acid residue, a dipeptide mimic, by replacing its central amide moiety with an (E) Cβ═Cγ alkene unit. Specifically, we have examined by DFT calculations, X-ray diffraction in the crystalline state, and FT-IR absorption/NMR spectroscopies in solution the extended vs folded preferences of analogues of this prototype system either unmodified or possessing single or multiple methyl group substituents on each of its four -CH2-CH═CH-CH2- main-chain carbon atoms. The theoretical and experimental results obtained clearly point to the conclusion that increasing the number of adequately positioned methylations will enhance the preference of the original sequence to fold, thus opening interesting perspectives in the design of conformationally constrained peptidomimetics.
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Affiliation(s)
- Giulia Marafon
- Department of Chemical Sciences , University of Padova , 35131 Padova , Italy
| | - Alessandro Moretto
- Department of Chemical Sciences , University of Padova , 35131 Padova , Italy.,Institute of Biomolecular Chemistry , Padova Unit, CNR , 35131 Padova , Italy
| | - David Zanuy
- Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering , Universitat Polytècnica de Catalunya , 08019 Barcelona , Spain
| | - Carlos Alemán
- Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering , Universitat Polytècnica de Catalunya , 08019 Barcelona , Spain.,Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12 , 08028 Barcelona Spain
| | - Marco Crisma
- Institute of Biomolecular Chemistry , Padova Unit, CNR , 35131 Padova , Italy
| | - Claudio Toniolo
- Department of Chemical Sciences , University of Padova , 35131 Padova , Italy.,Institute of Biomolecular Chemistry , Padova Unit, CNR , 35131 Padova , Italy
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5
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Drouillat B, Peggion C, Biondi B, Wright K, Couty F, Crisma M, Formaggio F, Toniolo C. Heterochiral Ala/(
αMe)Aze
sequential oligopeptides:
S
ynthesis and conformational study. J Pept Sci 2019; 25:e3165. [DOI: 10.1002/psc.3165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Bruno Drouillat
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | | | - Barbara Biondi
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Karen Wright
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | - François Couty
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | - Marco Crisma
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Fernando Formaggio
- Department of ChemistryUniversity of Padova Padova 35131 Italy
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Claudio Toniolo
- Department of ChemistryUniversity of Padova Padova 35131 Italy
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
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6
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Konda M, Ghosh T, Mobin SM, Das AK. Intertwined gababutin-based supramolecular double helix. NEW J CHEM 2019. [DOI: 10.1039/c8nj05009k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A dimer-assembly driven supramolecular double helix is observed for the gababutin-based short peptide sequence and this architecture exhibits electrochemical features.
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Affiliation(s)
- Maruthi Konda
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Tapas Ghosh
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Shaikh M. Mobin
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
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7
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Pal S, Prabhakaran EN. Hydrogen bond surrogate stabilized water soluble 310-helix from a disordered pentapeptide containing coded α-amino acids. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.05.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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8
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Crisma M, Formaggio F, Alemán C, Torras J, Ramakrishnan C, Kalmankar N, Balaram P, Toniolo C. The fully‐extended conformation in peptides and proteins. Pept Sci (Hoboken) 2018. [DOI: 10.1002/bip.23100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
- Department of ChemistryUniversity of PadovaPadova35131 Italy
| | - Carlos Alemán
- Departament d'Enginyeria QuímicaEEBE, Universitat Politècnica de CatalunyaBarcelona08019 Spain
- Barcelona Research Center in Multiscale Science and EngineeringUniversitat Politècnica de CatalunyaBarcelona08019 Spain
| | - Joan Torras
- Departament d'Enginyeria QuímicaEEBE, Universitat Politècnica de CatalunyaBarcelona08019 Spain
- Barcelona Research Center in Multiscale Science and EngineeringUniversitat Politècnica de CatalunyaBarcelona08019 Spain
| | | | - Neha Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK CampusBangalore560065 India
| | | | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
- Department of ChemistryUniversity of PadovaPadova35131 Italy
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9
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Konda M, Jadhav RG, Maiti S, Mobin SM, Kauffmann B, Das AK. Understanding the conformational analysis of gababutin based hybrid peptides. Org Biomol Chem 2018; 16:1728-1735. [DOI: 10.1039/c8ob00035b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A new class of gababutin-based tetrapeptide shows a C12/C10 hydrogen-bonded hybrid turn.
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Affiliation(s)
- Maruthi Konda
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Rohit G. Jadhav
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Sayan Maiti
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Shaikh M. Mobin
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Brice Kauffmann
- Université de Bordeaux
- CNRS
- UMS 3033
- INSERM US001 Institut Européen de Chimie et de Biologie (IECB)
- 33600 Pessac
| | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
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10
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Paul A, Kumar S, Kalita S, Ghosh AK, Mondal AC, Mandal B. A Peptide Based Pro-drug Disrupts Alzheimer’s Amyloid into Non-toxic Species and Reduces Aβ Induced Toxicity In Vitro. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9602-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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11
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Krieger V, Ciglia E, Thoma R, Vasylyeva V, Frieg B, de Sousa Amadeu N, Kurz T, Janiak C, Gohlke H, Hansen FK. α-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds. Chemistry 2017; 23:3699-3707. [PMID: 28090689 DOI: 10.1002/chem.201605100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 12/13/2022]
Abstract
α-Peptoids, or N-substituted glycine oligomers, are an important class of peptidomimetic foldamers with proteolytic stability. Nevertheless, the presence of cis/trans-amide bond conformers, which contribute to the high flexibility of α-peptoids, is considered as a major drawback. A modified peptoid backbone with an improved control of the amide bond geometry could therefore help to overcome this limitation. Herein, we have performed the first thorough analysis of the folding propensities of α-aminoxy peptoids (or N-substituted 2-aminoxyacetic acid oligomers). To this end, the amide bond geometry and the conformational properties of a series of model α-aminoxy peptoids were investigated by using 1D and 2D NMR experiments, X-ray crystallography, natural bond orbital (NBO) analysis, circular dichroism (CD) spectroscopy, and molecular dynamics (MD) simulations revealing a unique preference for cis-amide bonds even in the absence of cis-directing side chains. The conformational analysis based on the MD simulations revealed that α-aminoxy peptoids can adopt helical conformations that can mimic the spatial arrangement of peptide side chains in a canonical α-helix. Given their ease of synthesis and conformational properties, α-aminoxy peptoids represent a new member of the peptoid family capable of controlling the amide isomerism while maintaining the potential for side-chain diversity.
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Affiliation(s)
- Viktoria Krieger
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Emanuele Ciglia
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Roland Thoma
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Vera Vasylyeva
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Nader de Sousa Amadeu
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Thomas Kurz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Christoph Janiak
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Finn K Hansen
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
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12
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Makwana KM, Mahalakshmi R. Capping β-hairpin with N-terminal d-amino acid stabilizes peptide scaffold. Biopolymers 2017; 106:260-6. [PMID: 26999275 DOI: 10.1002/bip.22837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022]
Abstract
Various strategies exist to stabilize de novo designed synthetic peptide β-hairpins or β-sheets structures, especially at the non-hydrogen bonding position. However, strategies to stabilize strand termini, which are affected by fraying, are highly limited. Here, by substituting N-terminal aliphatic amino acid with its mirror image counterpart, we achieve a significant increase in scaffold stabilization, resulting from the formation of a terminal aliphatic-aromatic hydrophobic CH…pi cluster. Our extensive solution NMR studies support the incorporation of an N-terminal d-aliphatic amino acid in the design of short β-hairpins, while successfully retaining the overall structural scaffold. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 260-266, 2016.
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Affiliation(s)
- Kamlesh M Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, Madhya Pradesh, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, Madhya Pradesh, India
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13
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Toniolo C, Crisma M, Formaggio F, Alemán C, Ramakrishnan C, Kalmankar N, Balaram P. Intramolecular backbone···backbone hydrogen bonds in polypeptide conformations. The other way around: ɛ-turn. Biopolymers 2017; 108. [DOI: 10.1002/bip.22911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/17/2016] [Accepted: 06/29/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Claudio Toniolo
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Carlos Alemán
- Departament d'Enginyeria Quimica; ETSEIB, Universitat Politècnica de Catalunya; Barcelona 08028 Spain
| | | | - Neha Kalmankar
- National Centre for Biological Sciences (TIFR); GKVK Campus Bangalore 560065 India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
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14
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Konda M, Bhowmik S, Mobin SM, Biswas S, Das AK. Modulating Hydrogen Bonded Self-assembled Patterns and Morphological Features by a Change in Side Chain of Third Amino Acid of Synthetic γ- Amino Acid Based Tripeptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maruthi Konda
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Soumitra Bhowmik
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Shaikh M. Mobin
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Sagar Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
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