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Gupta SK, Banerjee S, Prabhakaran EN. Understanding the anomaly of cis-trans isomerism in Pro-His sequence. Bioorg Med Chem Lett 2022; 76:128985. [PMID: 36165914 DOI: 10.1016/j.bmcl.2022.128985] [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: 06/21/2022] [Revised: 08/05/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022]
Abstract
The anomalous absence of cisPro stabilizing CαHαXaa···πAro interactions at Xaa-Pro-Aro exclusively when Aro is His, is understood by NMR structural analyses of model peptides, as due to i → i backbone-side chain C6 H-bond that forms uniquely when Aro is His, which significantly decreases its χ1-g- population essential for CαHαXaa···πAro formation.
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Affiliation(s)
- Sunil K Gupta
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Erode N Prabhakaran
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.
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2
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Nandi S, Sarkar R, Jaiswar A, Roy S, Haldar D. Miniature β-Hairpin Mimetic by Intramolecular Hydrogen Bond and C-H···π Interactions. ACS OMEGA 2022; 7:17245-17252. [PMID: 35647431 PMCID: PMC9134230 DOI: 10.1021/acsomega.2c01168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Canonically, protein β-hairpin motifs are stabilized by intramolecular hydrogen bonds. Here, we attempt to develop a rational design recipe for a miniature hairpin structure stabilized by hydrogen bonding as well as C-H···π interaction and try to understand how such a stabilization effect varies with different functional groups at each terminus. Database analysis shows that the α-amino acids with an aromatic side chain will not favor that kind of C-H···π stabilized hairpin structure. However, hybrid tripeptides with an N-terminal Boc-Trp-Aib corner residue and C-terminal aromatic ω-amino acids fold into the hairpin conformation with a central β-turn/open-turn that is reinforced by a C-H···π interaction. The CCDC database analysis further confirms that this C-H···π stabilized hairpin motif is general for Boc-protected tripeptides containing Aib in the middle and aromatic functionality at the C-terminus. The different α-amino acids like Leu/Ala/Phe/Pro/Ser at the N-terminus have a minor influence on the C-H···π interaction and stabilities of the folded structures in solid-state. However, the hybrid peptides exhibit different degrees of conformational heterogeneity both in the solid and solution phase, which is common for this kind of flexible small molecule. Conformational heterogeneity in the solution phase including the C-H···π stabilized β-hairpin structures are characterized by the molecular dynamics (MD) simulations explaining their plausible origin at an atomistic level.
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Affiliation(s)
- Sujay
Kumar Nandi
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Raju Sarkar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Akhilesh Jaiswar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Susmita Roy
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Debasish Haldar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
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3
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Gupta SK, Banerjee S, Prabhakaran EN. van der Waals interactions to control amide cis– trans isomerism. NEW J CHEM 2022. [DOI: 10.1039/d2nj01457b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discover the presence of local van der Waals (vdW) interactions at the cis amide bond in crystals of isobutyroyl–Pro–Val–OMe.
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Affiliation(s)
- Sunil K. Gupta
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka–560012, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka–560012, India
| | - Erode N. Prabhakaran
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka–560012, India
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4
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Karmakar B, Saha B, Jana K, Gupta Bhattacharya S. Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus. J Biol Chem 2021; 295:17852-17864. [PMID: 33454019 DOI: 10.1074/jbc.ra120.015801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/14/2020] [Indexed: 11/06/2022] Open
Abstract
Aspergillus terreus is an allergenic fungus, in addition to causing infections in both humans and plants. However, the allergens in this fungus are still unknown, limiting the development of diagnostic and therapeutic strategies. We used a proteomic approach to search for allergens, identifying 16 allergens based on two-dimensional immunoblotting with A. terreus susceptible patient sera. We further characterized triose-phosphate isomerase (Asp t 36), one of the dominant IgE (IgE)-reactive proteins. The gene was cloned and expressed in Escherichia coli. Phylogenetic analysis showed Asp t 36 to be highly conserved with close similarity to the triose-phosphate isomerase protein sequence from Dermatophagoides farinae, an allergenic dust mite. We identified four immunodominant epitopes using synthetic peptides, and mapped them on a homology-based model of the tertiary structure of Asp t 36. Among these, two were found to create a continuous surface patch on the 3D structure, rendering it an IgE-binding hotspot. Biophysical analysis indicated that Asp t 36 shows similar secondary structure content and temperature sensitivity with other reported triose-phosphate isomerase allergens. In vivo studies using a murine model displayed that the recombinant Asp t 36 was able to stimulate airway inflammation, as demonstrated by an influx of eosinophils, goblet cell hyperplasia, elevated serum Igs, and induction of Th2 cytokines. Collectively, our results reveal the immunogenic property of Asp t 36, a major allergen from A. terreus, and define a new fungal allergen more broadly. This allergen could serve as a potent candidate for investigating component resolved diagnosis and immunotherapy.
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Affiliation(s)
- Bijoya Karmakar
- Division of Plant Biology, Bose Institute (Main Campus), Kolkata, India
| | - Bodhisattwa Saha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
| | - Kuladip Jana
- Division of Molecular Medicines, Bose Institute (Centenary Building), Kolkata, India
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5
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Ganguly HK, Basu G. Conformational landscape of substituted prolines. Biophys Rev 2020; 12:25-39. [PMID: 31953795 PMCID: PMC7040156 DOI: 10.1007/s12551-020-00621-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The cyclic side chain of the amino acid proline confers unique conformational restraints on its backbone and side chain dihedral angles. This affects two equilibria-one at the backbone (cis/trans) and the other at the side chain (endo/exo). Substitutions on the proline ring impose additional steric and stereoelectronic effects that can further modulate both these equilibria, which in turn can also affect the backbone dihedral angle (ϕ, ψ) preferences. In this review, we have explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. The impact of incorporating these derivatives within model peptides and proteins are also discussed for selected cases. Several of these substituents have been used to introduce bioorthogonal functionality and modulate structure-specific ligand recognition or used as spectroscopic probes. The incorporation of these diversely applicable functional groups, coupled with their ability to define an amino acid conformation via stereoelectronic effects, have a broad appeal among chemical biologists, molecular biophysicists, and medicinal chemists.
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Affiliation(s)
- Himal Kanti Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
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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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Dasgupta R, Ganguly HK, Modugula EK, Basu G. Type VIa β-turn-fused helix N-termini: A novel helix N-cap motif containing cis proline. Biopolymers 2016; 108. [PMID: 27428516 DOI: 10.1002/bip.22919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/07/2016] [Accepted: 07/14/2016] [Indexed: 11/05/2022]
Abstract
Helix N-capping motifs often form hydrogen bonds with terminal amide groups which otherwise would be free. Also, without an amide hydrogen, proline (trans) is over-represented at helix N-termini (N1 position) because this naturally removes the need to hydrogen bond one terminal amide. However, the preference of cisPro, vis-à-vis helix N-termini, is not known. We show that cisPro (αR or PPII ) often appears at the N-cap position (N0) of helices. The N-cap cisPro(αR ) is associated with a six-residue sequence motif - X(-2) -X(-1) -cisPro-X(1) -X(2) -X(3) - with preference for Glu/Gln at X(-1) , Phe/Tyr/Trp at X(1) and Ser/Thr at X(3) . The motif, formed by the fusion of a helix and a type VIa β-turn, contains a hydrogen bond between the side chain of X(-1) and the side chain/backbone of X(3) , a α-helical hydrogen bond between X(-2) and X(2) and stacking interaction between cisPro and an aromatic residue at X(1) . NMR experiments on peptides containing the motif and its variants showed that local interactions associated with the motif, as found in folded proteins, were not enough to significantly tilt the cis/trans equilibrium towards cisPro. This suggests that some other evolutionary pressure must select the cisPro motif (over transPro) at helix N-termini. Database analysis showed that >C = O of the pre-cisPro(αR ) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(αR ) motif is preferred at helix N-termini because it allows the helix to participate in long-range interactions that may be structurally and functionally important.
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Affiliation(s)
- Rubin Dasgupta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Himal K Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - E K Modugula
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
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8
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Sircar G, Jana K, Dasgupta A, Saha S, Gupta Bhattacharya S. Epitope Mapping of Rhi o 1 and Generation of a Hypoallergenic Variant: A CANDIDATE MOLECULE FOR FUNGAL ALLERGY VACCINES. J Biol Chem 2016; 291:18016-29. [PMID: 27358405 DOI: 10.1074/jbc.m116.732032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Indexed: 11/06/2022] Open
Abstract
Efficacy of allergen-specific immunotherapy is often severely impaired by detrimental IgE-mediated side effects of native allergen during vaccination. Here, we present the molecular determinants for IgE recognition of Rhi o 1 and eventually converting the allergen into a hypoallergenic immunogen to restrain health hazards during desensitization. Rhi o 1 is a respiratory fungal allergen. Despite having cross-reactivity with cockroach allergen, we observed that non-cross-reactive epitope predominantly determined IgE binding to Rhi o 1. Denaturation and refolding behavior of the allergen confirmed that its IgE reactivity was not essentially conformation-dependent. A combinatorial approach consisting of computational prediction and a peptide-based immunoassay identified two peptides ((44)TGEYLTQKYFNSQRNN and (311)GAEKNWAGQYVVDCNK) of Rhi o 1 that frequently reacted with IgE antibodies of sensitized patients. Interestingly, these peptides did not represent purely linear IgE epitopes but were presented in a conformational manner by forming a spatially clustered surface-exposed epitope conferring optimal IgE-binding capacity to the folded allergen. Site-directed alanine substitution identified four residues of the IgE epitope that were crucial for antibody binding. A multiple mutant (T49A/Y52A/K314A/W316A) showing 100-fold lower IgE binding and reduced allergenic activity was generated. The TYKW mutant retained T-cell epitopes, as evident from its lymphoproliferative capacity but down-regulated pro-allergic IL-5 secretion. The TYKW mutant induced enhanced focusing of blocking IgG antibodies specifically toward the IgE epitope of the allergen. Anti-TYKW mutant polyclonal IgG antibodies competitively inhibited binding of IgE antibodies to Rhi o 1 up to 70% and suppressed allergen-mediated histamine release by 10-fold. In conclusion, this is a simple yet rational strategy based on epitope mapping data to develop a genetically modified hypoallergenic variant showing protective antibody response for immunotherapeutic applications.
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Affiliation(s)
- Gaurab Sircar
- From the Division of Plant Biology, Bose Institute (Main Campus), 93/1 Acharya Prafulla Chandra Road, Kolkata-700009, India
| | | | - Angira Dasgupta
- the Department of Chest Medicine, BR Singh Hospital and Centre for Medical Education and Research, Kolkata-700014, India
| | - Sudipto Saha
- the Bioinformatics Centre, Bose Institute (Centenary Building), P 1/12, C. I. T. Road, Scheme-VIIM, Kolkata-700054, India, and
| | - Swati Gupta Bhattacharya
- From the Division of Plant Biology, Bose Institute (Main Campus), 93/1 Acharya Prafulla Chandra Road, Kolkata-700009, India,
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9
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Barman A, Batiste B, Hamelberg D. Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins. J Chem Theory Comput 2015; 11:1854-63. [DOI: 10.1021/ct501036r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Arghya Barman
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Bruce Batiste
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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10
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García-González I, Mata L, Corzana F, Jiménez-Osés G, Avenoza A, Busto JH, Peregrina JM. Synthesis and Conformational Analysis of Hybrid α/β-Dipeptides IncorporatingS-Glycosyl-β2,2-Amino Acids. Chemistry 2014; 21:1156-68. [DOI: 10.1002/chem.201405318] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 12/27/2022]
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11
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Pandey AK, Thomas KM, Forbes C, Zondlo NJ. Tunable control of polyproline helix (PPII) structure via aromatic electronic effects: an electronic switch of polyproline helix. Biochemistry 2014; 53:5307-14. [PMID: 25075447 PMCID: PMC4139158 DOI: 10.1021/bi500696k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Indexed: 01/10/2023]
Abstract
Aromatic rings exhibit defined interactions via the unique aromatic π face. Aromatic amino acids interact favorably with proline residues via both the hydrophobic effect and aromatic-proline interactions, C-H/π interactions between the aromatic π face and proline ring C-H bonds. The canonical aromatic amino acids Trp, Tyr, and Phe strongly disfavor a polyproline helix (PPII) when they are present in proline-rich sequences because of the large populations of cis amide bonds induced by favorable aromatic-proline interactions (aromatic-cis-proline and proline-cis-proline-aromatic interactions). We demonstrate the ability to tune polyproline helix conformation and cis-trans isomerism in proline-rich sequences using aromatic electronic effects. Electron-rich aromatic residues strongly disfavor polyproline helix and exhibit large populations of cis amide bonds, while electron-poor aromatic residues exhibit small populations of cis amide bonds and favor polyproline helix. 4-Aminophenylalanine is a pH-dependent electronic switch of polyproline helix, with cis amide bonds favored as the electron-donating amine, but trans amide bonds and polyproline helix preferred as the electron-withdrawing ammonium. Peptides with block proline-aromatic PPXPPXPPXPP sequences exhibited electronically switchable pH-dependent structures. Electron-poor aromatic amino acids provide special capabilities to integrate aromatic residues into polyproline helices and to serve as the basis of aromatic electronic switches to change structure.
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Affiliation(s)
- Anil K. Pandey
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Krista M. Thomas
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christina
R. Forbes
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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