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Debnath S, Ghosh S, Kumar D, Vasudev PG, Satpati P, Chatterjee S. Effect of differential backbone di-substitution of gamma amino acid residues on the conformation and assembly of their Fmoc derivatives in solid and solution states. Chem Asian J 2022; 17:e202200356. [PMID: 35603989 DOI: 10.1002/asia.202200356] [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: 04/06/2022] [Revised: 05/23/2022] [Indexed: 11/11/2022]
Abstract
We studied the effect of variable backbone dimethyl-substitution of γ amino acid residues (γ 2,2 , γ 3,3 and γ 4,4 ) on the conformation and assembly, in crystals and solution of their Fmoc derivatives. Crystal structure of γ 2,2 and γ 4,4 derivatives showed distinct conformations (open/close for γ 2,2 /γ 4,4 ) that differed in torsion angles, hydrogen-bonding and most importantly the π-π Fmoc-stacking interactions (relatively favorable for γ 4,4 -close). Fmoc derivatives existed in an equilibrium between major-monomeric (low energy, non-hydrogen bonded) and minor-dimeric (high energy, hydrogen bonded) populations in solution. Rate of major/minor population exchange was dependent on the position of substitution, highest being for γ 4,4 derivative. In solution, assembly of Fmoc derivatives was solvent dependent, but it was independent of the position of geminal substitution. Crystallization was primarily governed by the stabilization of high-energy dimer by favorable π-π stacking involving Fmoc moieties. High free-energy of the dimers (γ 2,2 -close, γ 3,3 -open/close) offset favorable stacking interactions and hindered crystallization.
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Affiliation(s)
- Swapna Debnath
- Indian Institute of Technology Guwahati, Department of chemistry, INDIA
| | - Suvankar Ghosh
- Indian Institute of Technology Guwahati, Bioscience and Bioengineering, INDIA
| | - Dinesh Kumar
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Prema G Vasudev
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Priyadarshi Satpati
- Indian Institute of Technology Guwahati, Bioscience and BIoengineering, INDIA
| | - Sunanda Chatterjee
- Indian Institute of Technology Guwahati, CHEMISTRY, IIT GUWAHATI, 781039, GUWAHATI, INDIA
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Mahalakshmi R. Aromatic interactions in β-hairpin scaffold stability: A historical perspective. Arch Biochem Biophys 2018; 661:39-49. [PMID: 30395808 DOI: 10.1016/j.abb.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/21/2023]
Abstract
Non-covalent interactions between naturally occurring aromatic residues have been widely exploited as scaffold stabilizing agents in de novo designed peptides and in Nature - inspired structures. Our understanding of the factors driving aromatic interactions and their observed interaction geometries have advanced remarkably with improvements in conventional structural studies, availability of novel molecular methods and in silico studies, which have together provided atomistic information on aromatic interactions and interaction strengths. This review attempts to recapitulate the early advances in our understanding of aromatic interactions as stabilizing agents of peptide β-hairpins.
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Affiliation(s)
- Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, India.
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Brodaczewska N, Košťálová Z, Uhrín D. (3, 2)D 1H, 13C BIRD r,X-HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2018; 70:115-122. [PMID: 29327222 DOI: 10.1007/s10858-018-0163-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of 1H chemical shifts; larger dispersion of 13C chemical shifts is often used to reduce this overlap, while still providing the proton-proton correlation information e.g. in the form of a 2D 1H, 13C HSQC-TOCSY experiment. For this methodology to work, 13C chemical shift must be resolved. In case of 13C chemical shifts overlap, 1H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D 1H, 13C BIRDr,X-HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F1 dimension. The required high-resolution in the 13C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.
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Affiliation(s)
- Natalia Brodaczewska
- EastChem School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Rd, Edinburgh, EH9 3FJ, UK
| | - Zuzana Košťálová
- EastChem School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Rd, Edinburgh, EH9 3FJ, UK
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Dušan Uhrín
- EastChem School of Chemistry, University of Edinburgh Joseph Black Building, David Brewster Rd, Edinburgh, EH9 3FJ, UK.
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Makwana KM, Mahalakshmi R. Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β-Hairpins. Chemistry 2016; 22:4147-56. [DOI: 10.1002/chem.201504428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/15/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Kamlesh Madhusudan 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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Makwana KM, Mahalakshmi R. Nature of aryl-tyrosine interactions contribute to β-hairpin scaffold stability: NMR evidence for alternate ring geometry. Phys Chem Chem Phys 2016; 17:4220-30. [PMID: 25569770 DOI: 10.1039/c4cp04991h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The specific contribution of the acidic-aromatic β-sheet favouring amino acid tyrosine to the stability of short octapeptide β-hairpin structures is presented here. Solution NMR analysis in near-apolar environments suggests the energetically favourable mode of interaction to be T-shaped face-to-edge (FtE) and that a Trp-Tyr interacting pair is the most stabilizing. Alternate aryl geometries also exist in solution, which readily equilibrate between a preferred π···π conformation to an aromatic-amide conformation, without any change in the backbone structure. While the phenolic ring is readily accommodated at the "edge" of FtE aryl interactions, it exhibits an overall lowered contribution to scaffold stability in the "face" orientation. Such differential tyrosine interactions are key to its dual nature in proteins.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal-462023, India.
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Adhikari B, Singh C, Shah A, Lough AJ, Kraatz H. Amino Acid Chirality and Ferrocene Conformation Guided Self‐Assembly and Gelation of Ferrocene–Peptide Conjugates. Chemistry 2015; 21:11560-72. [DOI: 10.1002/chem.201501395] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Bimalendu Adhikari
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
| | - Charanpreet Singh
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
| | - Afzal Shah
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
- Present address: Department of Chemistry, Quaid‐i‐Azam University, 45320 (Pakistan)
| | - Alan J. Lough
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6 (Canada)
| | - Heinz‐Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6 (Canada)
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Makwana KM, Mahalakshmi R. NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp-Trp Interactions in Designed β-Hairpin Peptides: Terminal Switch from L to D Amino Acid as a Strategy for β-Hairpin Capping. J Phys Chem B 2015; 119:5376-85. [PMID: 25849307 DOI: 10.1021/acs.jpcb.5b00554] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Interaction among the side chains of aromatic amino acids is a well-known mechanism of protein and peptide structure stabilization, particularly in β sheets. Using short β-hairpin models bearing the sequence Ac-Leu-Xxx-Val-DPro-Gly-Leu-Trp-Val-NH2, we report the surprising observation of significant destabilization in aryl–tryptophan interactions, which results in poorly folded peptide populations accompanied by lowering of stability. We find that such destabilization arises from forced occupancy of the indole ring in the shielded Edge position, in T-shaped aryl geometries. We demonstrate that this destabilizing effect can be efficiently salvaged by replacing the N-terminal LLeu with DLeu, which causes an increase in the folded hairpin population, while retaining Trp in the Edge position. Our observation of unique cross strand NOEs and data from temperature-dependent NMR and CD measurements reveals the formation of a locally stabilized aliphatic–aromatic network, leading to an overall increase in ΔGF° by ∼ −0.6 to −1.2 kcal/mol. Our results suggest that a contextual evaluation of stabilization by tryptophan is necessary in β hairpins. Furthermore, we report for the first time that the use of D isomers of aliphatic amino acids at the terminus is stabilizing, which can serve as a new strategy for increasing β-hairpin stability.
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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, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India
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Chandrappa S, Madhusudana Reddy MB, Sonti R, Basuroy K, Raghothama S, Balaram P. Directing peptide conformation with centrally positioned pre-organized dipeptide segments: studies of a 12-residue helix and β-hairpin. Amino Acids 2014; 47:291-301. [DOI: 10.1007/s00726-014-1858-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/14/2014] [Indexed: 01/27/2023]
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Sonti R, Rao KNS, Chidanand S, Gowd KH, Raghothama S, Balaram P. Conformational Analysis of a 20-Membered Cyclic Peptide Disulfide fromConus virgowith a WPW Segment: Evidence for an Aromatic-Proline Sandwich. Chemistry 2014; 20:5075-86. [DOI: 10.1002/chem.201303687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Indexed: 11/06/2022]
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Makwana KM, Mahalakshmi R. Comparative analysis of cross strand aromatic–Phe interactions in designed peptide β-hairpins. Org Biomol Chem 2014; 12:2053-61. [DOI: 10.1039/c3ob42247j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Examination of the preferential interaction geometries of the aromatic amino acids Phe, Tyr and Trp with the benzyl ring of Phe in designed octapeptide hairpin scaffolds reveals stabilizing contributions of a Trp–Phe pair, even in amphipathic solvents.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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Welch WRW, Keiderling TA, Kubelka J. Structural analyses of experimental 13C edited amide I' IR and VCD for peptide β-sheet aggregates and fibrils using DFT-based spectral simulations. J Phys Chem B 2013; 117:10359-69. [PMID: 23924239 DOI: 10.1021/jp405613r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the preceding paper, computational models based on density functional theory (DFT) were presented to characterize the sensitivity of vibrational spectroscopic methods (IR, VCD, and Raman) to structural features of β-sheets. Isotopically edited amide I' IR for peptides labeled with (13)C in multiple different sites provides the most structurally distinct signatures of strand alignment, while VCD is sensitive to the sheet twist and intersheet stacking. In this report, we simulate the IR and VCD spectra for models approximating structures of four β-sheet forming peptides previously experimentally studied using these methods with (13)C isotopic editing. Various register alignments are tested. Agreement with experiment is evaluated based on frequency shifts of both the (12)C and (13)C IR amide I' signals, relative intensity patterns, and VCD spectra where available. While for the simulation of IR spectra canonical planar sheets provide a sufficient model system, for VCD simulation twisted, stacked sheets are required in order to reproduce strong couplet-like amide I' VCD. Effects of the solvent (water) and amino acid side chains are also tested by using a simplified, electrostatic solvent model and atomic partial charges for the side chains. Very good agreement with experimental spectra is obtained, particularly for the relative (12)C and (13)C band frequencies. All four peptide models are shown to be antiparallel as had previously been assumed. However, in some cases our simulations are consistent with different register alignment of strands than originally proposed.
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Affiliation(s)
- William R W Welch
- Department of Chemistry, University of Wyoming , Laramie, Wyoming 82071, United States
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The Role of Aromatic-Aromatic Interactions in Strand-Strand Stabilization of β-Sheets. J Mol Biol 2013; 425:3522-35. [PMID: 23810905 DOI: 10.1016/j.jmb.2013.06.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/12/2013] [Accepted: 06/18/2013] [Indexed: 11/21/2022]
Abstract
Aromatic-aromatic interactions have long been believed to play key roles in protein structure, folding, and binding functions. However, we still lack full understanding of the contributions of aromatic-aromatic interactions to protein stability and the timing of their formation during folding. Here, using an aromatic ladder in the β-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), as a case study, we find that aromatic π stacking plays a greater role in the Phe65-Phe71 cross-strand pair, while in another pair, Phe50-Phe65, hydrophobic interactions are dominant. The Phe65-Phe71 pair spans β-strands 4 and 5 in the β-barrel, which lack interstrand hydrogen bonding, and we speculate that it compensates energetically for the absence of strand-strand backbone interactions. Using perturbation analysis, we find that both aromatic-aromatic pairs form after the transition state for folding of CRABP1, thus playing a role in the final stabilization of the β-sheet rather than in its nucleation as had been earlier proposed. The aromatic interaction between strands 4 and 5 in CRABP1 is highly conserved in the intracellular lipid-binding protein (iLBP) family, and several lines of evidence combine to support a model wherein it acts to maintain barrel structure while allowing the dynamic opening that is necessary for ligand entry. Lastly, we carried out a bioinformatics analysis and found 51 examples of aromatic-aromatic interactions across non-hydrogen-bonded β-strands outside the iLBPs, arguing for the generality of the role played by this structural motif.
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Sonti R, Gopi HN, Muddegowda U, Ragothama S, Balaram P. A Designed Three-Stranded β-Sheet in an α/β Hybrid Peptide. Chemistry 2013; 19:5955-65. [DOI: 10.1002/chem.201204327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Indexed: 01/25/2023]
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