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Yadav S, Bharti S, Srivastava P, Mathur P. PepEngine: A Manually Curated Structural Database of Peptides Containing α, β- Dehydrophenylalanine (ΔPhe) and α-Amino Isobutyric Acid (Aib). Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10362-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Misra R, Rudnick-Glick S, Adler-Abramovich L. From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non-Canonical Amino Acids. Macromol Biosci 2021; 21:e2100090. [PMID: 34142442 DOI: 10.1002/mabi.202100090] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/06/2021] [Indexed: 12/27/2022]
Abstract
The engineering of biological molecules is the fundamental concept behind the design of complex materials with desirable functions. Over the last few decades, peptides and proteins have emerged as useful building blocks for well-defined nanostructures with controlled size and dimensions. Short peptides in particular have received much attention due to their inherent biocompatibility, lower synthetic cost, and ease of tunability. In addition to the diverse self-assembling properties of short peptides comprising coded amino acids and their emerging applications in nanotechnology, there is now growing interest in the properties of peptides composed of non-canonical amino acids. Such non-natural oligomers have been shown in recent years to form well-defined secondary structures similar to natural proteins, with the ability to self-assemble to generate a wide variety of nanostructures with excellent biostability. This review describes recent events in the development of supramolecular assemblies of peptides composed completely of non-coded amino acids and their hybrid analogues. Special attention is paid to understanding the supramolecular assemblies at the atomic level and to considering their potential applications in nanotechnology.
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Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Safra Rudnick-Glick
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
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3
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Goyal R, Jerath G, Akhil R, Chandrasekharan A, Puppala ER, Ponneganti S, Sarma A, Naidu VGM, Santhoshkumar TR, Ramakrishnan V. Geometry encoded functional programming of tumor homing peptides for targeted drug delivery. J Control Release 2021; 333:16-27. [PMID: 33722612 DOI: 10.1016/j.jconrel.2021.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/24/2021] [Accepted: 03/07/2021] [Indexed: 01/10/2023]
Abstract
Poly-peptide molecules have shown promising applications in drug delivery and tumor targeting. A series of tumor homing peptides were designed by exhaustively sampling low energy geometrical basins of amino acids at specific sites of a peptide molecule to induce a conformational lock. This peptide library was pruned to a limited set of eight molecules, employing electrostatic interactions, docking, and molecular dynamics simulations. These designed and optimized peptides were synthesized and tested on various cell lines, including breast cancer (MDA-MB-231), cervical cancer (HeLa), osteosarcoma (U2-OS), and non-cancerous mammary epithelial cells (MCF-10A) using confocal microscopy and flow cytometry. Peptides show differential uptake in cancerous MDA-MB-231, HeLa, U2-OS, and non-cancerous MCF-10A cells. Confocal imaging verified their ability to penetrate even in 3D tumorospheres of MDA-MB-231 cells. Further, experiments of mitochondrial membrane potential depolarization and Caspase-3 activation confirmed that their cytotoxic effects are by apoptosis. Homing ability of the designed peptides in in vivo system and fluorescence imaging with clinical samples of human origin have further confirmed that the in vitro studies are qualitatively identical and quantitatively comparable in their ability to selectively recognize tumor cells. Overall, we present a roadmap for the functional programming of peptide-based homing and penetrating molecules that can perform selective tumor targeting.
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Affiliation(s)
- Ruchika Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Gaurav Jerath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - R Akhil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Aneesh Chandrasekharan
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
| | - Eswara Rao Puppala
- National Institute of Pharmaceutical Education and Research Guwahati, Guwahati 781101, Assam, India
| | - Srikanth Ponneganti
- National Institute of Pharmaceutical Education and Research Guwahati, Guwahati 781101, Assam, India
| | - Anupam Sarma
- Dr. Bhubaneswar Borooah Cancer Institute, Tata Memorial Centre (Mumbai), Guwahati 781016, Assam, India
| | - V G M Naidu
- National Institute of Pharmaceutical Education and Research Guwahati, Guwahati 781101, Assam, India
| | - T R Santhoshkumar
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India.
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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4
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Ben Haj Salah K, Das S, Ruiz N, Andreu V, Martinez J, Wenger E, Amblard M, Didierjean C, Legrand B, Inguimbert N. How are 1,2,3-triazoles accommodated in helical secondary structures? Org Biomol Chem 2019; 16:3576-3583. [PMID: 29693098 DOI: 10.1039/c8ob00686e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
1,4-Disubstituted-1,2,3-triazole (Tz) is widely used in peptides as a trans-amide bond mimic, despite having hazardous effects on the native peptide activity. The impact of amide bond substitution by Tz on peptide secondary structures is scarcely documented. We performed a Tz scan, by systematically replacing peptide bonds following the Aib residues with Tz on two model peptaibols: alamethicin F50/5 and bergofungin D, which adopt stable α- and 310 helices, respectively. We observed that the Tz insertion, whatever its position in the peptide sequences, abolished their antimicrobial activity. The structural consequences of this insertion were further investigated using CD, NMR and X-ray diffraction. Importantly, five crystal structures that were incorporated with Tz were solved, showing various degrees of alteration of the helical structures, from minor structural perturbation of the helix to partial disorder. Together, these results showed that Tz insertions impair helical secondary structures.
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Affiliation(s)
- Khoubaib Ben Haj Salah
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS, Université de Perpignan Via Domitia, Laboratoire d'Excellence «CORAIL». Bâtiment T, 58 avenue P. Alduy, 66860 Perpignan, France.
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5
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Kalita M, Archana A, Dimri A, Vasudev PG, Ramapanicker R. Synthesis of peptides containing oxo amino acids and their crystallographic analysis. J Pept Sci 2019; 25:e3148. [PMID: 30697868 DOI: 10.1002/psc.3148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/21/2018] [Accepted: 01/04/2019] [Indexed: 01/04/2023]
Abstract
An isolated uncharged hydrogen bond acceptor such as the carbonyl functionality of an aldehyde or a keto group is absent in natural amino acids. Although glutamine and asparagine are known to hydrogen bond through the amide carbonyl group in their side chains, they also possess the amide NH2 group, which can act as a hydrogen bond donor. This makes the structural study of peptides containing an oxo residue, with an isolated carbonyl group in the side chain, interesting. Here, we report the synthesis of δ- and ε-oxo amino acids and their incorporation into oligopeptides as the N-terminal residue. The resultant oxo peptides were extensively studied using X-ray crystallography to understand the interactions offered by the oxo group in peptide crystals. We find that the oxo groups are capable of providing additional hydrogen bonding opportunities to the peptides, resulting in increased intermolecular interactions in crystals. The study thus offers avenues for the utilization of oxo residues to introduce intermolecular interactions in synthetic peptides.
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Affiliation(s)
- Mrinal Kalita
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Archana Archana
- Metabolic and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Astha Dimri
- Metabolic and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Prema G Vasudev
- Metabolic and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Ramesh Ramapanicker
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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6
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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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7
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Burra G, Thakur AK. Inhibition of polyglutamine aggregation by SIMILAR huntingtin N-terminal sequences: Prospective molecules for preclinical evaluation in Huntington's disease. Biopolymers 2017; 108. [DOI: 10.1002/bip.23021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 04/03/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Gunasekhar Burra
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
| | - Ashwani Kumar Thakur
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
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Ruckthong L, Peacock AFA, Pascoe CE, Hemmingsen L, Stuckey JA, Pecoraro VL. d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils. Chemistry 2017; 23:8232-8243. [PMID: 28384393 DOI: 10.1002/chem.201700660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Indexed: 12/31/2022]
Abstract
Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of ZnII Cl(CSL16D C)32- to the published structure of ZnII (H2 O)(GRAND-CSL12AL16L C)3- . Moreover, spectroscopic analysis indicates that the CdII geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate CdII ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: Department Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, ThungKhru, Bangkok, 10140, Thailand
| | - Anna F A Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Cherilyn E Pascoe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
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9
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Vasudev PG, Aravinda S, Shamala N. Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel β-sheet in crystals. J Pept Sci 2016; 22:166-73. [PMID: 26856690 DOI: 10.1002/psc.2854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/03/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
The crystal structure of a tripeptide Boc-Leu-Val-Ac12 c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac12 c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C(α,α) -dialkylated residue Ac12 c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel β-sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac12 c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel β-sheet in crystals, twisted or helical β-sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted β-sheet assembly in crystals.
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Affiliation(s)
- Prema G Vasudev
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
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Aravinda S, Raghavender US, Rai R, Harini VV, Shamala N, Balaram P. Analysis of designed β-hairpin peptides: molecular conformation and packing in crystals. Org Biomol Chem 2013; 11:4220-31. [DOI: 10.1039/c3ob25777k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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11
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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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12
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Sonti R, Rai R, Ragothama S, Balaram P. NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded β-Sheet Peptide. J Phys Chem B 2012; 116:14207-15. [DOI: 10.1021/jp3034769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rajesh Sonti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
- NMR Research Centre, Indian Institute of Science, Bangalore, India 560012
| | - Rajkishor Rai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | | | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
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13
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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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14
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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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15
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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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16
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Chandrappa S, Aravinda S, Raghothama S, Sonti R, Rai R, Harini VV, Shamala N, Balaram P. Helix and hairpin nucleation in short peptides using centrally positioned conformationally constrained dipeptide segments. Org Biomol Chem 2012; 10:2815-23. [DOI: 10.1039/c2ob06817f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Gebreslasie HG, Jacobsen Ø, Görbitz CH. N-(tert-butoxycarbonyl)-α-aminoisobutyryl-α-aminoisobutyric acid methyl ester: two polymorphic forms in the space group P2(1)/n. Acta Crystallogr C 2011; 67:o283-7. [PMID: 21817793 DOI: 10.1107/s0108270111024322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 06/21/2011] [Indexed: 11/11/2022] Open
Abstract
The title compound (systematic name: methyl 2-{2-[(tert-butoxycarbonyl)amino]-2-methylpropanamido}-2-methylpropanoate), C(14)H(26)N(2)O(5), (I), crystallizes in the monoclinic space group P2(1)/n in two polymorphic forms, each with one molecule in the asymmetric unit. The molecular conformation is essentially the same in both polymorphs, with the α-aminoisobutyric acid (Aib) residues adopting ϕ and ψ values characteristic of α-helical and mixed 3(10)- and α-helical conformations. The helical handedness of the C-terminal residue (Aib2) is opposite to that of the N-terminal residue (Aib1). In contrast to (I), the closely related peptide Boc-Aib-Aib-OBn (Boc is tert-butoxycarbonyl and Bn is benzyl) adopts an α(L)-P(II) backbone conformation (or the mirror image conformation). Compound (I) forms hydrogen-bonded parallel β-sheet-like tapes, with the carbonyl groups of Aib1 and Aib2 acting as hydrogen-bond acceptors. This seems to represent an unusual packing for a protected dipeptide containing at least one α,α-disubstituted residue.
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18
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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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19
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Noguchi S. Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B. Biopolymers 2010; 93:1003-10. [PMID: 20623666 DOI: 10.1002/bip.21514] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Under physiological conditions, the deamidation and isomerization of asparagine to isoaspartate (isoAsp) proceeds nonenzymatically via succinimide. Although a large number of proteins have been reported to contain isoAsp, information concerning the three-dimensional structure of proteins containing isoaspartate is still limited. We have crystallized isoAsp containing Ustilago sphaerogena ribonuclease U2B, and determined the crystal structure at 1.32 Å resolution. The structure revealed that the formation of isoAsp32 induces a single turn unfolding of the α-helix from Asp29 to Asp34, and the region from Asp29 to Arg35 forms a U-shaped loop structure. The electron density map shows that isoAsp32 retained the L-configuration at the C(α) atom. IsoAsp32 is in gauche conformation about a C(α)--C(β) bond, and the polypeptide chain bends by ∼90° at isoAsp32. IsoAsp32 protrudes from the surface of the protein, and the abnormal β-peptide bond in the main-chain and α-carboxylate in the side-chain is fully exposed. The structure suggests that the deamidation of the Asn and the isoAsp formation in proteins could confer immunogenicity.
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Affiliation(s)
- Shuji Noguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan.
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20
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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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21
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Wang D, Friedmann M, Gattin Z, Jaun B, van Gunsteren W. The Propensity of α-Aminoisobutyric Acid (=2-Methylalanine; Aib) to Induce Helical Secondary Structure in an α-Heptapeptide: A Computational Study. Helv Chim Acta 2010. [DOI: 10.1002/hlca.200900420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Raghavender US, Aravinda S, Rai R, Shamala N, Balaram P. Peptide hairpin nucleation with the obligatory Type I' beta-turn Aib-DPro segment. Org Biomol Chem 2010; 8:3133-5. [PMID: 20532330 DOI: 10.1039/c004577m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The alpha-aminoisobutyric acid-D-proline (Aib-(D)Pro) dipeptide is an obligatory Type I' beta-turn forming segment that nucleates hairpin formation.
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23
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Wu L, McElheny D, Takekiyo T, Keiderling TA. Geometry and Efficacy of Cross-Strand Trp/Trp, Trp/Tyr, and Tyr/Tyr Aromatic Interaction in a β-Hairpin Peptide. Biochemistry 2010; 49:4705-14. [DOI: 10.1021/bi100491s] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ling Wu
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
| | - Takahiro Takekiyo
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
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Kantharaju, Raghothama S, Aravinda S, Shamala N, Balaram P. Helical conformations of hexapeptides containing N-terminus diproline segments. Biopolymers 2010; 94:360-70. [DOI: 10.1002/bip.21395] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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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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Peacock A, Stuckey J, Pecoraro V. Switching the Chirality of the Metal Environment Alters the Coordination Mode in Designed Peptides. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Punitha V, Raman SS, Parthasarathi R, Subramanian V, Rao JR, Nair BU, Ramasami T. Molecular dynamics investigations on the effect of D amino acid substitution in a triple-helix structure and the stability of collagen. J Phys Chem B 2009; 113:8983-92. [PMID: 19518060 DOI: 10.1021/jp808690m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies on the structure and stability of peptides and proteins during l-->d configurational change are certainly important for the designing of peptides with new biological activity and protein engineering. The l-->d amino acid (d AA) changes have been observed in aged proteins such as collagen. Hence, in this study, an attempt has been made to explore the effect of the replacement of l amino acid (l AA) in the model collagen-like peptides with d AA and the origin of structural stability (destability) has been traced using the molecular dynamics (MD) method employing the AMBER force field. Our results reveal that the substitution of d AA produces a large local disruption to the triple-helical structure. Formation of a kink (bulge) at the site of substitution is observed from the detailed analysis of MD trajectory. However, this local perturbation of kinked helix changes the direction of the helices and affects the relative orientation of the respective AA residues for helix-helix interaction, enough to affect the overall stability of the model collagen-like peptide. The destabilization energy per d Ala substitution is 7.87 kcal/mol, which is similar to the value for the Gly-->Ala mutation in collagen. Since the Gly-->Ala mutation is involved in genetic disorders such as osteogenesis imperfecta (OI), the l-->d configurational change may produce a similar effect on collagen.
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Affiliation(s)
- V Punitha
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific Industrial Research, Sardar Patel Road, Adyar, Chennai 600 020, India
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28
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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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29
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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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30
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Petrovic AG, Polavarapu PL, Mahalakshmi R, Balaram P. Characterization of folded conformations in a tetrapeptide containing two tryptophan residues by vibrational circular dichroism. Chirality 2009; 21 Suppl 1:E76-85. [DOI: 10.1002/chir.20779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Vasudev PG, Chatterjee S, Ramakrishnan C, Shamala N, Balaram P. Conformational choices for the stereochemically constrained γ-amino acid residue gabapentin: Theoretical studies and correlation with experimental results. Biopolymers 2009; 92:426-35. [DOI: 10.1002/bip.21214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Peacock AFA, Stuckey JA, Pecoraro VL. Switching the chirality of the metal environment alters the coordination mode in designed peptides. Angew Chem Int Ed Engl 2009; 48:7371-4. [PMID: 19579245 PMCID: PMC3014729 DOI: 10.1002/anie.200902166] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The effects of switching the chirality of a single layer of amino acids in a three stranded coiled coil has been investigated. X-ray crystallography reveals that this modification is well tolerated and does not alter the designed structure. In contrast, spectroscopic studies of cadmium binding to both the L- and D- enantiomers of the penicillamine, provide evidence that this switch dramatically alters the metal binding capability, the resulting coordination environment and the position of binding.
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Affiliation(s)
- Anna F. A. Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Jeanne A. Stuckey
- Life Sciences Institute, University and Michigan, Ann Arbor, MI 48109 (USA)
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Peacock AFA, Hemmingsen L, Pecoraro VL. Using diastereopeptides to control metal ion coordination in proteins. Proc Natl Acad Sci U S A 2008; 105:16566-71. [PMID: 18940928 PMCID: PMC2575460 DOI: 10.1073/pnas.0806792105] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Indexed: 11/18/2022] Open
Abstract
Here, we report a previously undescribed approach for controlling metal ion coordination geometry in biomolecules by reorientating amino acid side chains through substitution of L- to D-amino acids. These diastereopeptides allow us to manipulate the spatial orientation of amino acid side chains to alter the sterics of metal binding pockets. We have used this approach to design the de novo metallopeptide, Cd(TRIL12L(D)L16C)(3)(-), which is an example of Cd(II) bound to 3 L-Cys as exclusively trigonal CdS(3), as characterized by a combination of (113)Cd NMR and (111m)Cd PAC spectroscopy. We subsequently show that the physical properties of such a site, such as the high pK(a2) for Cd(II) binding of 15.1, is due to the nature of the coordination number and not the ligating group. Further more this approach allowed for the design of a construct, GRANDL12L(D)L16CL26AL30C, capable of independently binding 2 equivalents of Cd(II) to 2 very similar Cys sites as exclusively 3- and 4-, CdS(3) and CdS(3)O, respectively. Demonstrating that we are capable of controlling the Cd(II) coordination number in these 2 sites solely by varying the nature of a noncoordinating second coordination sphere amino acid, with D-leucine and L-alanine resulting in exclusively 3- and 4-coordinate structures, respectively. Cd(II) was found to selectively bind to the 4-coordinate CdS(3)O site, demonstrating that a protein can be designed that displays metal-binding selectivity based solely on coordination number control and not on the chemical identity of coordinating ligands.
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Affiliation(s)
- Anna F. A. Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055; and
| | - Lars Hemmingsen
- Department of Natural Sciences, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055; and
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Vasudev PG, Rai R, Shamala N, Balaram P. Conformations of beta-amino acid residues in peptides: X-ray diffraction studies of peptides containing the achiral residue 1-aminocyclohexaneacetic acid, beta3,3Ac6c. Biopolymers 2008; 90:138-50. [PMID: 18273891 DOI: 10.1002/bip.20957] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The conformational preferences of the 3,3-disubstituted beta-amino acid residue, 1-aminocyclohexaneacetic acid (beta3,3Ac6c) have been investigated by determining the crystal structures of the parent amino acid, the hydrochloride derivative, 10 protected derivatives and di and tripeptides. The symmetrical cyclohexyl substituent at the beta-position restricts the values of the torsion angles phi (N--C(beta)) and theta (C(beta)--C(alpha)) to approximately gauche values (+/-60 degrees ). Relatively few intramolecularly hydrogen bonded conformations are observed. In the dipeptide Boc-beta(3,3)Ac6c-beta(3,3)Ac6c-NHMe a C6 hydrogen bond is observed. In Piv-Pro-beta(3,3)Ac6c-NHMe a C11 hydrogen bonded hybrid alphabeta turn is characterized. In a majority of cases the amino group occupies the axial position in the cyclohexane ring. The conformations observed are compared with crystallographically observed structures for other beta-residues, including beta(2,2)Ac6c.
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Affiliation(s)
- Prema G Vasudev
- Department of Physics, Indian Institute of Science, Bangalore 560 012, India
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35
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Chatterjee B, Saha I, Raghothama S, Aravinda S, Rai R, Shamala N, Balaram P. Designed peptides with homochiral and heterochiral diproline templates as conformational constraints. Chemistry 2008; 14:6192-204. [PMID: 18491347 DOI: 10.1002/chem.200702029] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).
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Affiliation(s)
- Bhaswati Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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36
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Chatterjee S, Vasudev PG, Ananda K, Raghothama S, Shamala N, Balaram P. Multiple Conformational States in Crystals and in Solution in αγ Hybrid Peptides. Fragility of the C12 Helix in Short Sequences. J Org Chem 2008; 73:6595-606. [DOI: 10.1021/jo8009819] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Kuppanna Ananda
- 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
| | - 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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37
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Aravinda S, Shamala N, Balaram P. Aib Residues in Peptaibiotics and Synthetic Sequences: Analysis of Nonhelical Conformations. Chem Biodivers 2008; 5:1238-62. [PMID: 18649312 DOI: 10.1002/cbdv.200890112] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Vasudev PG, Shamala N, Balaram P. Nucleation, growth, and form in crystals of peptide helices. J Phys Chem B 2008; 112:1308-14. [PMID: 18173258 DOI: 10.1021/jp077231d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A model for the nucleation of crystallization in peptide helices is presented. The crystal structures of four polymorphic forms of a hydrophobic helical decapeptide Boc-Leu-Aib-Phe-Phe-Leu-Aib-Ala-Ala-Leu-Aib-OMe (I) exemplify alternative packing modes in cylindrical molecules. Three crystal forms of peptide I are monoclinic P2(1), while one is orthorhombic P22121. The five different helical molecules characterized have very similar backbone conformations over much of the peptide length. A survey of 117 helical peptide structures with a length >/=8 residues reveals a preponderance of the triclinic (P1), monoclinic (P2(1)), and orthorhombic (P2(1)2(1)2(1)) crystal forms. Models for the formation of critical nuclei are based on helix association driven by solvophobic forces, resulting in the formation of raftlike structures. Raft association can be further driven by the imperative of minimizing solvent accessible surface area with the formation of blocks, which can be subsequently fitted in Lego set fashion by multiple hydrogen bond interactions in the head-to-tail region. This model provides a rationalization for observed crystal formation based on a postulated structure for an embryonic nucleus, which is determined by aggregation patterns and unconstrained by the dictates of symmetry.
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Affiliation(s)
- Prema G Vasudev
- Department of Physics, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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39
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Hegde RP, Aravinda S, Rai R, Kaul R, Vijayalakshmi S, Rao RB, Shamala N, Balaram P. Conformation of di-n-propylglycine residues (Dpg) in peptides: crystal structures of a type I′β-turn forming tetrapeptide and an α-helical tetradecapeptide. J Pept Sci 2007; 14:648-59. [DOI: 10.1002/psc.962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Chatterjee S, Roy RS, Balaram P. Expanding the polypeptide backbone: hydrogen-bonded conformations in hybrid polypeptides containing the higher homologues of alpha-amino acids. J R Soc Interface 2007; 4:587-606. [PMID: 17251160 PMCID: PMC2373382 DOI: 10.1098/rsif.2006.0203] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2006] [Accepted: 12/01/2006] [Indexed: 11/12/2022] Open
Abstract
Half a century has passed since the hydrogen-bonded secondary structures of polypeptides and proteins were first recognized. An extraordinary wealth of conformational information is now available on peptides and proteins, which are formed of alpha-amino acid residues. More recently, the discovery of well-folded structures in oligopeptides containing beta-amino acids has focused a great deal of current interest on the conformational properties of peptides constructed from higher homologues (omega) of alpha-amino acids. This review examines the nature of intramolecularly hydrogen-bonded conformations of hybrid peptides formed by amino acid residues, with a varying number of backbone atoms. The beta-turn, a ubiquitous structural feature formed by two residue (alphaalpha) segments in proteins and peptides, is stabilized by a 10-atom (C10) intramolecular 4-->1 hydrogen bond. Hybrid turns may be classified by comparison with their alphaalpha counterparts. The available crystallographic information on hydrogen-bonded hybrid turns is surveyed in this review. Several recent examples demonstrate that individual omega-amino acid residues and hybrid dipeptide segments may be incorporated into the regular structures of alpha-peptides. Examples of both peptide helices and hairpins are presented. The present review explores the relationships between folded conformations in hybrid sequences and their counterparts in all alpha-residue sequences. The use of stereochemically constrained omega-residues promises to expand the range of peptide design strategies to include omega-amino acids. This approach is exemplified by well-folded structures like the C12 (alphagamma) and C14 (gammagamma) helices formed in short peptides containing multiply substituted gamma-residues. The achiral gamma-residue gabapentin is a readily accessible building block in the design of peptides containing gamma-amino acids. The construction of globular polypeptide structures using diverse hybrid sequences appears to be a realistic possibility.
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Affiliation(s)
| | | | - P Balaram
- Molecular Biophysics Unit, Indian Institute of ScienceBangalore 560012, India
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41
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Rai R, Vasudev PG, Ananda K, Raghothama S, Shamala N, Karle IL, Balaram P. Hybrid Peptides: Expanding the β Turn in Peptide Hairpins by the Insertion of β-, γ-, and δ-Residues. Chemistry 2007; 13:5917-26. [PMID: 17393543 DOI: 10.1002/chem.200601562] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The beta turn segment in designed peptide hairpins has been expanded by the insertion of beta-, gamma- and delta-amino acids at the i+2 position. The model octapeptides Boc-Leu-Phe-Val-DPro-Ac6c-Leu-Phe-Val-OMe (1), Boc-Leu-Phe-Val-DPro-beta3-Ac6c-Leu-Phe-Val-OMe (2), and Boc-Leu-Phe-Val-DPro-Gpn-Leu-Phe-Val-OMe (3) have been shown to adopt beta hairpin conformations in methanol by the observation of key diagnostic nuclear Overhauser effects. Boc-Leu-Val-Val-DPro-delta-Ava-Leu-Val-Val-OMe (4) adopts a beta hairpin conformation in crystals; this is stabilized by three cross-strand hydrogen bonds as demonstrated by X-ray diffraction. The canonical C10 turn in an alpha-alpha segment is expanded to C11, C12, and C13 turns in alpha-beta, alpha-gamma, and alpha-delta segments, respectively. The crystal structures of Piv-LPro-beta3-Ac6c-NHMe (5) and Boc-Ac6c-Gpn-Ac6c-OMe (6) reveal intramolecularly hydrogen-bonded C11 and C12 conformations, respectively. Computer modeling of octapeptide sequences that contain centrally positioned hybrid-turn segments, by using turn parameters derived from the structures of peptides 5 and 6, establishes the stereochemical acceptability of the beta hairpins in the cases of peptides 2 and 3. Accommodation of omega-amino acids into the turn segments is achieved by the adoption of gauche conformations around the backbone C--C bonds.
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Affiliation(s)
- Rajkishor Rai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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42
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Nanda V, Andrianarijaona A, Narayanan C. The role of protein homochirality in shaping the energy landscape of folding. Protein Sci 2007; 16:1667-75. [PMID: 17600146 PMCID: PMC2203351 DOI: 10.1110/ps.072867007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as alpha-helices and beta-sheets. However, many examples exist in nature where novel polypeptide topologies use both l- and d-amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and all-atom polypeptide chains. We formulate a rectangular lattice chain model in both two and three dimensions, where monomers are chiral, having the effect of restricting local conformation. Syndiotactic chains with alternating chirality of adjacent monomers have a very large ensemble of accessible conformations characterized predominantly by extended structures. Isotactic chains on the other hand, have far fewer possible conformations and a significant fraction of these are compact. Syndiotactic chains are often unable to access maximally compact states available to their isotactic counterparts of the same length. Similar features are observed in all-atom models of isotactic versus syndiotactic polyalanine. Our results suggest that protein isotacticity has evolved to increase the enthalpy of chain collapse by facilitating compact helical states and to reduce the entropic cost of folding by restricting the size of the unfolded ensemble of competing states.
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Affiliation(s)
- Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA.
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43
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Rai R, Raghothama S, Sridharan R, Balaram P. Tuning the beta-turn segment in designed peptide beta-hairpins: construction of a stable type I' beta-turn nucleus and hairpin-helix transition promoting segments. Biopolymers 2007; 88:350-61. [PMID: 17154289 DOI: 10.1002/bip.20649] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Designed octapeptides Boc-Leu-Val-Val-Aib-(D)Xxx-Leu-Val-Val-OMe ((D)Xxx = (D)Ala, 3a;(D)Val, 3c and (D)Pro, 5a) and Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (3b) have been investigated to construct models of a stable type I' beta-turn nucleated hairpin and to generate systems for investigating helix-hairpin conformational transitions. Peptide 5a, which contains a central Aib-(D)Pro segment, is shown to adopt a stable type I' beta-turn nucleated hairpin structure, stabilized by four cross-strand hydrogen bonds. The stability of the structure in diverse solvents is established by the observation of all diagnostic NOEs expected in a beta-hairpin conformation. Replacement of (D)Pro5 by (D)Ala/(D)Val (3a-c) results in sequences that form beta-hairpins in hydrogen bonding solvents like CD(3)OH and DMSO-d(6). However, in CDCl(3) evidence for population of helical conformations is obtained. Peptide 6b (Boc-Leu-Phe-Val-Aib-Aib-Leu-Phe-Val-OMe), which contains a centrally positioned Aib-Aib segment, provides a clear example of a system, which exhibits a helical conformation in CDCl(3) and a significant population of both helices and hairpins in CD(3)OH and DMSO-d(6). The coexistence of multiple conformations is established by the simultaneous observation of diagnostic NOEs. Control over stereochemistry of the central beta-turn permits generation of models for robust beta-hairpins and also for the construction of systems that may be used to probe helix-hairpin conformational transitions.
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Affiliation(s)
- Rajkishor Rai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Vasudev PG, Ananda K, Chatterjee S, Aravinda S, Shamala N, Balaram P. Hybrid Peptide Design. Hydrogen Bonded Conformations in Peptides Containing the Stereochemically Constrained γ-Amino Acid Residue, Gabapentin. J Am Chem Soc 2007; 129:4039-48. [PMID: 17348653 DOI: 10.1021/ja068910p] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The crystal structure of 12 peptides containing the conformationally constrained 1-(aminomethyl)cyclohexaneacetic acid, gabapentin (Gpn), are reported. In all the 39 Gpn residues conformationally characterized so far, the torsion angles about the Calpha-Cbeta and Cbeta-Cgamma bonds are restricted to the gauche conformation (+/-60 degrees ). The Gpn residue is constrained to adopt folded conformations resulting in the formation of intramolecularly hydrogen-bonded structures even in short peptides. The peptides Boc-Ac6c-Gpn-OMe 1 and Boc-Gpn-Aib-Gpn-Aib-OMe 2 provide examples of C7 conformation; peptides Boc-Gpn-Aib-OH 3, Boc-Ac6c-Gpn-OH 4, Boc-Val-Pro-Gpn-OH 5, Piv-Pro-Gpn-Val-OMe 6, and Boc-Gpn-Gpn-Leu-OMe 7 provide examples of C9 conformation; peptide Boc-Ala-Aib-Gpn-Aib-Ala-OMe 8 provides an example of C12 conformation and peptides Boc-betaLeu-Gpn-Val-OMe 9 and Boc-betaPhe-Gpn-Phe-OMe 10 provide examples of C13 conformation. Gpn peptides provide examples of backbone expanded mimetics for canonical alpha-peptide turns like the gamma (C7) and the beta (C10) turns. The hybrid betagamma sequences provide an example of a mimetic of the C13 alpha-turn formed by three contiguous alpha-amino acid residues. Two examples of folded tripeptide structures, Boc-Gpn-betaPhe-Leu-OMe 11 and Boc-Aib-Gpn-betaPhg-NHMe 12, lacking internal hydrogen bonds are also presented. An analysis of available Gpn residue conformations provides the basis for future design of folded hybrid peptides.
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Affiliation(s)
- Prema G Vasudev
- Department of Physics, Indian Institute of Science, Bangalore-560012, India
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Nanda V, DeGrado WF. Computational design of heterochiral peptides against a helical target. J Am Chem Soc 2006; 128:809-16. [PMID: 16417370 DOI: 10.1021/ja054452t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polypeptides incorporating D-amino acids occasionally occur in nature and are an important class of pharmaceutical molecules. With the use of heterochiral Monte Carlo (HCMC), a method inspired by the de novo design of proteins, we develop peptide scaffolds for interacting with a molecular target, a left-handed alpha-helix. The HCMC approach concurrently seeks to optimize a peptide sequence, its internal conformation, and its docked conformation with a target surface. Several major classes of interactions are observed: (1) homochiral interactions between two alphaL helices, (2) heterochiral interactions between an alphaL and an alphaR helix, and (3) heterochiral interactions between the alphaL target and novel nonhelical structures. We explore the application of HCMC to simulating the preferential enantioselectivity of heterochiral complexes. Implications for biomimetic design in molecular recognition are discussed.
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Affiliation(s)
- Vikas Nanda
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA.
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Roy RS, Gopi HN, Raghothama S, Gilardi RD, Karle IL, Balaram P. Peptide hairpins with strand segments containing alpha- and beta-amino acid residues: cross-strand aromatic interactions of facing Phe residues. Biopolymers 2006; 80:787-99. [PMID: 15895435 PMCID: PMC1380308 DOI: 10.1002/bip.20294] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The incporation of beta-amino acid residues into the strand segments of designed beta-hairpin leads to the formation of polar sheets, since in the case of beta-peptide strands, all adjacent carbonyl groups point in one direction and the amide groups orient in the opposite direction. The conformational analysis of two designed peptide hairpins composed of alpha/beta-hybrid segments are described: Boc-Leu-betaPhe-Val-(D)-Pro-Gly-Leu-betaPhe-Val-OMe (1) and Boc-betaLeu-Phe-betaVal-D-Pro-Gly-betaLeu-Phe-betaVal-OMe (2). A 500-MHz 1H-NMR (nuclear magnetic resonance) analysis in methanol supports a significant population of hairpin conformations in both peptides. Diagnostic nuclear Overhauser effects (NOEs) are observed in both cases. X-ray diffraction studies on single crystals of peptide 1 reveal a beta-hairpin conformation in both the molecules, which constitute the crystallographic asymmetric unit. Three cross-strand hydrogen bonds and a nucleating type II' beta-turn at the D-Pro-Gly segment are observed in the two independent molecules. In peptide 1, the betaPhe residues at positions 2 and 7 occur at the nonhydrogen-bonding position, with the benzyl side chains pointing on opposite faces of the beta-sheet. The observed aromatic centroid-to-centroid distances are 8.92 A (molecule A) and 8.94 A (molecule B). In peptide 2, the aromatic rings must occupy facing positions in antiparallel strands, in the NMR-derived structure. Peptide 1 yields a normal "hairpin-like" CD spectrum in methanol with a minimum at 224 nm. The CD spectrum of peptide 2 reveals a negative band at 234 nm and a positive band at 221 nm, suggestive of an exciton split doublet. Modeling of the facing Phe side chains at the hydrogen-bonding position of a canonical beta-hairpin suggests that interring separation is approximately 4.78 A for the gauche+ gauche- (g+ g-) rotamer. A previously reported peptide beta-hairpin composed of only alpha-amino acids, Boc-Leu-Phe-Val-D-Pro-Gly-Leu-Phe-Val-OMe also exhibited an anomalous far-UV (ultraviolet) CD (circular dichroism) spectrum, which was interpreted in terms of interactions between facing aromatic chromophores, Phe 2 and Phe 7 (C. Zhao, P. L. Polavarapu, C. Das, and P. Balaram, Journal of the American Chemical Society, 2000, Vol 122, pp. 8228-8231).
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Affiliation(s)
- Rituparna S Roy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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Rai R, Raghothama S, Balaram P. Design of a Peptide Hairpin Containing a Central Three-Residue Loop. J Am Chem Soc 2006; 128:2675-81. [PMID: 16492054 DOI: 10.1021/ja056861v] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The construction of a designed beta-hairpin structure, containing a central three-residue loop has been successfully achieved in the synthetic nonapeptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-(D)Ala-Leu-Phe-Val-OMe (2). The design is based on expanding the two-residue loop established in the peptide beta-hairpin Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1). Characterization of the registered beta-hairpins in peptides 1 and 2 is based on the observation of key nuclear Overhauser effects (NOEs) in CDCl(3) and CD(3)OH. Solvent titration and temperature dependence of NH chemical shifts establish the identity of NH groups involved in interstrand hydrogen bonding. In peptide 2, the antiparallel registry is maintained, with the formation of a (D)Pro-(L)Pro-(D)Ala loop, stabilized by a 5-->1 hydrogen bond between Val3 CO and Leu7 NH groups (C(13), alpha-turn) and a 3-->1 hydrogen bond between (D)Pro4 CO and (d)Ala6 NH groups (C(7), gamma-turn). NMR derived structures suggest that in peptide 2, (d)Ala(6) adopts an alpha(L) conformation. In peptide 1, the (D)Pro-(L)Pro segment adopts a type II' beta-turn. Replacement of (D)Ala (6) in peptide 2 by (L)Ala in peptide 3 yields a beta-hairpin conformation, with a central (D)Pro-(L)Pro two-residue loop. Strand slippage at the C-terminus results in altered registry of the antiparallel strands.
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Affiliation(s)
- Rajkishor Rai
- Molecular Biophysics Unit and NMR Research Center, Indian Institute of Science, Bangalore
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Sengupta A, Aravinda S, Shamala N, Raja KMP, Balaram P. Structural studies of model peptides containing β-, γ- and δ-amino acids. Org Biomol Chem 2006; 4:4214-22. [PMID: 17312978 DOI: 10.1039/b609863k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-betaGly-NHMe (2), Piv-Pro-betaGly-OMe (3), Piv-Pro-deltaAva-OMe (4) and Boc-Pro-gammaAbu-OH (5) are described (Piv: pivaloyl; NHMe: N-methylamide; betaGly: beta-glycine; OMe: O-methyl ester; deltaAva: delta-aminovaleric acid; gammaAbu: gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-betaGly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the deltaAva residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H...O hydrogen bond.
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Affiliation(s)
- Anindita Sengupta
- Department of Physics, Indian Institute of Science, Bangalore, 560 012, India
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Sengupta A, Roy RS, Sabareesh V, Shamala N, Balaram P. Aggregation modes in sheets formed by protected β-amino acids and β-peptides. Org Biomol Chem 2006; 4:1166-73. [PMID: 16525563 DOI: 10.1039/b516088j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of four protected beta-amino acid residues, Boc-(S)-beta3-HAla-NHMe (1); Boc-(R)-beta3-HVal-NHMe (2); Boc-(S)-beta3-HPhe-NHMe (3); Boc-(S)-beta3-HPro-OH (6) and two beta-dipeptides, Boc-(R)-beta3-HVal-(R)-beta3-HVal-OMe (4); Boc-(R)-beta3-HVal-(S)-beta3-HVal-OMe (5) have been determined. Gauche conformations about the C(beta)-C(alpha) bonds (theta approximately +/-60 degrees) are observed for the beta3-HPhe residues in and all four beta3-HVal residues in the dipeptides and . Trans conformations (theta is approximately 180 degrees) are observed for beta3-HAla residues in both independent molecules in and for the beta3-HVal and beta3-HPro residues in and , respectively. In the cases of compounds , molecules associate in the crystals via intermolecular backbone hydrogen bonds leading to the formation of sheets. The polar strands formed by beta3-residues aggregate in both parallel (1,3,5) and antiparallel (2,4 fashion. Sheet formation accommodates both the trans and gauche conformations about the C(beta)-C(alpha) bonds.
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Affiliation(s)
- Anindita Sengupta
- Department of Physics, Indian Institute of Science, Bangalore, 560 012, India
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Mahalakshmi R, Shanmugam G, Polavarapu PL, Balaram P. Circular Dichroism of Designed Peptide Helices and β-Hairpins: Analysis of Trp- and Tyr-Rich Peptides. Chembiochem 2005; 6:2152-8. [PMID: 16261550 DOI: 10.1002/cbic.200500152] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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