1
|
Nandi SK, Mondal S, Mondal S, Gumtya M, Haldar D. Structure–mechanical property relationship of a pentapeptide crystal. CrystEngComm 2021. [DOI: 10.1039/d1ce00738f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A peptide having miniature (P)310/α-helix conformation, forms intermolecular H-bonded supramolecular helical bundle structure which further self-assembled to interdigited supramolecular sheet-like structure that eventually from the brittle crystal.
Collapse
Affiliation(s)
- Sujay Kumar Nandi
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India
| | - Saikat Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India
- Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research, Kolkata, Mohanpur-741246, West Bengal, India
| | - Sahabaj Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India
| | - Milan Gumtya
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India
| | - Debasish Haldar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India
- Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research, Kolkata, Mohanpur-741246, West Bengal, India
| |
Collapse
|
2
|
Debnath M, Sarkar R, Nandi SK, Haldar D. C-Terminal -Aib-L-Leu-OMe Segment Promotes Schellman Loop from α-Peptides with Alternating L-Leu and Aib Residues in the Crystal State. ChemistrySelect 2017. [DOI: 10.1002/slct.201701577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mintu Debnath
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246, West Bengal India
| | - Rajib Sarkar
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246, West Bengal India
| | - Sujay Kumar Nandi
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246, West Bengal India
| | - Debasish Haldar
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246, West Bengal India
| |
Collapse
|
3
|
Pike SJ, Raftery J, Webb SJ, Clayden J. Conformational analysis of helical aminoisobutyric acid (Aib) oligomers bearing C-terminal ester Schellman motifs. Org Biomol Chem 2016; 12:4124-31. [PMID: 24831537 DOI: 10.1039/c4ob00268g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of Schellman motifs on the adoption of stable 310 helical conformations in a series of aminoisobutyric (Aib) oligomers has been studied in the solid state and solution. The destabilising effect of the Schellman motif (a local inversion of helical screw-sense due to a C-terminal ester residue) was quantified in the solid state using X-ray crystallography through analysis of the torsion angles and their deviation from those observed in an ideal 310 helix. Investigation of the intramolecular hydrogen-bonding interactions in the solid state led to the identification of a fully extended C5 conformation in one oligomer, which is a novel folding motif for Aib oligomers. The effect of ester groups with differing steric demands on intermolecular hydrogen-bonding contacts in the solid state was also ascertained. In solution, the adoption of a 310 conformation in Aib oligomers appeared to be more finely tuned, depending on a number of factors, including chain length and the steric demands of the C-terminal destabilising Schellman motif.
Collapse
Affiliation(s)
- Sarah J Pike
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | | | | | | |
Collapse
|
4
|
Shepherd NE, Hoang HN, Abbenante G, Fairlie DP. Left- and Right-Handed Alpha-Helical Turns in Homo- and Hetero-Chiral Helical Scaffolds. J Am Chem Soc 2009; 131:15877-86. [DOI: 10.1021/ja9065283] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas E. Shepherd
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Giovanni Abbenante
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| |
Collapse
|
5
|
Ousaka N, Inai Y. Transfer of Noncovalent Chiral Information along an Optically Inactive Helical Peptide Chain: Allosteric Control of Asymmetry of the C-Terminal Site by External Molecule that Binds to the N-Terminal Site. J Org Chem 2008; 74:1429-39. [DOI: 10.1021/jo801686m] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Naoki Ousaka
- Department of Environmental Technology and Urban Planning and Department of Frontier Materials, Shikumi College, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yoshihito Inai
- Department of Environmental Technology and Urban Planning and Department of Frontier Materials, Shikumi College, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
6
|
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]
|
7
|
Dutt A, Drew MG, Pramanik A. Conformational and self-assembly studies of helix forming hexapeptides containing two α-amino isobutyric acids. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.11.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
8
|
Ananda K, Vasudev PG, Sengupta A, Raja KMP, Shamala N, Balaram P. Polypeptide helices in hybrid peptide sequences. J Am Chem Soc 2006; 127:16668-74. [PMID: 16305256 DOI: 10.1021/ja055799z] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new class of polypeptide helices in hybrid sequences containing alpha-, beta-, and gamma-residues is described. The molecular conformations in crystals determined for the synthetic peptides Boc-Leu-Phe-Val-Aib-betaPhe-Leu-Phe-Val-OMe 1 (betaPhe: (S)-beta3-homophenylalanine) and Boc-Aib-Gpn-Aib-Gpn-OMe 2(Gpn: 1-(aminomethyl)cyclohexaneacetic acid) reveal expanded helical turns in the hybrid sequences (alpha alphabeta)n and (alphagamma)n. In 1, a repetitive helical structure composed of C14 hydrogen-bonded units is observed, whereas 2 provides an example of a repetitive C12 hydrogen-bonded structure. Using experimentally determined backbone torsion angles for the hydrogen-bonded units formed by hybrid sequences, we have generated energetically favorable hybrid helices. Conformational parameters are provided for C11, C12, C13, C14, and C15 helices in hybrid sequences.
Collapse
Affiliation(s)
- Kuppanna Ananda
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | | | | | | | | | |
Collapse
|
9
|
|
10
|
Karle IL, Das C, Balaram P. Effects of hydrogen-bond deletion on peptide helices: structural characterization of depsipeptides containing lactic acid. Biopolymers 2001; 59:276-89. [PMID: 11473352 DOI: 10.1002/1097-0282(20011005)59:4<276::aid-bip1024>3.0.co;2-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The insertion of alpha-hydroxy acids into peptide chains provides a convenient means for investigating the effects of hydrogen bond deletion on polypeptide secondary structures. The crystal structures of three oligopeptides containing L-lactic acid (Lac) residue have been determined. Peptide 1, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe (Boc: tert-butyloxycarbonyl; Aib: alpha- aminoisobutyric acid; OMe: methyl ester), and peptide 2, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Leu-OMe, adopt completely helical conformations in the crystalline state with the Lac(6) residue comfortably accommodated in the center of a helix. The distance between the O atoms of Leu(3) CO group and the Lac(6) O (ester) in both the structures is 3.1-3.3 A. The NMR and CD studies of peptide 1 and its all-amide analogue 4, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe, provide firm evidence for a continuous helical conformation in solution in both the cases. In a 14-residue peptide 3, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Val-Ala-Leu-Aib-Val-Lac-Leu-OMe, residues Val(1)-Leu(10) adopt a helical conformation. Aib(11) is the site of chiral reversal resulting in helix termination by formation of a Schellman motif. Residues 12-14 adopt nonhelical conformations. The loss of the hydrogen bond near the C-terminus appears to facilitate the chiral reversal at Aib(11). Published 2001 John Wiley & Sons, Inc. Biopolymers 59: 276-289, 2001
Collapse
Affiliation(s)
- I L Karle
- Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC, 20375-5341, USA
| | | | | |
Collapse
|
11
|
Abstract
The design of a peptide that contains two distinct elements of secondary structure, helix and beta-hairpin, is described. Two designed 17-residue peptides: Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Gly-Gly-Leu-Phe-Val-D-Pro-Gly-Leu-Phe-Val-OMe (I) and Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Gly-Gly-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe (II) have been conformationally characterized by NMR spectroscopy. Peptides I and II contain a seven-residue helical module at the N terminus and a eight-residue beta-hairpin module at the C terminus, which are connected by a conformationally flexible Gly-Gly segment. The choice of the secondary-structure modules is based upon prior crystallographic and spectroscopic analysis of the individual modules. Analysis of 500 MHz 1H NMR data, recorded as solutions in methanol, suggests that the observed pattern of chemical shifts, 3JHN CalphaH values, temperature coefficients of the NH chemical shifts, and backbone inter-residue nuclear Overhauser effects favor helical structures for residues 1-7 and beta-hairpin structures for residues 10-17. The spectroscopic data are compatible with termination of the helical segment by formation of a Schellman motif; this restricts Gly(8) to a left-handed alpha-helical conformation. Gly(9) is the only residue with multiple conformational possibilities in phi,psi space. Possible orientations of the two secondary-structure modules are considered. This study validates the use of stereochemically rigid peptide modules as prefabricated elements in the construction of synthetic protein mimics.
Collapse
Affiliation(s)
- C Das
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
| | | | | |
Collapse
|
12
|
Aravinda S, Shamala N, Pramanik A, Das C, Balaram P. An unusual C-H...O hydrogen bond mediated reversal of polypeptide chain direction in a synthetic peptide helix. Biochem Biophys Res Commun 2000; 273:933-6. [PMID: 10891350 DOI: 10.1006/bbrc.2000.3026] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An unusual C-terminal conformation has been detected in a synthetic decapeptide designed to analyze the stereochemistry of helix termination in polypeptides. The crystal structure of the decapeptide Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe reveals a helical segment spanning residues 1-7 and helix termination by formation of a Schellman motif, generated by (D)Ala(8) adopting the left-handed helical (alpha(L)) conformation. The extended conformation at (D)Leu(9) results in a compact folded structure, stabilized by a potentially strong C-H. O hydrogen bond between Ala(4) C(alpha)H and (D)Leu(9) CO. The parameters for C-H. O interaction are Ala(4) C(alpha)H. O=C (D)Leu(9) distance 3.27 A, C(alpha)-H. O angle 176 degrees, and O. H(alpha) distance 2.29 A. This structure suggests that insertion of contiguous D-residues may provide a handle for the generation of designed structures containing more than one helical segment folded in a compact manner.
Collapse
Affiliation(s)
- S Aravinda
- Department of Physics, Indian Institute of Science, Bangalore-, 560012, India
| | | | | | | | | |
Collapse
|