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Debnath S, Vignesh SR, Satpati P, Chatterjee S. Position of Geminal Substitution of γ Amino Acid Residues Modulates Their Ability to Form Isolated Non‐Helical C
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β‐turn Mimics. ChemistrySelect 2023. [DOI: 10.1002/slct.202204255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Swapna Debnath
- Department of Chemistry Indian Institute of Technology, Guwahati Guwahati Assam India
| | - S. R. Vignesh
- Biosciences and Bioengineering Indian Institute of Technology Guwahati, Guwahati Assam India
| | - Priyadarshi Satpati
- Biosciences and Bioengineering Indian Institute of Technology Guwahati, Guwahati Assam India
| | - Sunanda Chatterjee
- Department of Chemistry Indian Institute of Technology, Guwahati Guwahati Assam India
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2
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Dolenc J, Haywood EJ, Zhu T, Smith LJ. Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds. J Chem Inf Model 2022; 62:6704-6714. [PMID: 35816656 PMCID: PMC9795546 DOI: 10.1021/acs.jcim.2c00516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecular dynamics (MD) simulations have been used to characterize the effects of backbone N-amination of residues in a model β-hairpin peptide. This modification is of considerable interest as N-aminated peptides have been shown to inhibit amyloid-type aggregation. Six derivatives of the β-hairpin peptide, which contain one, two, or four N-aminated residues, have been studied. For each peptide 100 ns MD simulations starting from the folded β-hairpin structure were performed. The effects of the N-amination prove to be very sequence dependent. N-Amination of a residue involved in interstrand hydrogen bonding (Val3) leads to unfolding of the β-hairpin, whereas N-amination of a residue toward the C-terminus (Leu11) gives fraying at the termini of the peptide. In the other derivatives the peptide remains folded, with increasing levels of N-amination reducing the right-handed twist of the β-hairpin and favoring population of a type II' rather than a type I' β-turn. MD simulations (100 ns) have also been run for each peptide starting from an unfolded extended chain. Here, the peptide with four N-aminated residues shows the most folding into the β-hairpin (34%). Analysis of the simulations shows that N-amination favors the population of β (φ, ψ) conformations by the preceding residue due to, at least in part, a network of weak NH2(i)-CO(i) and NH2(i)-CO(i-2) hydrogen bonds. It also leads to a reduction of misfolding because of changes in the hydrogen-bonding potential. Both of these features help funnel the peptide to the folded β-hairpin structure. The conformational insights provided through this work give a firm foundation for the design of N-aminated peptide inhibitors for modulating protein-protein interactions and aggregation.
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Affiliation(s)
- Jožica Dolenc
- Chemistry
- Biology
- Pharmacy Information Center, ETH Zurich, Zurich CH-8093, Switzerland
| | - Esme J. Haywood
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Tingting Zhu
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Lorna J. Smith
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, (L.J.S.)
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3
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Kumar S, Borish K, Dey S, Nagesh J, Das A. Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides. Phys Chem Chem Phys 2022; 24:18408-18418. [PMID: 35880873 DOI: 10.1039/d2cp01306a] [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
Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 27-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.
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Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
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4
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Moharana TR, Nagaraj R. In silico folding of hydrophobic peptides that form β-hairpin structures in solution. J Pept Sci 2022; 28:e3427. [PMID: 35595709 DOI: 10.1002/psc.3427] [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: 01/19/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022]
Abstract
Peptides designed with residues that have a high propensity to occur in β-turns form β-hairpin structures in apolar as well as in polar organic solvents such as dimethyl sulfoxide (DMSO). Due to limited solubility, their conformations have not been investigated experimentally in water. We have examined the conformations of four of such designed peptides that fold into well-defined β-hairpin structures facilitated by β-turns, in the crystalline state and in solution, by molecular dynamics simulations (MDS). The peptides folded into β-hairpin structures in water, starting from the fully extended conformation. However, in DMSO, neither folding nor unfolding was observed during MDS, when the starting structures were unfolded and folded, respectively. The lack of folding in DMSO was investigated by constructing folding free energy landscapes by umbrella sampling. The folding free energy landscape is smooth in water while in DMSO folded and unfolded structures are separated by high-energy barriers. The folding free energy is less in DMSO compared to water due to a more stable unfolded structure in DMSO compared to water, which in turn is due to stabilization of the unfolded state by hydrophobic interactions in DMSO. This finding will be helpful to researchers to accurately model and/or design small peptide structures in water and organic solvents.
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5
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Stanojlovic V, Müller A, Moazzam A, Hinterholzer A, Ożga K, Berlicki Ł, Schubert M, Cabrele C. A Conformationally Stable Acyclic β-Hairpin Scaffold Tolerating the Incorporation of Poorly β-Sheet-Prone Amino Acids. Chembiochem 2022; 23:e202100604. [PMID: 34856053 PMCID: PMC9299858 DOI: 10.1002/cbic.202100604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Indexed: 11/09/2022]
Abstract
The β-hairpin is a structural element of native proteins, but it is also a useful artificial scaffold for finding lead compounds to convert into peptidomimetics or non-peptide structures for drug discovery. Since linear peptides are synthetically more easily accessible than cyclic ones, but are structurally less well-defined, we propose XWXWXpPXK(/R)X(R) as an acyclic but still rigid β-hairpin scaffold that is robust enough to accommodate different types of side chains, regardless of the secondary-structure propensity of the X residues. The high conformational stability of the scaffold results from tight contacts between cross-strand cationic and aromatic side chains, combined with the strong tendency of the d-Pro-l-Pro dipeptide to induce a type II' β-turn. To demonstrate the robustness of the scaffold, we elucidated the NMR structures and performed molecular dynamics (MD) simulations of a series of peptides displaying mainly non-β-branched, poorly β-sheet-prone residues at the X positions. Both the NMR and MD data confirm that our acyclic β-hairpin scaffold is highly versatile as regards the amino-acid composition of the β-sheet face opposite to the cationic-aromatic one.
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Affiliation(s)
- Vesna Stanojlovic
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Anna Müller
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Ali Moazzam
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
- School of ChemistryCollege of ScienceUniversity of TehranP.O. Box 14155–6619TehranIran
| | - Arthur Hinterholzer
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Katarzyna Ożga
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Łukasz Berlicki
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Mario Schubert
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Chiara Cabrele
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
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6
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Zhong Y, Tang Q, Miller DP, Zurek E, Liu R, Lu ZL, Gong B. Major Factors for the Persistent Folding of Hybrid α, β, γ-Hybrid Peptides Into Hairpins. Front Chem 2020; 8:530083. [PMID: 33134269 PMCID: PMC7550740 DOI: 10.3389/fchem.2020.530083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
Factors responsible for the persistent adoption of hairpin conformations by hybrid oligopeptides, each having a central β/α dipeptide segment flanked by aromatic γ-amino acid (γAr) residues, are probed. Our recent studies revealed that tetrapeptide 1 and 2, having central dipeptide segments consisting of β-alanine (β-Ala) and glycine (Gly), and L-β-homophenylalanine (L-β-homoPhe) and Gly residues, respectively, that are flanked by γAr residues, fold into well-defined, expanded β-turns with doubly H-bonded γAr residues. Replacing the γAr residues of 1 and 2 with L-Val and L-Leu residues results in tetrapetides 1 ' and 2 ' that fail to fold into defined conformations, which confirms the decisive role played by the H-bonded γAr residues in the promoting folding of 1 and 2. Attaching L-Val and L-Leu residues to the termini of 1 affords hexapeptide 1a. With an additional H-bond between its L-Val and L-Leu residues, peptide 1a folds into a hairpin with higher stability than that of 1, indicating that the expanded β-turn can nucleate and stabilize β-hairpin with longer β-strands. Attaching L-Val and L-Leu residues to the termini of 2 affords hexapeptide 2a. Substituting the L-β-homoPhe residue of 2a with a D-β-homoPhe residue gives hexapeptide 2b. Surprisingly, hexapeptide 2a fold into a hairpin showing the similar stability as those of tetrapeptides 1 and 2. Hexapeptide 2b, with its combination of a D-β-homoPhe residue and the L-Val/L-Leu pair, fold into a hairpin that is significantly more stable than the other hybrid peptides, demonstrating that a combination of hetero-chirality between the β-amino acid residue of the dipeptide loop and the α-amino acid residues of the β-strands enhances the stability of the resultant β-hairpin.
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Affiliation(s)
- Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Quan Tang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Daniel P. Miller
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
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7
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Tang Q, Zhong Y, Miller DP, Liu R, Zurek E, Lu ZL, Gong B. Reverse Turn Foldamers: An Expanded β-Turn Motif Reinforced by Double Hydrogen Bonds. Org Lett 2020; 22:1003-1007. [DOI: 10.1021/acs.orglett.9b04547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quan Tang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department of Chemistry, Hofstra University, Hempstead, New York 11549, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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8
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Sarojini V, Cameron AJ, Varnava KG, Denny WA, Sanjayan G. Cyclic Tetrapeptides from Nature and Design: A Review of Synthetic Methodologies, Structure, and Function. Chem Rev 2019; 119:10318-10359. [PMID: 31418274 DOI: 10.1021/acs.chemrev.8b00737] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small cyclic peptides possess a wide range of biological properties and unique structures that make them attractive to scientists working in a range of areas from medicinal to materials chemistry. However, cyclic tetrapeptides (CTPs), which are important members of this family, are notoriously difficult to synthesize. Various synthetic methodologies have been developed that enable access to natural product CTPs and their rationally designed synthetic analogues having novel molecular structures. These methodologies include the use of reversible protecting groups such as pseudoprolines that restrict conformational freedom, ring contraction strategies, on-resin cyclization approaches, and optimization of coupling reagents and reaction conditions such as temperature and dilution factors. Several fundamental studies have documented the impacts of amino acid configurations, N-alkylation, and steric bulk on both synthetic success and ensuing conformations. Carefully executed retrosynthetic ring dissection and the unique structural features of the linear precursor sequences that result from the ring dissection are crucial for the success of the cyclization step. Other factors that influence the outcome of the cyclization step include reaction temperature, solvent, reagents used as well as dilution levels. The purpose of this review is to highlight the current state of affairs on naturally occurring and rationally designed cyclic tetrapeptides, including strategies investigated for their syntheses in the literature, the conformations adopted by these molecules, and specific examples of their function. Using selected examples from the literature, an in-depth discussion of the synthetic techniques and reaction parameters applied for the successful syntheses of 12-, 13-, and 14-membered natural product CTPs and their novel analogues are presented, with particular focus on the cyclization step. Selected examples of the three-dimensional structures of cyclic tetrapeptides studied by NMR, and X-ray crystallography are also included.
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Affiliation(s)
- Vijayalekshmi Sarojini
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology , Wellington 6140 , New Zealand
| | - Alan J Cameron
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | - Kyriakos G Varnava
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | | | - Gangadhar Sanjayan
- Division of Organic Chemistry , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411 008 , India
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9
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Cameron AJ, Squire CJ, Edwards PJB, Harjes E, Sarojini V. Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides. Chem Asian J 2017; 12:3195-3202. [PMID: 29098772 DOI: 10.1002/asia.201701422] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/30/2017] [Indexed: 12/31/2022]
Abstract
Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H2 N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution.
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Affiliation(s)
- Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Christopher J Squire
- School of Biological Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
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10
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Baravkar SB, Kotmale AS, Shaikh SR, Gonnade RG, Sanjayan GJ. Structural Insights into the Hydrogen-Bonding and Folding Pattern in Ant-Ant-Pro-Gly Tetrapeptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sachin B. Baravkar
- Division of Organic Chemistry; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Amol S. Kotmale
- Central NMR facility; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Samir R. Shaikh
- Center for Materials Characterization; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Rajesh G. Gonnade
- Center for Materials Characterization; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Gangadhar J. Sanjayan
- Division of Organic Chemistry; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
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11
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Pellach M, Mondal S, Harlos K, Mance D, Baldus M, Gazit E, Shimon LJW. A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure. Angew Chem Int Ed Engl 2017; 56:3252-3255. [PMID: 28191715 PMCID: PMC5412914 DOI: 10.1002/anie.201609877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Indexed: 11/29/2022]
Abstract
The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level.
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Affiliation(s)
- Michal Pellach
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
| | - Karl Harlos
- Division of Structural BiologyWellcome Trust Centre for Human GeneticsUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUK
| | - Deni Mance
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Ehud Gazit
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
- Department of Materials Science and EngineeringIby and Aladar Fleischman Faculty of EngineeringTel Aviv UniversityRamat Aviv69978Israel
| | - Linda J. W. Shimon
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovot76100Israel
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12
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Pellach M, Mondal S, Harlos K, Mance D, Baldus M, Gazit E, Shimon LJW. A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michal Pellach
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Karl Harlos
- Division of Structural Biology; Wellcome Trust Centre for Human Genetics; University of Oxford; Roosevelt Drive Oxford OX3 7BN UK
| | - Deni Mance
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
- Department of Materials Science and Engineering; Iby and Aladar Fleischman Faculty of Engineering; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support; Weizmann Institute of Science; Rehovot 76100 Israel
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13
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Metrano A, Abascal NC, Mercado BQ, Paulson EK, Hurtley AE, Miller SJ. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc 2017; 139:492-516. [PMID: 28029251 PMCID: PMC5312972 DOI: 10.1021/jacs.6b11348] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/30/2022]
Abstract
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.
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Affiliation(s)
- Anthony
J. Metrano
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Nadia C. Abascal
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Eric K. Paulson
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Anna E. Hurtley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
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14
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Bakker DJ, Dey A, Tabor DP, Ong Q, Mahé J, Gaigeot MP, Sibert EL, Rijs AM. Fingerprints of inter- and intramolecular hydrogen bonding in saligenin–water clusters revealed by mid- and far-infrared spectroscopy. Phys Chem Chem Phys 2017; 19:20343-20356. [DOI: 10.1039/c7cp01951c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Saligenin (2-(hydroxymethyl)phenol) exhibits both strong and weak intramolecular electrostatic interactions.
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Affiliation(s)
- Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Arghya Dey
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Daniel P. Tabor
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Qin Ong
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Edwin L. Sibert
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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15
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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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16
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Konda M, Bhowmik S, Mobin SM, Biswas S, Das AK. Modulating Hydrogen Bonded Self-assembled Patterns and Morphological Features by a Change in Side Chain of Third Amino Acid of Synthetic γ- Amino Acid Based Tripeptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maruthi Konda
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Soumitra Bhowmik
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Shaikh M. Mobin
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Sagar Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
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17
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Kang YK, Yoo IK. Propensities of peptides containing the Asn-Gly segment to form β-turn and β-hairpin structures. Biopolymers 2016; 105:653-64. [DOI: 10.1002/bip.22863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
| | - In Kee Yoo
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
- LG Research Park, LG Household & Health Care; Daejeon 34114 Republic of Korea
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18
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Wani NA, Gupta VK, Singh UP, Aravinda S, Rai R. Folded Structure Stabilized by C 7, C 10and C 12Hydrogen Bonds in αγ Hybrid Peptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Naiem Ahmad Wani
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
| | - Vivek Kumar Gupta
- X-ray Crystallography Laboratory; Post-Graduate Department of Physics and Electronics; University of Jammu; Jammu Tawi 180 006 India
| | - Umesh Prasad Singh
- CSIR-Indian Institute of Chemical Biology; 4, Raja, S.C. Mullick Road Kolkata- 700032 India
| | - Subrayashastry Aravinda
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
| | - Rajkishor Rai
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
- Academy of Scientific and Innovative Research; New Delhi India
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19
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Ingole TS, Vijayadas KN, Chaitanya KN, Kotmale AS, Gawade RL, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Disruption of Native β-Turns: Consequence of Folding Competition between Native and Orthanilic Acid Proline-BasedPseudoβ-Turn. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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20
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Kang YK, Park HS. Propensities to form the β-turn and β-hairpin structures of d-Pro-Gly and Aib- d-Ala containing peptides: a computational study. NEW J CHEM 2016. [DOI: 10.1039/c6nj00614k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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Madhusudan Makwana K, Mahalakshmi R. Implications of aromatic-aromatic interactions: From protein structures to peptide models. Protein Sci 2015; 24:1920-33. [PMID: 26402741 DOI: 10.1002/pro.2814] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022]
Abstract
With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed.
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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
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
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22
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Matsumoto M, Lee SJ, Gagné MR, Waters ML. Cross-strand histidine-aromatic interactions enhance acyl-transfer rates in beta-hairpin peptide catalysts. Org Biomol Chem 2015; 12:8711-8. [PMID: 25254932 DOI: 10.1039/c4ob01754d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A reactive tagging methodology was used to select the species most reactive to an acylation reagent from a solid phase library of beta hairpin peptides. Hits bearing an electron-rich aromatic residue across strand from a reactive histidine were found to competitively become N-acylated. In addition to displaying rapid N-acylation rates the hit peptide was additionally deacylated in the presence of a nucleophile, thus closing a putative catalytic cycle. Variants of the hit peptide were studied to elucidate both the magnitude (up to 18,000-fold over background, kcat/kuncat = 94,000,000, or 45-fold over Boc-histidine methyl ester) and mechanism of acyl transfer catalysis. A combination of CH-π, cation-π and HisH(+)-O interactions in the cationic imidazole transition state is implicated in the rate acceleration, in addition to the fidelity of the beta hairpin fold. Moreover, NMR structural data on key intermediates or models thereof suggest that a key feature of this catalyst is the ability to access several different stabilizing conformations along the catalysis reaction coordinate.
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Affiliation(s)
- M Matsumoto
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina 27599-3290, USA.
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23
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Kang YK, Park HS. Hairpin formation promoted by the heterochiral dinipecotic acid segment: A DFT study. Biopolymers 2015; 103:609-17. [PMID: 26015319 DOI: 10.1002/bip.22687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/22/2015] [Accepted: 05/22/2015] [Indexed: 01/16/2023]
Abstract
Conformational preferences for the turn and β-hairpin structures of Ala-based peptides [Ac-Ala(n)-(R)-Nip-(S)-Nip-Ala(n)-X (n = 0-2; X = NHMe or NMe2)] containing nipecotic acid (Nip) residues were carried out using the density functional M06-2X and the implicit solvation model SMD in CH2Cl2 and/or water. The turn structure of the (R)-Nip-(S)-Nip segment with a C10 H-bond between two terminal groups was found to be most preferred (populated at 98.9%) in CH2Cl2; this structure is consistent with IR and (1)H NMR results. The stabilities of the β-hairpins containing the (R)-Nip-(S)-Nip segment as a turn motif relative to the extended structures increased with peptide sequence length. The relative strengths of the H-bonds between the carbonyl oxygen and the amide hydrogen appeared to be responsible for stabilizing the turn and β-hairpin structures in CH2Cl2. In addition, the (R)-Nip-(S)-Nip segment exhibited the capability to be incorporated into one of the two β-turn motifs of gramicidin S (GS). The structure of this GS derivative (GS-Nip2 ) was generally similar to the native peptide but was less hydrophobic and it is therefore expected to exhibit lower hemolytic activity; however, further experiments are needed to evaluate its antimicrobial activity. The structure of GS-Nip2 was somewhat more flexible than GS in solvents of higher polarity. Thus, our calculated results regarding the turn and β-hairpin motifs of the (R)-Nip-(S)-Nip segment indicate that this structure might be useful for the design of bioactive macrocyclic peptides containing β-hairpin mimics as well as binding epitopes in protein-protein and protein-nucleic acid recognitions.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team, Chungbuk National University, Cheongju, Chungbuk, 362-763, Republic of Korea
| | - Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, 690-708, Republic of Korea
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24
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Akagawa K, Sakai N, Kudo K. Histidine-Containing Peptide Catalysts Developed by a Facile Library Screening Method. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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25
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Akagawa K, Sakai N, Kudo K. Histidine-containing peptide catalysts developed by a facile library screening method. Angew Chem Int Ed Engl 2014; 54:1822-6. [PMID: 25521645 DOI: 10.1002/anie.201410268] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/17/2014] [Indexed: 11/12/2022]
Abstract
Although peptide catalysts have a high potential for the use as organocatalysts, the optimization of peptide sequences is laborious and time-consuming. To address this issue, a facile screening method for finding efficient aminocatalysts from a peptide library has been developed. In the screening for the Michael addition of a malonate to an enal, a dye-labeled product is immobilized on resin-bound peptides through reductive amination to visualize active catalysts. This procedure allows for the monitoring of the reactivity of entire peptides without modifying the resin beads beforehand. Peptides containing histidine at an appropriate position were identified by this method. A novel function of the histidyl residue, which enhances the binding of a substrate to the catalyst by capturing an iminium intermediate, was indicated.
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Affiliation(s)
- Kengo Akagawa
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan)
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26
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Gopinath P, Ramkumar V, Muraleedharan KM. Peptide turns through just ‘one atom’! A sulfamide group nucleates folding and stabilizes new supramolecular topologies in short peptides. CrystEngComm 2014. [DOI: 10.1039/c4ce01938e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide segments with centrally placed sulfamide groups showed a remarkable tendency to adopt a turn conformation and exhibited supramolecular topologies like ‘helical stacks’ and ‘hairpin sheets’ through a highly coordinated array of strong and weak hydrogen bonds.
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27
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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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28
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Vijayadas KN, Nair RV, Gawade RL, Kotmale AS, Prabhakaran P, Gonnade RG, Puranik VG, Rajamohanan PR, Sanjayan GJ. Ester vs. amide on folding: a case study with a 2-residue synthetic peptide. Org Biomol Chem 2013; 11:8348-56. [DOI: 10.1039/c3ob41967c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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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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30
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Kang YK, Byun BJ. Computationally designed β-turn foldamers of γ-peptides based on 2-(aminomethyl)cyclohexanecarboxylic acid. Biopolymers 2012; 97:1018-25. [DOI: 10.1002/bip.22119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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Chung MK, Lee SJ, Waters ML, Gagné MR. Self-Assembled Multi-Component Catenanes: The Effect of Multivalency and Cooperativity on Structure and Stability. J Am Chem Soc 2012; 134:11430-43. [DOI: 10.1021/ja302347q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mee-Kyung Chung
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Stephen J. Lee
- U.S. Army Research Office, P.O. Box 12211, Research Triangle Park, North
Carolina 27709, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Michel R. Gagné
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
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32
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Akagawa K, Sugiyama M, Kudo K. Asymmetric Michael addition of boronic acids to a γ-hydroxy-α,β-unsaturated aldehyde catalyzed by resin-supported peptide. Org Biomol Chem 2012; 10:4839-43. [DOI: 10.1039/c2ob25431j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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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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34
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Rajagopal A, Aravinda S, Raghothama S, Shamala N, Balaram P. Aromatic interactions in model peptide β-hairpins: Ring current effects on proton chemical shifts. Biopolymers 2011; 98:185-94. [DOI: 10.1002/bip.22003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/05/2011] [Accepted: 10/13/2011] [Indexed: 11/08/2022]
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35
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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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36
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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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37
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Kapoerchan V, Spalburg E, de Neeling A, Mars-Groenendijk R, Noort D, Otero J, Ferraces-Casais P, Llamas-Saiz A, van Raaij M, van Doorn J, van der Marel G, Overkleeft H, Overhand M. Gramicidin S Derivatives Containingcis- andtrans-Morpholine Amino Acids (MAAs) as Turn Mimetics. Chemistry 2010; 16:4259-65. [DOI: 10.1002/chem.200902984] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Rathore RS. Study on β-sheet packing, stabilized by aromatic interactions in a tri-peptide crystal. Z KRIST-CRYST MATER 2009. [DOI: 10.1524/zkri.219.9.567.44043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The role of unconventional aromatic interactions in the β-sheet packing, inside the crystal, has been highlighted. Crystal structure of terminally blocked tri-peptide, Z-L-Ala-L-Ala-L-Leu-pNA has been determined. There are four different conformers of tri-peptide inside the unit-cell, in space group P1. All the four independent molecules are described by semi-extended backbone conformations which form an anti-parallel β-sheet. The inter β-sheet packing is predominantly stabilized by C—H…π and π…π interactions. In π…π interactions, the center-to-center distance between aromatic rings varies from 3.8 Å to 4.6 Å while the closest distance of approach ranges from 3.4 Å to 3.8 Å. The associations of aromatic-aromatic rings are described by either face-to-face or inclined arrangements.
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39
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Eidenschink L, Kier BL, Huggins KNL, Andersen NH. Very short peptides with stable folds: building on the interrelationship of Trp/Trp, Trp/cation, and Trp/backbone-amide interaction geometries. Proteins 2009; 75:308-22. [PMID: 18831035 PMCID: PMC2656586 DOI: 10.1002/prot.22240] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
By combining a favorable turn sequence with a turn flanking Trp/Trp interaction and a C-terminal H-bonding interaction between a backbone amide and an i-2 Trp ring, a particularly stable (DeltaG(U) > 7 kJ/mol) truncated hairpin, Ac-WI-(D-Pro-D-Asn)-KWTG-NH(2), results. In this construct and others with a W-(4-residue turn)-W motif in severely truncated hairpins, the C-terminal Trp is the edge residue in a well-defined face-to-edge (FtE) aryl/aryl interaction. Longer hairpins and those with six-residue turns retain the reversed "edge-to-face" (EtF) Trp/Trp geometry first observed for the trpzip peptides. Mutational studies suggest that the W-(4-residue turn)-W interaction provides at least 3 kJ/mol of stabilization in excess of that due to the greater beta-propensity of Trp. The pi-cation, and Trp/Gly-H(N) interactions have been defined. The latter can give rise to >3 ppm upfield shifts for the Gly-H(N) in -WX(n)G- units both in turns (n = 2) and at the C-termini (n = 1) of hairpins. Terminal YTG units result in somewhat smaller shifts (extrapolated to 2 ppm for 100% folding). In peptides with both the EtF and FtE W/W interaction geometries, Trp to Tyr mutations indicate that Trp is the preferred "face" residue in aryl/aryl pairings, presumably because of its greater pi basicity.
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Affiliation(s)
- Lisa Eidenschink
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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40
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Saha I, Chatterjee B, Shamala N, Balaram P. Crystal structures of peptide enantiomers and racemates: probing conformational diversity in heterochiral Pro-Pro sequences. Biopolymers 2009; 90:537-43. [PMID: 18335426 DOI: 10.1002/bip.20982] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Multiple conformational states in heterochiral diproline sequences have been characterized in the solid state by the determination of the crystal structures of seven tripeptides in enantiomeric and racemic forms. The sequences of the type Piv-DPro-LPro-DXxx-NHMe (D-L-D) [DXxx=DVal 1, DLeu 3, and DPhe 5] and their corresponding enatiomeric L-D-L sequences [LXxx=LVal 2, LLeu 4, and LPhe 6] have been investigated. Single crystals have been obtained for the pure enantiomers 1, 2, 3, 4 and for the racemates 1/2, 3/4, and 5/6. For Xxx=Leu, mirror image conformations (type II/II' beta-turns) at Pro-Leu segment are obtained. For Xxx=Val, a LPro-DPro type II beta-turn in 2 and an open/extended structure is obtained in the solvated form of the enantiomer 1. For Xxx=Phe, suitable crystals could not be obtained for enatiomeric peptides. The racemate 5/6 revealed a cis peptide bond between the diproline segment with the absence of any intramolecular hydrogen bonds. Crystal structures of enantiomers and racemates prove useful in characterizing the multiple conformational states that are accessible to Pro-Pro segments.
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Affiliation(s)
- Indranil Saha
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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41
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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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Oku H, Yamada K, Katakai R. Conformational change from antiparallel beta-sheet to alpha-helix in a series of depsipeptide, -(Leu-Leu-Lac)(n)-: syntheses, spectroscopic studies, and crystal structures of Boc-Leu-Lac-OEt and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2). Biopolymers 2008; 89:270-83. [PMID: 18067154 DOI: 10.1002/bip.20904] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The depsipeptides Boc-Leu-Lac-OEt (1) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2) (2 and 3, respectively) (Boc = tert-butyloxycarbonyl, Lac = L-lactic acid residue) has been synthesized and studied by crystallographic, CD spectroscopic, and ESI-MS analyses. In the packing cells, those three compounds adopt beta-strand conformations. Each molecule is linked into a dimer (1) or an infinite assembly (2 and 3) by tight hydrogen bonds of the type NH...O==C. Interestingly, the hexamer, 3 shows the first example of antiparallel pleated beta-sheet crystal structure for a depsipeptide molecule. In the packing cells, especially for 3, the ester groups O--C==O are perpendicularly oriented to the amide groups NH--C==O and beta-sheet planes to avoid the interaction between --O--(ester) and O==C. Therefore, when the chain length become longer, the O...O==C repulsion interaction works as a beta-sheet breaker and hence promotes an alpha-helical structure as observed for Boc-(Leu-Leu-Lac)(3)-Leu-Leu-OEt (4) (Oku et al. Biopolymers 2004, 75, 242-254) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 4-6) (5-7) (Katakai et al., Biopolymers 1996, 38, 285-290), in which the O...O==C repulsion does not cause significant structural changes in alpha-helical main chains. Therefore from the structural and spectroscopic analyses, we have found governing factors for the specificity in the beta-sheet and alpha-helix decision in this series of depsipeptides, -(Leu-Leu-Lac)(n)-.
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Affiliation(s)
- Hiroyuki Oku
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Gunma, Japan.
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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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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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Mahalakshmi R, Sengupta A, Raghothama S, Shamala N, Balaram P. Tryptophan rich peptides: influence of indole rings on backbone conformation. Biopolymers 2007; 88:36-54. [PMID: 17091496 DOI: 10.1002/bip.20625] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Synthetic peptides with defined secondary structure scaffolds, namely hairpins and helices, containing tryptophan residues, have been investigated in this study to probe the influence of a large number of aromatic amino acids on backbone conformations. Solution NMR investigations of Boc-W-L-W-(D)P-G-W-L-W-OMe (peptide 1), designed to form a well-folded hairpin, clearly indicates the influence of flanking aromatic residues at the (D)Pro-Gly region on both turn nucleation and strand propagation. Indole-pyrrolidine interactions in this peptide lead to the formation of the less-frequent type I' turn at the (D)Pro-Gly segment and frayed strand regions, with the strand residues adopting local helical conformations. An analog of peptide 1 with an Aib-Gly turn-nucleated hairpin (Boc-W-L-W-U-G-W-L-W-OMe (peptide 2)) shows a preference for helical structures in solution, in both chloroform and methanol. Peptides with either one (Boc-W-L-W-U-W-L-W-OMe (peptide 3)) or two (Boc-U-W-L-W-U-W-L-W-OMe (peptide 4)) helix-nucleating Aib residues give rise to the well-folded helical conformations in the chloroform solution. The results are indicative of a preference for helical folding in peptides containing a large number of Trp residues. Investigation of a tetrapeptide analog of peptide 2, Boc-W-U-G-W-OMe (peptide 5), in solution and in the crystal state (by X-ray diffraction), also indicates a preference for a helical fold. Additionally, peptide 5 is stabilized in crystals by both aromatic interactions and an array of weak interactions. Examination of Trp-rich sequences in protein structures, however, reveals no secondary structure preference, suggesting that other stabilizing interactions in a well-folded protein may offset the influence of indole rings on backbone conformations.
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Rai R, Aravinda S, Kanagarajadurai K, Raghothama S, Shamala N, Balaram P. Diproline Templates as Folding Nuclei in Designed Peptides. Conformational Analysis of Synthetic Peptide Helices Containing Amino Terminal Pro-Pro Segments. J Am Chem Soc 2006; 128:7916-28. [PMID: 16771506 DOI: 10.1021/ja060674v] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (alphaR) conformation for the segment residues 2 to 5, stabilized by one 4-->1 hydrogen bond and two 5-->1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P(II)) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alphaR-alphaR conformation, whereas in the latter, a P(II)-alphaR structure is established. The conformational equilibrium shifts in favor of the P(II)-alphaR structure in solvents like methanol and DMSO. A significant population of the Pro(1)-Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro-Pro segment: trans alphaR-alphaR, trans P(II)-alphaR and cis P(II)-alphaR. Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alphaR-alphaR conformation followed by a helix. Modeling and energy minimization studies suggest that both P(II)-alphaR and alphaR-alphaR conformations have very similar energies in the model hexapeptide 1.
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Affiliation(s)
- Rajkishor Rai
- Molecular Biophysics Unit, Department of Physics and NMR Research Centre, Indian Institute of Science, Bangalore, 560 012, India
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Seidler NW, Craig HD, Squire TJ. Endogenous plastic composite material in the Alzheimer's brain. Med Hypotheses 2006; 67:467-70. [PMID: 16678976 DOI: 10.1016/j.mehy.2006.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Accepted: 02/15/2006] [Indexed: 11/17/2022]
Abstract
Accumulation of amyloid beta (Abeta) peptide in brain is the hallmark of Alzheimer's disease (AD). The resulting plaques though fibrous in nature may also consist of additional structures currently poorly defined. We hypothesize that plastic composite material contributes to plaque formation. This material is organized by polymers of acrolein, which is an oxidized lipid fragment found in AD. Acrolein, a 3-carbon compound, contains a carbonyl and a vinyl group that participate in polymerization via fundamental latex chemistry. The redox and surfactant properties of Abeta allow it to catalyze the polymerization of acrolein. We previously reported observations of thin plastic fragments of Abeta-polyacrolein. The current paper outlines the proposed steps in forming these plastic fragments. Endogenous plastic composite material may significantly contribute to the pathogenesis of AD.
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Affiliation(s)
- N W Seidler
- Kansas City University of Medicine and Biosciences, Department of Biochemistry, 1750 Independence Avenue, Kansas City, MO 64106, USA.
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Mahalakshmi R, Raghothama S, Balaram P. NMR analysis of aromatic interactions in designed peptide beta-hairpins. J Am Chem Soc 2006; 128:1125-38. [PMID: 16433528 DOI: 10.1021/ja054040k] [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: 11/29/2022]
Abstract
Designed octapeptide beta-hairpins containing a central (D)Pro-Gly segment have been used as a scaffold to place the aromatic residues Tyr and Trp at various positions on the antiparallel beta-strands. Using a set of five peptide hairpins, aromatic interactions have been probed across antiparallel beta-sheets, in the non-hydrogen bonding position (Ac-L-Y-V-(D)P-G-L-Y/W-V-OMe: peptides 1 and 2), diagonally across the strands (Boc-Y/W-L-V-(D)P-G-W-L-V-OMe: peptides 3 and 6), and along the strands at positions i and i + 2 (Boc-L-L-V-(D)P-G-Y-L-W-OMe: peptide 4). Two peptides served as controls (Boc-L-L-V-(D)P-G-Y-W-V-OMe: peptide 5; Boc-L-Y-V-(D)P-G-L-L-V-OMe: peptide 7) for aromatic interactions. All studies have been carried out using solution NMR methods in CDCl(3) + 10% DMSO-d(6) and have been additionally examined in CD(3)OH for peptides 1 and 2. Inter-ring proton-proton nuclear Overhauser effects (NOEs) and upfield shifted aromatic proton resonances have provided firm evidence for specific aromatic interactions. Calculated NMR structures for peptides 1 and 2, containing aromatic pairs at facing non-hydrogen bonded positions, revealed that T-shaped arrangements of the interacting pairs of rings are favored, with ring current effects leading to extremely upfield chemical shifts and temperature dependences for specific aromatic protons. Anomalous far-UV CD spectra appeared to be a characteristic feature in peptides where the two aromatic residues are spatially proximal. The observation of the close approach of aromatic rings in organic solvents suggests that interactions of an electrostatic nature may be favored. This situation may be compared to the case of aqueous solutions, where clustering of aromatic residues is driven by solvophobic (hydrophobic) forces.
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Roy RS, Gopi HN, Raghothama S, Karle IL, Balaram P. Hybrid peptide hairpins containing alpha- and omega-amino acids: conformational analysis of decapeptides with unsubstituted beta-, gamma-, and delta-residues at positions 3 and 8. Chemistry 2006; 12:3295-302. [PMID: 16453362 PMCID: PMC1435683 DOI: 10.1002/chem.200500742] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The effects of inserting unsubstituted omega-amino acids into the strand segments of model beta-hairpin peptides was investigated by using four synthetic decapeptides, Boc-Leu-Val-Xxx-Val-D-Pro-Gly-Leu-Xxx-Val-Val-OMe: peptide 1 (Xxx=Gly), peptide 2 (Xxx=betaGly=betahGly=homoglycine, beta-glycine), peptide 3 (Xxx=gammaAbu=gamma-aminobutyric acid), peptide 4 (Xxx=deltaAva=delta-aminovaleric acid). 1H NMR studies (500 MHz, methanol) reveal several critical cross-strand NOEs, providing evidence for beta-hairpin conformations in peptides 2-4. In peptide 3, the NMR results support the formation of the nucleating turn, however, evidence for cross-strand registry is not detected. Single-crystal X-ray diffraction studies of peptide 3 reveal a beta-hairpin conformation for both molecules in the crystallographic asymmetric unit, stabilized by four cross-strand hydrogen bonds, with the gammaAbu residues accommodated within the strands. The D-Pro-Gly segment in both molecules (A,B) adopts a type II' beta-turn conformation. The circular dichroism spectrum for peptide 3 is characterized by a negative CD band at 229 nm, whereas for peptides 2 and 4, the negative band is centered at 225 nm, suggesting a correlation between the orientation of the amide units in the strand segments and the observed CD pattern.
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Affiliation(s)
- Rituparna S. Roy
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 (India)
| | - Hosahudya N. Gopi
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 (India)
| | | | - Isabella L. Karle
- Laboratory for the Structure of Matter, Naval Research Laboratory Washington, DC 20375-5341 (USA)
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 (India)
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Nanozipper formation in the solid state from a self-assembling tripeptide with a single tryptophan residue. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.02.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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