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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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Zou J, Zhou M, Xiao X, Liu R. Advance in Hybrid Peptides Synthesis. Macromol Rapid Commun 2022; 43:e2200575. [PMID: 35978269 DOI: 10.1002/marc.202200575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/24/2022] [Indexed: 11/08/2022]
Abstract
Hybrid peptides with heterogeneous backbone are a class of peptide mimics with adjustable proteolytic stability obtained from incorporating unnatural amino acid residues into peptide backbone. α/β-peptides and peptide/peptoid hybrids are two types of hybrid peptides that are widely studied for diverse applications, and several synthetic methods have been developed. In this mini review, the advance in hybrid peptide synthesis is summarized, including solution-phase method, solid-phase method, and novel polymerization method. Conventional solution-phase method and solid-phase method generally result in oligomers with defined sequences, while polymerization methods have advantages in preparing peptide hybrid polymers with high molecular weight with simple operation and low cost. In addition, the future development of polymerization method to realize the control of the peptide hybrid polymer sequence is discussed.
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Affiliation(s)
- Jingcheng Zou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Min Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ximian Xiao
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Runhui Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
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3
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Debnath S, Ghosh S, Pandit G, Satpati P, Chatterjee S. Effect of Differential Geminal Substitution of γ Amino Acid Residues at the ( i + 2) Position of αγ Turn Segments on the Conformation of Template β-Hairpin Peptides. J Org Chem 2021; 86:11310-11323. [PMID: 34479402 DOI: 10.1021/acs.joc.1c00351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The effect of insertion of three geminally dimethyl substituted γ amino acid residues [γ2,2 (4-amino-2,2-dimethylbutanoic acid), γ3,3 (4-amino-3,3-dimethylbutanoic acid), and γ4,4 (4-amino-4,4-dimethylbutanoic acid)] at the (i + 2) position of a two-residue αγ C12 turn segment in a model octapeptide sequence Leu-Phe-Val-Aib-Xxx-Leu-Phe-Val (where Xxx = γ amino acid residues) has been investigated in this study. Solution conformational studies (NMR, CD, and IR) and ab initio calculations indicated that γ3,3 and γ4,4 residues were well accommodated in the β-hairpin nucleating αγ C12 turns, which gave rise to well-registered hairpins, in contrast to γ2,2, which was unable to form a tight C12 β-hairpin nucleating turn and promote a well-registered β-hairpin. Geminal disubstitution at the Cα carbon in γ2,2 led to unfavorable steric contacts, disabling its accommodation in the αγ C12 hairpin nucleating turn unlike the γ3,3 and γ4,4 residues. Geminal substitutions at different carbons along the backbone constrained backbone torsion angles for the three γ amino acid residues differently, generating diverse conformational preferences in them. Folded hairpins were energetically more stable (∼8 to 9 kcal/mol) than the unfolded peptides. Conformational preference of the peptides was independent of the N-terminal protecting group. Such fundamental understanding will instrumentalize the future directed design of foldamers.
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Affiliation(s)
- Swapna Debnath
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Suvankar Ghosh
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Gopal Pandit
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Priyadarshi Satpati
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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4
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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Lou S, Wang X, Yu Z, Shi L. Peptide Tectonics: Encoded Structural Complementarity Dictates Programmable Self-Assembly. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802043. [PMID: 31380179 PMCID: PMC6662064 DOI: 10.1002/advs.201802043] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/20/2019] [Indexed: 05/23/2023]
Abstract
Programmable self-assembly of peptides into well-defined nanostructures represents one promising approach for bioinspired and biomimetic synthesis of artificial complex systems and functional materials. Despite the progress made over the past two decades in the development of strategies for precise manipulation of the self-assembly of peptides, there is a remarkable gap between current peptide assemblies and biological systems in terms of structural complexity and functions. Here, the concept of peptide tectonics for the creation of well-defined nanostructures predominately driven by the complementary association at the interacting interfaces of tectons is introduced. Peptide tectons are defined as peptide building blocks exhibiting structural complementarity at the interacting interfaces of commensurate domains and undergoing programmable self-assembly into defined supramolecular structures promoted by complementary interactions. Peptide tectons are categorized based on their conformational entropy and the underlying mechanism for the programmable self-assembly of peptide tectons is highlighted focusing on the approaches for incorporating the structural complementarity within tectons. Peptide tectonics not only provides an alternative perspective to understand the self-assembly of peptides, but also allows for precise manipulation of peptide interactions, thus leading to artificial systems with advanced complexity and functions and paves the way toward peptide-related functional materials resembling natural systems.
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Affiliation(s)
- Shaofeng Lou
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Xinmou Wang
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
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Buß O, Muller D, Jager S, Rudat J, Rabe KS. Improvement in the Thermostability of a β-Amino Acid Converting ω-Transaminase by Using FoldX. Chembiochem 2017; 19:379-387. [PMID: 29120530 DOI: 10.1002/cbic.201700467] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 12/19/2022]
Abstract
ω-Transaminases (ω-TAs) are important biocatalysts for the synthesis of active, chiral pharmaceutical ingredients containing amino groups, such as β-amino acids, which are important in peptidomimetics and as building blocks for drugs. However, the application of ω-TAs is limited by the availability and stability of enzymes with high conversion rates. One strategy for the synthesis and optical resolution of β-phenylalanine and other important aromatic β-amino acids is biotransformation by utilizing an ω-transaminase from Variovorax paradoxus. We designed variants of this ω-TA to gain higher process stability on the basis of predictions calculated by using the FoldX software. We herein report the first thermostabilization of a nonthermostable S-selective ω-TA by FoldX-guided site-directed mutagenesis. The melting point (Tm ) of our best-performing mutant was increased to 59.3 °C, an increase of 4.0 °C relative to the Tm value of the wild-type enzyme, whereas the mutant fully retained its specific activity.
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Affiliation(s)
- Oliver Buß
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Delphine Muller
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Sven Jager
- Computational Biology, Technische Universität Darmstadt, Schnittspahnstrasse 2, 64287, Darmstadt, Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces I, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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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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8
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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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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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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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Sivakama Sundari C, Bikshapathy E, Nagaraj R. Self-assembly of a peptide with a tandem repeat of the Aβ16-22 sequence linked by a β turn-promoting dipeptide sequence. Biopolymers 2015; 104:790-803. [DOI: 10.1002/bip.22753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 09/21/2015] [Accepted: 10/10/2015] [Indexed: 12/31/2022]
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12
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Lengyel GA, Reinert ZE, Griffith BD, Horne WS. Comparison of backbone modification in protein β-sheets by α→γ residue replacement and α-residue methylation. Org Biomol Chem 2015; 12:5375-81. [PMID: 24909436 DOI: 10.1039/c4ob00886c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The mimicry of protein tertiary structure by oligomers with unnatural backbones is a significant contemporary research challenge. Among common elements of secondary structure found in natural proteins, sheets have proven the most difficult to address. Here, we report the systematic comparison of different strategies for peptide backbone modification in β-sheets with the goal of identifying the best method for replacing a multi-stranded sheet in a protein tertiary fold. The most effective sheet modifications examined led to native-like tertiary folding behavior with a thermodynamic folded stability comparable to the prototype protein on which the modified backbones are based.
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Affiliation(s)
- George A Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Portillo A, Hashemi M, Zhang Y, Breydo L, Uversky VN, Lyubchenko YL. Role of monomer arrangement in the amyloid self-assembly. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:218-28. [PMID: 25542374 DOI: 10.1016/j.bbapap.2014.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/24/2014] [Accepted: 12/10/2014] [Indexed: 02/05/2023]
Abstract
Assembly of amyloid proteins into aggregates requires the ordering of the monomers in oligomers and especially in such highly organized structures as fibrils. This ordering is accompanied by structural transitions leading to the formation of ordered β-structural motifs in proteins and peptides lacking secondary structures. To characterize the effect of the monomer arrangements on the aggregation process at various stages, we performed comparative studies of the yeast prion protein Sup35 heptapeptide (GNNQQNY) along with its dimeric form CGNNQQNY-(d-Pro)-G-GNNQQNY. The (d-Pro)-G linker in this construct is capable of adopting a β-turn, facilitating the assembly of the dimer into the dimeric antiparallel hairpin structure (AP-hairpin). We applied Atomic Force Microscopy (AFM) techniques to follow peptide-peptide interactions at the single molecule level, to visualize the morphology of aggregates formed by both constructs, thioflavin T (ThT) fluorescence to follow the aggregation kinetics, and circular dichroism (CD) spectroscopy to characterize the secondary structure of the constructs. The ThT fluorescence data showed that the AP-hairpin aggregation kinetics is insensitive to the external environment such as ionic strength and pH contrary to the monomers the kinetics of which depends dramatically on the ionic strength and pH. The AFM topographic imaging revealed that AP-hairpins primarily assemble into globular aggregates, whereas linear fibrils are primary assemblies of the monomers suggesting that both constructs follow different aggregation pathways during the self-assembly. These morphological differences are in line with the AFM force spectroscopy experiments and CD spectroscopy measurements, suggesting that the AP-hairpin is structurally rigid regardless of changes of environmental factors.
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Affiliation(s)
- Alexander Portillo
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Leonid Breydo
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33647, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33647, USA; Department of Biological Science, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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14
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Structural preferences of two unnatural hybrid octapeptides with and without the crystal environment: a computational study. Theor Chem Acc 2014. [DOI: 10.1007/s00214-013-1444-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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15
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Sonti R, Gopi HN, Muddegowda U, Ragothama S, Balaram P. A Designed Three-Stranded β-Sheet in an α/β Hybrid Peptide. Chemistry 2013; 19:5955-65. [DOI: 10.1002/chem.201204327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Indexed: 01/25/2023]
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16
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Lengyel GA, Eddinger GA, Horne WS. Introduction of Cyclically Constrained γ-Residues Stabilizes an α-Peptide Hairpin in Aqueous Solution. Org Lett 2013; 15:944-7. [DOI: 10.1021/ol4001125] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- George A. Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Geoffrey A. Eddinger
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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17
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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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18
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Abstract
Progress in the quantum mechanics of biological molecules is being driven by computational advances. The notion of quantum kernels can be introduced to simplify the formalism of quantum mechanics, making it especially suitable for parallel computation of very large biological molecules. The essential idea is to mathematically break large biological molecules into smaller kernels that are calculationally tractable, and then to represent the full molecule by a summation over the kernels. The accuracy of the kernel energy method (KEM) is shown by systematic application to a great variety of molecular types found in biology. These include peptides, proteins, DNA and RNA. Examples are given that explore the KEM across a variety of chemical models, and to the outer limits of energy accuracy and molecular size. KEM represents an advance in quantum biology applicable to problems in medicine and drug design.
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van der Knaap M, Basalan F, van de Mei HC, Busscher HJ, van der Marel GA, Overkleeft HS, Overhand M. Synthesis and Biological Evaluation of Gramicidin S-Inspired Cyclic Mixedα/β-Peptides. Chem Biodivers 2012; 9:2494-506. [DOI: 10.1002/cbdv.201200277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Indexed: 11/06/2022]
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20
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Lengyel GA, Horne WS. Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β-Sheets by α/β-Peptides. J Am Chem Soc 2012; 134:15906-13. [DOI: 10.1021/ja306311r] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- George A. Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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21
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Sharma GVM, Yadav TA, Choudhary M, Kunwar AC. Design of β-Amino Acid with Backbone–Side Chain Interactions: Stabilization of 14/15-Helix in α/β-Peptides. J Org Chem 2012; 77:6834-48. [DOI: 10.1021/jo300865d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Gangavaram V. M. Sharma
- Organic and
Biomolecuar Chemistry
Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Thota Anupama Yadav
- Organic and
Biomolecuar Chemistry
Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Madavi Choudhary
- Centre for Nuclear Magnetic Resonance, CSIR-Indian Institute of Chemical Technology, Hyderabad
500 007, India
| | - Ajit C. Kunwar
- Centre for Nuclear Magnetic Resonance, CSIR-Indian Institute of Chemical Technology, Hyderabad
500 007, India
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22
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van der Knaap M, Otero JM, Llamas-Saiz A, van Raaij MJ, Lageveen LI, Busscher HJ, Grotenbreg GM, van der Marel GA, Overkleeft HS, Overhand M. Design, synthesis and structural analysis of mixed α/β-peptides that adopt stable cyclic hairpin-like conformations. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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23
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Segman-Magidovich S, Lee MR, Vaiser V, Struth B, Gellman SH, Rapaport H. Sheet-Like Assemblies of Charged Amphiphilic α/β-Peptides at the Air-Water Interface. Chemistry 2011; 17:14857-66. [DOI: 10.1002/chem.201101775] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Indexed: 11/10/2022]
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24
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Affiliation(s)
- W Seth Horne
- University of Pittsburgh, Department of Chemistry,
219 Parkman Ave., Pittsburgh, PA 15260, USA
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25
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Pilsl LKA, Reiser O. α/β-Peptide foldamers: state of the art. Amino Acids 2011; 41:709-18. [DOI: 10.1007/s00726-011-0894-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 03/18/2011] [Indexed: 11/24/2022]
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26
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Lengyel GA, Frank RC, Horne WS. Hairpin folding behavior of mixed α/β-peptides in aqueous solution. J Am Chem Soc 2011; 133:4246-9. [PMID: 21370877 DOI: 10.1021/ja2002346] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The invention of new strategies for the design of protein-mimetic oligomers that manifest the folding encoded in natural amino acid sequences is a significant challenge. In contrast to the α-helix, mimicry of protein β-sheets is less understood. We report here the aqueous folding behavior of a prototype α-peptide hairpin model sequence varied at cross-strand positions by incorporation of 16 different β-amino acid monomers. Our results provide a folding propensity scale for β-residues in a protein β-sheet context as well as high-resolution structures of several mixed-backbone α/β-peptide hairpins in water.
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Affiliation(s)
- George A Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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27
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Structural Chemistry of Peptides Containing Backbone Expanded Amino Acid Residues: Conformational Features of β, γ, and Hybrid Peptides. Chem Rev 2010; 111:657-87. [DOI: 10.1021/cr100100x] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Prema. G. Vasudev
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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28
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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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29
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Segman S, Lee MR, Vaiser V, Gellman S, Rapaport H. Highly Stable Pleated-Sheet Secondary Structure in Assemblies of Amphiphilic α/β-Peptides at the Air-Water Interface. Angew Chem Int Ed Engl 2009; 49:716-9. [DOI: 10.1002/anie.200904566] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Segman S, Lee MR, Vaiser V, Gellman S, Rapaport H. Highly Stable Pleated-Sheet Secondary Structure in Assemblies of Amphiphilic α/β-Peptides at the Air-Water Interface. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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An efficient synthetic approach towards trans-β2,3-amino acids and demonstration of their utility in the design of therapeutically important β2,3-peptides and α,β2,3-peptide aldehydes. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.09.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Dutt A, Dutta A, Kar S, Koley P, Drew MG, Pramanik A. Stabilization of two smallest possible diastereomeric β-hairpins in a water soluble tetrapeptide containing non-coded α-amino isobutyric acid (Aib) and m-amino benzoic acid. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.03.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Chatterjee S, Vasudev PG, Raghothama S, Ramakrishnan C, Shamala N, Balaram P. Expanding the Peptide β-Turn in αγ Hybrid Sequences: 12 Atom Hydrogen Bonded Helical and Hairpin Turns. J Am Chem Soc 2009; 131:5956-65. [DOI: 10.1021/ja900618h] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunanda Chatterjee
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Prema G. Vasudev
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Srinivasarao Raghothama
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Chandrasekharan Ramakrishnan
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Narayanaswamy Shamala
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Department of Physics, and NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
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34
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Barbaras D, Gademann K. Stable β Turns of Tripeptides in Water through Cation-π Interactions. Chembiochem 2008; 9:2398-401. [DOI: 10.1002/cbic.200800344] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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35
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Vasudev PG, Rai R, Shamala N, Balaram P. Conformations of beta-amino acid residues in peptides: X-ray diffraction studies of peptides containing the achiral residue 1-aminocyclohexaneacetic acid, beta3,3Ac6c. Biopolymers 2008; 90:138-50. [PMID: 18273891 DOI: 10.1002/bip.20957] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The conformational preferences of the 3,3-disubstituted beta-amino acid residue, 1-aminocyclohexaneacetic acid (beta3,3Ac6c) have been investigated by determining the crystal structures of the parent amino acid, the hydrochloride derivative, 10 protected derivatives and di and tripeptides. The symmetrical cyclohexyl substituent at the beta-position restricts the values of the torsion angles phi (N--C(beta)) and theta (C(beta)--C(alpha)) to approximately gauche values (+/-60 degrees ). Relatively few intramolecularly hydrogen bonded conformations are observed. In the dipeptide Boc-beta(3,3)Ac6c-beta(3,3)Ac6c-NHMe a C6 hydrogen bond is observed. In Piv-Pro-beta(3,3)Ac6c-NHMe a C11 hydrogen bonded hybrid alphabeta turn is characterized. In a majority of cases the amino group occupies the axial position in the cyclohexane ring. The conformations observed are compared with crystallographically observed structures for other beta-residues, including beta(2,2)Ac6c.
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Affiliation(s)
- Prema G Vasudev
- Department of Physics, Indian Institute of Science, Bangalore 560 012, India
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36
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Bautista AD, Craig CJ, Harker EA, Schepartz A. Sophistication of foldamer form and function in vitro and in vivo. Curr Opin Chem Biol 2007; 11:685-92. [PMID: 17988934 DOI: 10.1016/j.cbpa.2007.09.009] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 09/26/2007] [Indexed: 01/24/2023]
Abstract
Advances in the foldamer field in recent years are as diverse as the backbones of which they are composed. Applications have ranged from cellular penetration and membrane disruption to discrete molecular recognition, while efforts to control the complex geometric shape of foldamers has entered the realm of tertiary and quaternary structure. This review will provide recent examples of progress in the foldamer field, highlighting the significance of this class of compounds and the advances that have been made towards exploiting their full potential.
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Affiliation(s)
- Arjel D Bautista
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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37
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Zanuy D, Rodríguez-Ropero F, Nussinov R, Alemán C. Testing β-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study. J Struct Biol 2007; 160:177-89. [PMID: 17897839 DOI: 10.1016/j.jsb.2007.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 07/25/2007] [Accepted: 07/31/2007] [Indexed: 11/20/2022]
Abstract
The search for new building block templates useful for nanostructures design, targets protein motifs with a wide range of structures. Stabilizing these building blocks when extracted from their natural environment becomes a fundamental goal in order to successfully control their assembly. Targeted replacements of natural residues by conformationally constrained amino acids were shown to be a successful strategy to achieve such stabilization. In this work, the effect of replacing natural amino acids by non-proteogenic residues in a beta-helix building block has been evaluated using extensive molecular dynamics simulations. Here, we focus on systematic substitutions of valine residues present in beta-sheet segments of a beta-helical building block excised from Escherichia coli galactoside acetyltransferase, residues 131-165. Four different types of non-proteogenic amino acids have been considered for substitution: (i) one dehydroamino acid, (ii) two d-amino acids, (iii) one beta-amino acid and (iv) two alpha,alpha-dialkylamino acids. Our results indicate that the ability of non-proteogenic amino acids to stabilize small building block motifs is site-dependent. We conclude that if the replacement does not alter the energy balance between attractive non-covalent interactions and steric hindrance, synthetic residues are suitable candidates to nucleate beta-helix formation.
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Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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38
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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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39
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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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40
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Stereoselective synthesis of (−)-bulgecinine hydrochloride and its C-2 epimer from l-ascorbic acid. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.tetasy.2006.10.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Seebach D, Jaun B, Sebesta R, Mathad R, Flögel O, Limbach M, Sellner H, Cottens S. Synthesis, and Helix or Hairpin-Turn Secondary Structures of ‘Mixed’α/β-Peptides Consisting of Residues with Proteinogenic Side Chains and of 2-Amino-2-methylpropanoic Acid (Aib). Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690176] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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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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43
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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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44
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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.
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Affiliation(s)
- Kuppanna Ananda
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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45
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Lelais G, Seebach D, Jaun B, Mathad R, Flögel O, Rossi F, Campo M, Wortmann A. β-Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way toβ-Peptidic Zinc Fingers? Helv Chim Acta 2006. [DOI: 10.1002/hlca.339] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Lelais G, Seebach D, Jaun B, Mathad R, Flögel O, Rossi F, Campo M, Wortmann A. β-Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way toβ-Peptidic Zinc Fingers? Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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47
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Roy RS, Gopi HN, Raghothama S, Gilardi RD, Karle IL, Balaram P. Peptide hairpins with strand segments containing alpha- and beta-amino acid residues: cross-strand aromatic interactions of facing Phe residues. Biopolymers 2006; 80:787-99. [PMID: 15895435 PMCID: PMC1380308 DOI: 10.1002/bip.20294] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The incporation of beta-amino acid residues into the strand segments of designed beta-hairpin leads to the formation of polar sheets, since in the case of beta-peptide strands, all adjacent carbonyl groups point in one direction and the amide groups orient in the opposite direction. The conformational analysis of two designed peptide hairpins composed of alpha/beta-hybrid segments are described: Boc-Leu-betaPhe-Val-(D)-Pro-Gly-Leu-betaPhe-Val-OMe (1) and Boc-betaLeu-Phe-betaVal-D-Pro-Gly-betaLeu-Phe-betaVal-OMe (2). A 500-MHz 1H-NMR (nuclear magnetic resonance) analysis in methanol supports a significant population of hairpin conformations in both peptides. Diagnostic nuclear Overhauser effects (NOEs) are observed in both cases. X-ray diffraction studies on single crystals of peptide 1 reveal a beta-hairpin conformation in both the molecules, which constitute the crystallographic asymmetric unit. Three cross-strand hydrogen bonds and a nucleating type II' beta-turn at the D-Pro-Gly segment are observed in the two independent molecules. In peptide 1, the betaPhe residues at positions 2 and 7 occur at the nonhydrogen-bonding position, with the benzyl side chains pointing on opposite faces of the beta-sheet. The observed aromatic centroid-to-centroid distances are 8.92 A (molecule A) and 8.94 A (molecule B). In peptide 2, the aromatic rings must occupy facing positions in antiparallel strands, in the NMR-derived structure. Peptide 1 yields a normal "hairpin-like" CD spectrum in methanol with a minimum at 224 nm. The CD spectrum of peptide 2 reveals a negative band at 234 nm and a positive band at 221 nm, suggestive of an exciton split doublet. Modeling of the facing Phe side chains at the hydrogen-bonding position of a canonical beta-hairpin suggests that interring separation is approximately 4.78 A for the gauche+ gauche- (g+ g-) rotamer. A previously reported peptide beta-hairpin composed of only alpha-amino acids, Boc-Leu-Phe-Val-D-Pro-Gly-Leu-Phe-Val-OMe also exhibited an anomalous far-UV (ultraviolet) CD (circular dichroism) spectrum, which was interpreted in terms of interactions between facing aromatic chromophores, Phe 2 and Phe 7 (C. Zhao, P. L. Polavarapu, C. Das, and P. Balaram, Journal of the American Chemical Society, 2000, Vol 122, pp. 8228-8231).
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Affiliation(s)
- Rituparna S Roy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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Abstract
Peptoids of alpha- and beta-peptides (alpha- and beta-peptoids) can be obtained by shifting the amino acid side chains from the backbone carbon atoms of the monomer constituents to the peptide nitrogen atoms. They are, therefore, N-substituted poly-glycines and poly-beta-alanines, respectively. Due to the substituted nitrogen atoms, the ability for hydrogen bond formation between peptide bonds gets lost. It may be very interesting to see whether such non-natural oligomers could be regarded as foldamers, which fold into definite backbone conformers. In this paper, we provide a complete overview on helix formation in alpha- and beta-peptoids on the basis of systematic theoretical conformational analyses employing the methods of ab initio molecular orbital (MO) theory. It can be shown that the alpha- and beta-peptoid structures form helical structures with both trans and cis peptide bonds despite the missing hydrogen bonds. Obviously, the conformational properties of the backbone are more important for folding than the possibility of hydrogen bonding. There are close relationships between the helices of alpha-peptoids and poly-glycine and poly-proline helices of alpha-peptides, whereas the helices of beta-peptoids correspond to the well-known helical structures of beta-peptides as, for instance, the 3(1)-helix of beta-peptides with 14-membered hydrogen-bonded rings. Thus, alpha- and beta-peptoids enrich the field of foldamers and may be used as useful tools in peptide and protein design.
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Affiliation(s)
- Carsten Baldauf
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, D-04103 Leipzig, Germany
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Sengupta A, Roy RS, Sabareesh V, Shamala N, Balaram P. Aggregation modes in sheets formed by protected β-amino acids and β-peptides. Org Biomol Chem 2006; 4:1166-73. [PMID: 16525563 DOI: 10.1039/b516088j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of four protected beta-amino acid residues, Boc-(S)-beta3-HAla-NHMe (1); Boc-(R)-beta3-HVal-NHMe (2); Boc-(S)-beta3-HPhe-NHMe (3); Boc-(S)-beta3-HPro-OH (6) and two beta-dipeptides, Boc-(R)-beta3-HVal-(R)-beta3-HVal-OMe (4); Boc-(R)-beta3-HVal-(S)-beta3-HVal-OMe (5) have been determined. Gauche conformations about the C(beta)-C(alpha) bonds (theta approximately +/-60 degrees) are observed for the beta3-HPhe residues in and all four beta3-HVal residues in the dipeptides and . Trans conformations (theta is approximately 180 degrees) are observed for beta3-HAla residues in both independent molecules in and for the beta3-HVal and beta3-HPro residues in and , respectively. In the cases of compounds , molecules associate in the crystals via intermolecular backbone hydrogen bonds leading to the formation of sheets. The polar strands formed by beta3-residues aggregate in both parallel (1,3,5) and antiparallel (2,4 fashion. Sheet formation accommodates both the trans and gauche conformations about the C(beta)-C(alpha) bonds.
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Affiliation(s)
- Anindita Sengupta
- Department of Physics, Indian Institute of Science, Bangalore, 560 012, India
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