Self-Assembling Peptide Nanotubes from Enantiomeric Pairs of Cyclic Peptides with Alternating <scp>d</scp> and <scp>l</scp> Amino Acid Residues

Rosenthal-Aizman, Katri; Svensson, Gunnar; Undén, Anders

doi:10.1021/ja0372659

Cited by 71 publications

(42 citation statements)

References 12 publications

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“…A variety of CPs with flat ring-shaped structures consisting of even number of alternate L-and D-R-amino acids has been synthesized and characterized and their potential applications have been explored. [29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45] In 1972, Hassall proposed the self-assembly of CPs into tubelike conformation through backbone-backbone hydrogen bonding. 46 The same author validated the formation of tubelike structures by backbone-backbone hydrogen bonding using X-ray diffraction studies on the tetrapeptide of cyclo[-(LSer(OtBu)--Ala-Gly--Asp(OMe))-].…”

Section: Introductionmentioning

confidence: 99%

Studies on the Structure and Stability of Cyclic Peptide Based Nanotubes Using Oligomeric Approach: A Computational Chemistry Investigation

et al. 2010

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In this study, an attempt has been made to investigate the structure, dynamics, and stability of cyclic peptide nanotubes (CPNTs) formed by the self-assembly of cyclic peptides (CPs) using classical molecular dynamics (MD) simulation and semiempirical quantum chemistry calculation employing PM6 Hamiltonian with the dispersion correction and hydrogen-bonding interaction (DH2). The structure and energetics of monomer and various oligomeric CPNTs have been investigated by considering the (cyclo-[(D-Ala-L-Ala)(4)]) peptide as the model for CP. Although the formation of CPNTs has been intensively studied, the present study adds valuable information to the de novo design of CPNTs. Various geometrical parameters extracted from the MD simulation reveal that the terminal residues are loosely hydrogen bonded to the inner subunits regardless of degree of oligomerization. The hydrogen bonds present in the inner core regions are stronger than the terminal residues. As the degree of oligomerization increases, the stability of the tube increases due to the hydrogen-bonding and stacking interactions between the subunits. The results show that the binding free energy increases with the extent of oligomerization and reaches saturation beyond pentamer CPNT. In addition, hydrophobic and electrostatic interactions play crucial roles in the formation of CPNTs. Analysis of both structure and energetics of the formation of CPNTs unveils that the self-assembly of dimer, trimer, and tetramer CPNTs are the essential steps in the growth of CPNTs.

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Section: Introductionmentioning

confidence: 99%

Studies on the Structure and Stability of Cyclic Peptide Based Nanotubes Using Oligomeric Approach: A Computational Chemistry Investigation

et al. 2010

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“…Some theoretical studies by ab initio, semiempirical approaches and molecular dynamics (MD) have also been performed to reveal the importance of channels in sustaining biological systems and their potential utility in nanotechnology and biomaterials [21][22][23][24][25][26]. All these work made the structure-property relationship of channels an active area of investigation [27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

Zhu

Cheng

Liao

et al. 2008

J Comput Aided Mol Des

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In order to investigate the structures and properties of cyclic peptide nanotubes of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-], cyclo[(-D: -Phe-L: -Ala)( n = 4)-] was synthesized and self-assembled to nanotubes, and its structure and morphology of the nanotube were characterized by mass spectrometry (MS), fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). On the basis of these experimental results, the structures of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-] were characterized by molecular dynamics. In addition, the motion behaviors of H(2)O molecules in nanotubes were investigated by molecular dynamics using a COMPASS force field. Experimental results show that cyclo[(-D: -Phe-L: -Ala)( n = 4)-] peptides self-assemble into nanotube bundles. Molecular modeling results indicate that cyclic peptide nanotubes with n = 3, 4, 5 and 6 are very stable; these nanotubes have internal diameters of 5.9 A, 8.1 A, 10.8 A and 13.1 A and outer diameters of 18.2 A, 21.7 A, 23.4 A and 25.9 A respectively. Modeling results demonstrate that H(2)O molecules move in cooperation in single nanotube and they diffuse in one dimension, but they did not diffuse unilaterally due to the antiparallel ring stacking arrangement.

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“…[12,38] The steric clashes between closely neighbouring, bulky Tle homochiral residues may hamper the formation of self-assembled peptide nanotubes. [39] Tle has been successfully site-specifically incorporated into proteins by biosynthetic methodologies. [40] Results and Discussion Synthesis and characterization: For the large-scale production of enantiomerically pure l-Tle, an economically attractive and generally applicable chemoenzymatic synthesis developed by DSM Research a few years ago [41][42][43] was exploited.…”

Section: Introductionmentioning

confidence: 99%

Preferred Conformations of Peptides Containing tert‐Leucine, a Sterically Demanding, Lipophilic α‐Amino Acid with a Quaternary Side‐Chain C^β Atom

Formaggio

Baldini

Moretto

et al. 2005

Chemistry A European J

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Terminally protected homopeptides of tert-leucine, from the dimer to the hexamer, co-oligopeptides of tert-leucine in combination with alpha-aminoisobutyric acid or glycine residues up to the hexamer level, and simple dipeptides representing known scaffolds for catalysts in asymmetric organic reactions were prepared by solution methods and fully characterized. The results of conformation analysis, performed by use of FT-IR absorption, NMR, CD, and X-ray diffraction techniques, indicate that this hydrophobic alpha-amino acid with tetrasubstitution at the Cbeta atom is structurally versatile. We show that it prefers extended or semiextended conformations, but can also be accommodated in folded structures, provided that these are biased by the presence of helicogenic residues. The current large-scale production of Tle, combined with its conformational preferences unravelled in this work, should make this bulky, hydrophobic, Calpha-trisubstituted alpha-amino acid a regular building block of any strategy seeking to tailor peptides with improved catalytic and pharmacological properties.

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Self-Assembling Peptide Nanotubes from Enantiomeric Pairs of Cyclic Peptides with Alternating d and l Amino Acid Residues

Cited by 71 publications

References 12 publications

Studies on the Structure and Stability of Cyclic Peptide Based Nanotubes Using Oligomeric Approach: A Computational Chemistry Investigation

Studies on the Structure and Stability of Cyclic Peptide Based Nanotubes Using Oligomeric Approach: A Computational Chemistry Investigation

Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

Preferred Conformations of Peptides Containing tert‐Leucine, a Sterically Demanding, Lipophilic α‐Amino Acid with a Quaternary Side‐Chain C^β Atom

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Self-Assembling Peptide Nanotubes from Enantiomeric Pairs of Cyclic Peptides with Alternating d and l Amino Acid Residues

Cited by 71 publications

References 12 publications

Studies on the Structure and Stability of Cyclic Peptide Based Nanotubes Using Oligomeric Approach: A Computational Chemistry Investigation

Studies on the Structure and Stability of Cyclic Peptide Based Nanotubes Using Oligomeric Approach: A Computational Chemistry Investigation

Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

Preferred Conformations of Peptides Containing tert‐Leucine, a Sterically Demanding, Lipophilic α‐Amino Acid with a Quaternary Side‐Chain Cβ Atom

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Preferred Conformations of Peptides Containing tert‐Leucine, a Sterically Demanding, Lipophilic α‐Amino Acid with a Quaternary Side‐Chain C^β Atom