Theoretical investigation of the self-assembly of cyclo[(-β3-HGly)4-]

Tan, Hongwei; Qu, Wenwen; Chen, Guangju; Liu, Ruo‐Zhuang

doi:10.1016/s0009-2614(02)02031-6

Cited by 23 publications

(24 citation statements)

References 14 publications

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“…All cyclic peptides in these oligomers with C 4 symmetry maintain their original conformations with the NOH and CAO groups nearly at a right angle (90 Ϯ 3°) with respect to the plane of the ring. Along the C 4 axis, hardly any angular deflection between two adjacent cyclic peptides could be observed in both parallel and antiparallel oligomers, which differed from a helical feature of cyclo[(-␤ 3 -HGly-) 4 ] oligomers [22]. The symmetrical character is also in accord with the crystal structures of several antiparallel stacking cyclic d,l-␣-peptides [3].…”

Section: Structures Of the Parallel-stacked And Antiparallel-stacked supporting

confidence: 56%

“…Stronger support comes from more accurate calculations using density functional method B3LYP/6-31g for the modified parallel 4 ] calculated by B3LYP/6-31g and PBE1PBE/D95* also display the similar distribution of net charge. Clearly, the calculations show different variations as those of ␤ 3 cyclic peptide nanotube [22]. The reason for such a result lies in the unique structure of the cyclic d,l-␣-peptide.…”

Section: The Cooperativity Of Dl-␣-peptides Systemsmentioning

confidence: 90%

“…In ␤ 3 peptide nanotube, such charge transfer process will induce the charge redistribution in the whole tube. The accumulation of positive and negative charge at two termini of the tube will bring additional stability, which is thought to be the origin of the cooperative effect [22,25]. But the calculation results of the cyclo[(-l-Phe-d-Ala-) 4 ] oligomers using AM1 method reveal that there is no obvious variation of net charge in individual peptide rings whether they take parallel or antiparallel stacking mode.…”

Section: The Cooperativity Of Dl-␣-peptides Systemsmentioning

confidence: 99%

“…Moreover, our recent study found that the competition exists between parallel stacking and antiparallel stacking modes in lower oligomers of certain kinds of cyclic d,l-␣-peptide systems which could self-assemble through H-bonding interactions between both backbone-backbone and cross-strand side chains [20,21]. Another study of cyclic ␤ 3 -peptide tubular ensembles [22] demonstrated that there is a cooperative effect of weak interactions, which is thought as the essential driving force for this kind of cyclic peptide to form stable nanotubes. Thus far, the theoretical study on cyclic d,l-␣-peptide nanotubes has been mainly limited to dimers.…”

Section: Introductionmentioning

confidence: 99%

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The self‐assembled of cyclic D,L‐α‐peptide systems: Insights into the structure and energetics

Tan

Chen

et al. 2009

Int J of Quantum Chemistry

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Cyclic d,l-␣-peptides are able to self-assemble to nanotubes, although the inherent reason of the stability of this kind of nanotube as well as the intrinsic driving force of self-assembly of the cyclic d,l-␣-peptides still remain elusive. In this work, using several computational approaches, we investigated the structural and energy characteristics of a seriesThe results reveal that the thermodynamic stability, cooperativity, and self-assembly patterns of cyclic d,l-␣-peptide nanotubes are mainly determined by the interactions between cross-strand side chains instead of those between backbones. For cyclo[(-l-Phe-d-Ala-) 4 ] oligomers, the steric interaction between cross-strand side chains, especially the electrostatic repulsion between the phenyls in Phe residues, brings anticooperative effect into parallel stacking mode, which is responsible for the preference of self-assembling nanotube in antiparallel vs. parallel stacking orientation. Based on our results, a novel self-assembling mechanism is put forward-it is the l-l antiparallel dimer of cyclo [(-l-Phe-d-Ala-) 4 ], instead of the commonly presumed monomer, that acts as the basic building block in self assembly. It explains why these cyclic peptides uniquely self-assemble to form antiparallel nanotubes.

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Section: Structures Of the Parallel-stacked And Antiparallel-stacked supporting

confidence: 56%

Section: The Cooperativity Of Dl-␣-peptides Systemsmentioning

confidence: 90%

Section: The Cooperativity Of Dl-␣-peptides Systemsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The self‐assembled of cyclic D,L‐α‐peptide systems: Insights into the structure and energetics

Tan

Chen

et al. 2009

Int J of Quantum Chemistry

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“…56 The same type of calculations have been carried out to characterize the energetic and structural properties of cyclo[(-3 -HGly) 4 -] and its oligomers. 57 It has been found that the gradual increase in the oligomerization facilitates the enhancement of favorable interaction of the CPNT. It is observed from the molecular dynamics simulation study on CPNT consisting of eight cyclo[(L-Trp-DLeu) 3 -L-Gln-D-Leu] embedded in a fully hydrated DMPC bilayer that the embedded CPNT function as synthetic, integral transmembrane channels.…”

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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Selective Complexation of S‐block Cations with Nanotubular Silk Type Cyclopeptides: A DFT Study

Teimouri

Najari

Chermahini

et al. 2015

J Chinese Chemical Soc

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Density functional theory (DFT) was used to study the interaction of alkali metal cations (Li + , Na + and K + ) with cyclic peptides constructed from silk type macrocycles (Silk1, Silk2, Silk3, Silk4, Silk5 and Silk6). The calculated binding energies were used as a base for investigating the selectivity of the cyclic peptides in biniding to considered metals ions. The highest cation selectivity for Li + compared to the other alkali metal ions was observed. The orbital nature of different interactions between the metal cations and the cyclic peptides was analyzed using NBO analysis. The main types of driving force for host-guest interactions was investigated and it was found that the electron-donating O offers lone pair electrons to the contacting LP* of alkali metal cations.

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Theoretical investigation of the self-assembly of cyclo[(-β3-HGly)4-]

Cited by 23 publications

References 14 publications

The self‐assembled of cyclic D,L‐α‐peptide systems: Insights into the structure and energetics

The self‐assembled of cyclic D,L‐α‐peptide systems: Insights into the structure and energetics

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

Selective Complexation of S‐block Cations with Nanotubular Silk Type Cyclopeptides: A DFT Study

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