Theoretical Studies of Monomer and Dimer of Cyclo[(−<scp>l</scp>-Phe-<scp>d</scp>-Ala−)n] and Cyclo[(−<scp>l</scp>-Phe1-<scp>d</scp>-MeN-Ala2−)n] (n = 3−6)

Chen, Guangju; Su, Shujun; Liu, Ruo‐Zhuang

doi:10.1021/jp0114790

Cited by 54 publications

(48 citation statements)

References 19 publications

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“…The number of hydrogen bonds during the initial 1 ns of constrained MD is not plotted in the figure, as it is expected to be eight for all the systems. The quantum mechanical studies by Chen et al 10 showed that the conformation for the optimized cyclo [(-L-Phe-D-N-MeAla-) 4 -] is distorted to a certain extent compared to that for cyclo [(-L-Phe-D-Ala-) 4 -]. It was observed that the angles of NH and CO with respect to the ring plane in the capped ring depart farther than that found for the uncapped ring.…”

Section: Resultsmentioning

confidence: 99%

Self-Assembling Cyclic Peptides: Molecular Dynamics Studies of Dimers in Polar and Nonpolar Solvents

et al. 2006

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The self-assembly of cyclic D,L-R-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-) 4 -] 2 and cyclo [(-L-Trp-D-Leu-) 4 -] 2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the and ψ dihedral angles of a single uncapped ring in nonane lie in the -sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.

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Section: Resultsmentioning

confidence: 99%

Self-Assembling Cyclic Peptides: Molecular Dynamics Studies of Dimers in Polar and Nonpolar Solvents

et al. 2006

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“…Consequently, the semiempirical molecular orbital method is the only option. Our previous study has proved that cyclo[(-l-Phe-d-Ala-) 4 ] and its dimers optimized by both semiempirical molecular orbital AM1 method and density functional method B3LYP/6-31G* show similar characteristics in structures and energies [18]. In this work, we further confirmed the adaptability of AM1 method; thus the structural and energetic comparisons of H-bonds in the antiparallel l-l, d-d and parallel l-d dimers were performed by using either the semiempirical molecular orbital AM1 method and the density functional method B3LYP [32] with 6-31g, 6-31g ** basis sets and PBE1PBE25 [33]/6-31g ** .…”

Section: Model and Methodsmentioning

confidence: 99%

“…Based on the aforementioned discussion, the parallel dimer (l-d) and the antiparallel dimers [18] 4 ], and a series of tubular oligomers, from trimer to decamer, were constructed according to parallel, antiparallel and parallel-antiparallel mixing stacking schemes. All the oligomers retained C 4 symmetry and the distance between adjacent rings was initially set to ϳ5.0 Å.…”

Section: Model and Methodsmentioning

confidence: 99%

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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“…Recently, a new class of organic compounds has been reported in which amino acid unites make a macrocycle named cyclic peptide. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19] Cyclic peptides as a group of the cyclic compounds are of wide research interest. 10 These compounds have several biological activities such as antibacterial agent, [11][12][13] inhibitors of cell growth 14 enzymes, 15 antiviral, 16 antifungal, 17 immunosuppressant 18 antinociceptive properties 19 anthelmintic and cytotoxic agents.…”

Section: Introductionmentioning

confidence: 99%

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 Studies of Monomer and Dimer of Cyclo[(−l-Phe-d-Ala−)_n] and Cyclo[(−l-Phe¹-d-^MeN-Ala²−)_n] (n = 3−6)

Cited by 54 publications

References 19 publications

Self-Assembling Cyclic Peptides: Molecular Dynamics Studies of Dimers in Polar and Nonpolar Solvents

Self-Assembling Cyclic Peptides: Molecular Dynamics Studies of Dimers in Polar and Nonpolar Solvents

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

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

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Theoretical Studies of Monomer and Dimer of Cyclo[(−l-Phe-d-Ala−)n] and Cyclo[(−l-Phe1-d-MeN-Ala2−)n] (n = 3−6)

Cited by 54 publications

References 19 publications

Self-Assembling Cyclic Peptides: Molecular Dynamics Studies of Dimers in Polar and Nonpolar Solvents

Self-Assembling Cyclic Peptides: Molecular Dynamics Studies of Dimers in Polar and Nonpolar Solvents

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

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

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Theoretical Studies of Monomer and Dimer of Cyclo[(−l-Phe-d-Ala−)_n] and Cyclo[(−l-Phe¹-d-^MeN-Ala²−)_n] (n = 3−6)