Self-Assembling Organic Nanotubes

Bong, Dennis; Clark, Thomas D.; Granja, Juan R.; Ghadiri, M. Reza

doi:10.1002/1521-3773(20010316)40:6<988::aid-anie9880>3.3.co;2-e

Cited by 394 publications

(589 citation statements)

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“…Peptide nanotubes, which can be viewed as tailored synthetic ion channels, result from the self-assembly of cyclic peptides formed by alternated D-L-R-amino acids, 55,56 by means of a network of intermolecular hydrogen bonds. 57 The peptide nanotube considered here consisted of eight stacked cyclo [LW] 4 units, where underlined letters denote D-amino acids, immersed in a thermalized palmitoyl-oleoylphosphatidylcholine (POPC) bilayer formed by 48 lipid units, in equilibrium with 1572 water molecules. The complete molecular assembly was placed in a simulation cell of initial dimensions equal to 36 × 41 × 79 Å 3 .…”

Section: Computational Detailsmentioning

confidence: 99%

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

Hénin

Fiorin

Chipot

et al. 2009

J. Chem. Theory Comput.

395

494

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Abstract:A new implementation of the adaptive biasing force (ABF) method is described. This implementation supports a wide range of collective variables and can be applied to the computation of multidimensional energy profiles. It is provided to the community as part of a code that implements several analogous methods, including metadynamics. ABF and metadynamics have not previously been tested side by side on identical systems. Here, numerical tests are carried out on processes including conformational changes in model peptides and translocation of a halide ion across a lipid membrane through a peptide nanotube. On the basis of these examples, we discuss similarities and differences between the ABF and metadynamics schemes. Both approaches provide enhanced sampling and free energy profiles in quantitative agreement with each other in different applications. The method of choice depends on the dimension of the reaction coordinate space, the height of the barriers, and the relaxation times of degrees of freedom in the orthogonal space, which are not explicitly described by the chosen collective variables.

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Section: Computational Detailsmentioning

confidence: 99%

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

Hénin

Fiorin

Chipot

et al. 2009

J. Chem. Theory Comput.

395

494

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“…For this reason, contemporary studies of β-sheet interactions have generally focused on creating large supramolecular assemblies or aggregates involving extended edge-to-edge and face-to-face interactions. 10,11 A number of peptidic model systems that mimic β-sheet quaternary structure through the formation of dimers have been developed. 12,13 Most of these systems dimerize in noncompetitive organic solvents and are designed to allow hydrogen bonding from only one edge of the β-sheet, with the other edge being blocked to avoid uncontrolled aggregation.…”

Section: Introductionmentioning

confidence: 99%

Macrocyclic β-Sheet Peptides That Mimic Protein Quaternary Structure through Intermolecular β-Sheet Interactions

2007

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This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through β-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide β-strand, two Hao β-strand mimics [JACS 2000, 122, 7654] joined by one additional α-amino acid, and two δ-linked ornithine β-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID: 1mio]. 1 H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide selfassociates through edge-to-edge β-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of β-sheet dimers. In this tetrameric β-sheet sandwich, the macrocyclic peptide 3a is folded to form a β-sheet, the β-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b-3n, which are homologues of peptide 3a with 1-6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b-3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h-3n indicate that hydrophobic residues at positions R 3 and R 5 of the heptapeptide sequence are important in oligomerization.

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“…A conceptually straightforward strategy for constructing synthetic pores involves the stacking of macrocycles, an area that has witnessed impressive progress in recent years 16,17 . Of particular interest are molecular-scale ( < 2 nm) nanopores with fixed sizes, on the basis of which many fascinating properties resulting from confinement within a nanospace, such as selective transport of molecules and ions with significantly enhanced rate, could be realized.…”

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confidence: 99%

Self-assembling subnanometer pores with unusual mass-transport properties

et al. 2012

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A long-standing aim in molecular self-assembly is the development of synthetic nanopores capable of mimicking the mass-transport characteristics of biological channels and pores. Here we report a strategy for enforcing the nanotubular assembly of rigid macrocycles in both the solid state and solution based on the interplay of multiple hydrogen-bonding and aromatic π − π stacking interactions. The resultant nanotubes have modifiable surfaces and inner pores of a uniform diameter defined by the constituent macrocycles. The self-assembling hydrophobic nanopores can mediate not only highly selective transmembrane ion transport, unprecedented for a synthetic nanopore, but also highly efficient transmembrane water permeability. These results establish a solid foundation for developing synthetically accessible, robust nanostructured systems with broad applications such as reconstituted mimicry of defined functions solely achieved by biological nanostructures, molecular sensing, and the fabrication of porous materials required for water purification and molecular separations.

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Self-Assembling Organic Nanotubes

Cited by 394 publications

References 0 publications

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

Macrocyclic β-Sheet Peptides That Mimic Protein Quaternary Structure through Intermolecular β-Sheet Interactions

Self-assembling subnanometer pores with unusual mass-transport properties

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