Self-Assembly of a Functionalized Alkylated Isophthalic Acid at the Au(111)/Electrolyte Interface: Structure and Dynamics

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

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Structure Formation and Annealing of Isophthalic Acid at the Electrochemical Au(111)−Electrolyte Interface

The Journal of Physical Chemistry C ◽

10.1021/jp900279n ◽

2009 ◽

Vol 113 (18) ◽

pp. 7821-7825 ◽

Cited By ~ 18

Author(s):

Zhihai Li ◽

Thomas Wandlowski

Keyword(s):

Structure Formation ◽

Isophthalic Acid ◽

Electrolyte Interface

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ChemInform Abstract: Cation-Directed Self-Assembly of Lipophilic Nucleosides: The Cation′s Central Role in the Structure and Dynamics of a Hydrogen-Bonded Assembly.

ChemInform ◽

10.1002/chin.200217061 ◽

2010 ◽

Vol 33 (17) ◽

pp. no-no

Author(s):

Mangmang Cai ◽

Xiaodong Shi ◽

Valdimir Sidorov ◽

Daniele Fabris ◽

Yiu-fai Lam ◽

...

Keyword(s):

Self Assembly ◽

Structure And Dynamics ◽

Hydrogen Bonded

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Self‐Assembly of DNA and RNA Building Blocks Explored by Nitrogen‐14 NMR Crystallography: Structure and Dynamics

ChemPhysChem ◽

10.1002/cphc.201901214 ◽

2020 ◽

Vol 21 (10) ◽

pp. 1044-1051 ◽

Cited By ~ 1

Author(s):

Diego Carnevale ◽

Marcel Hollenstein ◽

Geoffrey Bodenhausen

Keyword(s):

Self Assembly ◽

Building Blocks ◽

Structure And Dynamics ◽

Dna And Rna ◽

Nmr Crystallography

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MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

Nucleic Acids Research ◽

10.1093/nar/gkaa200 ◽

2020 ◽

Vol 48 (9) ◽

pp. 5135-5146 ◽

Cited By ~ 7

Author(s):

Christopher Maffeo ◽

Aleksei Aksimentiev

Keyword(s):

Self Assembly ◽

De Novo ◽

Dna Nanotechnology ◽

Equilibrium Structure ◽

Molecular Graphics ◽

Structure And Dynamics ◽

Self Assembled ◽

Actual Shape ◽

And Function ◽

Assembly Principles

Abstract Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

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