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

2020 ◽  
Vol 48 (9) ◽  
pp. 5135-5146 ◽  
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.

scholarly journals MrDNA: A multi-resolution model for predicting the structure and dynamics of nanoscale DNA objects

2019 ◽  
Author(s):  
Christopher Maffeo ◽  
Aleksei Aksimentiev
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Dna Nanotechnology ◽  
Equilibrium Structure ◽  
Molecular Graphics ◽  
Dna Nanostructure ◽  
Structure And Dynamics ◽  
Resolution Model ◽  
Actual Shape ◽  
And Function

AbstractAlthough the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures 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 minutes or less, can produce an atomistic-resolution structure of an arbitrary DNA nanostructure with accuracy on par with that of a cryo-electron microscopy (cryo-EM) reconstruction. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of 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 a self-assembly principle other than origami, 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.

scholarly journals Self-assembly of large RNA structures: learning from DNA nanotechnology

2016 ◽  
Vol 2 (1) ◽  
Author(s):  
Jaimie Marie Stewart ◽  
Elisa Franco
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Dna Nanotechnology ◽  
De Novo Design ◽  
Dna Nanostructures ◽  
Rna Structures ◽  
Functional Nanostructures ◽  
Rna And Dna ◽  
Unique Chemical

AbstractNucleic acid nanotechnology offers many methods to build self-assembled structures using RNA and DNA. These scaffolds are valuable in multiple applications, such as sensing, drug delivery and nanofabrication. Although RNA and DNA are similar molecules, they also have unique chemical and structural properties. RNA is generally less stable than DNA, but it folds into a variety of tertiary motifs that can be used to produce complex and functional nanostructures. Another advantage of using RNA over DNA is its ability to be encoded into genes and to be expressed in vivo. Here we review existing approaches for the self-assembly of RNA and DNA nanostructures and specifically methods to assemble large RNA structures. We describe de novo design approaches used in DNA nanotechnology that can be ported to RNA. Lastly, we discuss some of the challenges yet to be solved to build micron-scale, multi stranded RNA scaffolds.

De novo design of Self-assembly Hydrogels based on Fmoc-diphenylalanine Providing with Drug Release

2021 ◽  
Author(s):  
Xiang Li ◽  
Huijun Zhang ◽  
Lingyan Liu ◽  
Chunyan Cao ◽  
Peng Wei ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Drug Delivery System ◽  
Delivery System ◽  
Self Assembly ◽  
De Novo ◽  
De Novo Design ◽  
Short Peptides ◽  
Self Assembled

The short peptides with self-assembled nanostructures are widely applied in the areas of drug delivery system and biomaterials. In this article, we create a new peptide-based hydrogelator (Fmoc-FFRRVR) based on...

scholarly journals Segregation and activation of myosin IIB creates a rear in migrating cells

2008 ◽  
Vol 183 (3) ◽  
pp. 543-554 ◽  
Author(s):  
Miguel Vicente-Manzanares ◽  
Margaret A. Koach ◽  
Leanna Whitmore ◽  
Marcelo L. Lamers ◽  
Alan F. Horwitz
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Coiled Coil ◽  
Myosin Isoforms ◽  
C Terminus ◽  
Filament Bundles ◽  
A Cell ◽  
Myosin Iia ◽  
And Function ◽  
Migrating Cells

We have found that MLC-dependent activation of myosin IIB in migrating cells is required to form an extended rear, which coincides with increased directional migration. Activated myosin IIB localizes prominently at the cell rear and produces large, stable actin filament bundles and adhesions, which locally inhibit protrusion and define the morphology of the tail. Myosin IIA forms de novo filaments away from the myosin IIB–enriched center and back to form regions that support protrusion. The positioning and dynamics of myosin IIA and IIB depend on the self-assembly regions in their coiled-coil C terminus. COS7 and B16 melanoma cells lack myosin IIA and IIB, respectively; and show isoform-specific front-back polarity in migrating cells. These studies demonstrate the role of MLC activation and myosin isoforms in creating a cell rear, the segregation of isoforms during filament assembly and their differential effects on adhesion and protrusion, and a key role for the noncontractile region of the isoforms in determining their localization and function.

Supramolecular Structure and Stability of the GNNQQNY β-Sheet Bilayer Filament: A Computational Study

2007 ◽  
Author(s):  
Jiyong Park ◽  
Byungnam Kahng ◽  
Wonmuk Hwang
Keyword(s):  
Self Assembly ◽  
Amyloid Fibrils ◽  
De Novo ◽  
Structural Information ◽  
Computational Study ◽  
Molecular Structures ◽  
Theoretical Approaches ◽  
Self Assembled ◽  
Β Sheet

Self-assembly of β-sheet forming peptides into filaments has drawn great interests in biomedical applications [1,2]; Hydrogels formed by filaments self-assembled from de novo designed peptides possess potential applications for cell culture scaffolds [3]. On the other hand, peptides derived from amyloidogenic proteins in neurodegenerative diseases such as Alzheimer’s and Parkinson’s also form similar β-sheet filaments in vitro. They share little sequence homology, yet filaments formed by these self-assembling peptides commonly have the cross-β structure, the key signature of the amyloid fibril. Detailed structural information of the self-assembled β-sheet filaments has been limited partly due to the difficulty in preparing ordered filament samples, and it has been only recently that solid-state nuclear magnetic resonance and x-ray techniques have revealed their molecular structure at the atomic level [4,5]. Although molecular structures of amyloid fibrils are becoming available, physical principles governing their self-assembly and the properties of the filaments are not well-understood, for which computational as well as theoretical approaches are desirable [6].

scholarly journals Self-assembly and regulation of protein cages from pre-organised coiled-coil modules

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fabio Lapenta ◽  
Jana Aupič ◽  
Marco Vezzoli ◽  
Žiga Strmšek ◽  
Stefano Da Vela ◽  
...  
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Coiled Coil ◽  
Dna Nanotechnology ◽  
De Novo Design ◽  
Single Chain ◽  
Sequential Order ◽  
Conformational Switch ◽  
Protein Cages ◽  
Protease Cleavage

AbstractCoiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes.

scholarly journals A de novo matrix for macroscopic living materials from bacteria

2021 ◽  
Author(s):  
Sara Molinari ◽  
Robert F. Tesoriero ◽  
Dong Li ◽  
Swetha Sridhar ◽  
Rong Cai ◽  
...  
Keyword(s):  
De Novo ◽  
Caulobacter Crescentus ◽  
Living Cells ◽  
Structure And Function ◽  
Self Organization ◽  
Morphological Properties ◽  
Interacting Protein ◽  
And Function ◽  
Assembly Principles ◽  
Living Materials

Engineered living materials (ELMs) embed living cells in a biopolymer matrix to create novel materials with tailored functions. While bottom-up assembly of macroscopic ELMs with a de novo matrix would offer the greatest control over material properties, we lack the ability to genetically encode a protein matrix that leads to collective self-organization. Here we report growth of ELMs from Caulobacter crescentus cells that display and secrete a self-interacting protein. This protein formed a de novo matrix and assembled cells into centimeter-scale ELMs. Discovery of design and assembly principles allowed us to tune the mechanical, catalytic, and morphological properties of these ELMs. This work provides novel tools, design and assembly rules, and a platform for growing ELMs with control over matrix and cellular structure and function.

Nanoscale Self-Assembly Using Ion and Electron Beam Techniques: A Rapid Review

MRS Advances ◽  
2020 ◽  
Vol 5 (64) ◽  
pp. 3507-3520
Author(s):  
Chunhui Dai ◽  
Kriti Agarwal ◽  
Jeong-Hyun Cho
Keyword(s):  
Electron Beam ◽  
Self Assembly ◽  
Ion Beam ◽  
Three Dimensional ◽  
The Self ◽  
Stress Generation ◽  
Rapid Review ◽  
High Yield ◽  
3D Nanostructures ◽  
Self Assembled

AbstractNanoscale self-assembly, as a technique to transform two-dimensional (2D) planar patterns into three-dimensional (3D) nanoscale architectures, has achieved tremendous success in the past decade. However, an assembly process at nanoscale is easily affected by small unavoidable variations in sample conditions and reaction environment, resulting in a low yield. Recently, in-situ monitored self-assembly based on ion and electron irradiation has stood out as a promising candidate to overcome this limitation. The usage of ion and electron beam allows stress generation and real-time observation simultaneously, which significantly enhances the controllability of self-assembly. This enables the realization of various complex 3D nanostructures with a high yield. The additional dimension of the self-assembled 3D nanostructures opens the possibility to explore novel properties that cannot be demonstrated in 2D planar patterns. Here, we present a rapid review on the recent achievements and challenges in nanoscale self-assembly using electron and ion beam techniques, followed by a discussion of the novel optical properties achieved in the self-assembled 3D nanostructures.

Self-Assembly of a Chiral Cubic Three-Connected Net from the High Symmetry Molecules C60 and SnI4

2020 ◽  
Author(s):  
Daniel B. Straus ◽  
Robert J. Cava
Keyword(s):  
Organic Synthesis ◽  
Self Assembly ◽  
Van Der Waals ◽  
Van Der Waals Forces ◽  
High Symmetry ◽  
Molecular Chirality ◽  
Chiral Materials ◽  
Self Assembled ◽  
Chiral Centers

The design of new chiral materials usually requires stereoselective organic synthesis to create molecules with chiral centers. Less commonly, achiral molecules can self-assemble into chiral materials, despite the absence of intrinsic molecular chirality. Here, we demonstrate the assembly of high-symmetry molecules into a chiral van der Waals structure by synthesizing crystals of C<sub>60</sub>(SnI<sub>4</sub>)<sub>2</sub> from icosahedral buckminsterfullerene (C<sub>60</sub>) and tetrahedral SnI4 molecules through spontaneous self-assembly. The SnI<sub>4</sub> tetrahedra template the Sn atoms into a chiral cubic three-connected net of the SrSi<sub>2</sub> type that is held together by van der Waals forces. Our results represent the remarkable emergence of a self-assembled chiral material from two of the most highly symmetric molecules, demonstrating that almost any molecular, nanocrystalline, or engineered precursor can be considered when designing chiral assemblies.

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

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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