scholarly journals Symmetry-Directed Self-Assembly of a Tetrahedral Protein Cage Mediated by de Novo-Designed Coiled Coils

ChemBioChem ◽  
2017 ◽  
Vol 18 (19) ◽  
pp. 1888-1892 ◽  
Author(s):  
Somayesadat Badieyan ◽  
Aaron Sciore ◽  
Joseph D. Eschweiler ◽  
Philipp Koldewey ◽  
Ajitha S. Cristie-David ◽  
...  
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Coiled Coils ◽  
Protein Cage

scholarly journals Front Cover: Symmetry-Directed Self-Assembly of a Tetrahedral Protein Cage Mediated by de Novo-Designed Coiled Coils (ChemBioChem 19/2017)

ChemBioChem ◽  
2017 ◽  
Vol 18 (19) ◽  
pp. 1871-1871 ◽  
Author(s):  
Somayesadat Badieyan ◽  
Aaron Sciore ◽  
Joseph D. Eschweiler ◽  
Philipp Koldewey ◽  
Ajitha S. Cristie-David ◽  
...  
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Coiled Coils ◽  
Front Cover ◽  
Protein Cage

Metal Ion Assisted Folding and Supramolecular Organization of a De Novo Designed Metalloprotein

2004 ◽  
Vol 57 (1) ◽  
pp. 33 ◽  
Author(s):  
Guido W. M. Vandermeulen ◽  
Christos Tziatzios ◽  
Dieter Schubert ◽  
Philip R. Andres ◽  
Alexander Alexeev ◽  
...  
Keyword(s):  
Protein Folding ◽  
Self Assembly ◽  
Metal Ion ◽  
De Novo ◽  
Coiled Coil ◽  
Coiled Coils ◽  
The Self ◽  
Supramolecular Organization ◽  
Low Concentrations ◽  
The Moment

This paper describes the supramolecular organization of a novel de novo designed metalloprotein, which consists of two N-terminal terpyridine modified coiled-coil protein folding motif sequences held together by an iron(II) ion. The self-assembly of the metalloprotein is the result of the interplay of metal ion complexation and protein folding, and can be manipulated by changes in concentration, temperature, and solvent. At low concentrations, folding and organization of the metalloprotein resembles that of the native coiled-coil peptide. Besides unimeric species, also dimeric and tetrameric metalloprotein assemblies were found. Several indications suggest that at least part of these unimeric species may exist as intramolecularly folded coiled-coils, however, unambiguous proof is lacking at the moment. At higher concentrations, folding and organization is dominated by the large octahedral [FeII(terpy)2] complexes (terpy = 2,2′:6′,2″-terpyridine) and considerable amounts of large, ill-defined aggregates are formed.

scholarly journals Methionine-stabilized nonclassical growth within self-assembled de novo gold nanoparticles in conjunction with secondary nucleation inhibition

2021 ◽  
Author(s):  
Jitendra Sahu ◽  
Shahbaz Lone ◽  
Kalyan Sadhu
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Noble Metal Nanoparticles ◽  
Secondary Nucleation ◽  
Unique Case ◽  
Primary Particles ◽  
Growth Reaction ◽  
Aurophilic Interaction ◽  
Key Steps

Abstract The key steps for seed mediated growth of noble metal nanoparticles involve primary and secondary nucleation, which depends upon the energy barrier and ligand supersaturation standards of the medium. Herein we report the unique case of methionine (Met) controlled growth reaction, which rather proceeds via impeding secondary nucleation in presence of citrate stabilized gold nanoparticle (AuNP). The interaction between freshly generated Au+ and thioether group of Met in the medium restricts the secondary nucleation process involving further Au+ reduction. This incomplete conversion of Au+ results in a significant enhancement of the zeta (ζ) potential even at low concentration of Met. Furthermore, the aurophilic interaction of Au+ controls the self-assembly process of the in situ generated emissive nucleated particles. Nucleation of primary particles on seed surface, their segregation and time dependent conversion to larger particles within self-assembly confirm the nonclassical growth, which has further been explored with Met containing bio-inspired peptides.

scholarly journals De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Won-Jing Wang ◽  
Devrim Acehan ◽  
Chien-Han Kao ◽  
Wann-Neng Jane ◽  
Kunihiro Uryu ◽  
...  
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Human Cells ◽  
De Novo Synthesis ◽  
Current Paradigm

Vertebrate centrioles normally propagate through duplication, but in the absence of preexisting centrioles, de novo synthesis can occur. Consistently, centriole formation is thought to strictly rely on self-assembly, involving self-oligomerization of the centriolar protein SAS-6. Here, through reconstitution of de novo synthesis in human cells, we surprisingly found that normal looking centrioles capable of duplication and ciliation can arise in the absence of SAS-6 self-oligomerization. Moreover, whereas canonically duplicated centrioles always form correctly, de novo centrioles are prone to structural errors, even in the presence of SAS-6 self-oligomerization. These results indicate that centriole biogenesis does not strictly depend on SAS-6 self-assembly, and may require preexisting centrioles to ensure structural accuracy, fundamentally deviating from the current paradigm.

scholarly journals Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils

2018 ◽  
Vol 9 (18) ◽  
pp. 4308-4316 ◽  
Author(s):  
Mike C. Groth ◽  
W. Mathis Rink ◽  
Nils F. Meyer ◽  
Franziska Thomas
Keyword(s):  
De Novo ◽  
Kinetic Studies ◽  
Competitive Binding ◽  
Coiled Coils ◽  
Binding Mechanism ◽  
Strand Displacement

Strand displacement in heterodimeric coiled coils follows a competitive binding mechanism and can be predicted by the ratio of KD values.

scholarly journals Capacity of the Golgi Apparatus for Biogenesis from the Endoplasmic Reticulum

2003 ◽  
Vol 14 (12) ◽  
pp. 5011-5018 ◽  
Author(s):  
Sapna Puri ◽  
Adam D. Linstedt
Keyword(s):  
Endoplasmic Reticulum ◽  
Golgi Apparatus ◽  
Self Assembly ◽  
De Novo ◽  
Brefeldin A ◽  
The Other ◽  
Matrix Proteins ◽  
Er Export ◽  
Golgi Matrix

It is unclear whether the mammalian Golgi apparatus can form de novo from the ER or whether it requires a preassembled Golgi matrix. As a test, we assayed Golgi reassembly after forced redistribution of Golgi matrix proteins into the ER. Two conditions were used. In one, ER redistribution was achieved using a combination of brefeldin A (BFA) to cause Golgi collapse and H89 to block ER export. Unlike brefeldin A alone, which leaves matrix proteins in relatively large remnant structures outside the ER, the addition of H89 to BFA-treated cells caused ER accumulation of all Golgi markers tested. In the other, clofibrate treatment induced ER redistribution of matrix and nonmatrix proteins. Significantly, Golgi reassembly after either treatment was robust, implying that the Golgi has the capacity to form de novo from the ER. Furthermore, matrix proteins reemerged from the ER with faster ER exit rates. This, together with the sensitivity of BFA remnants to ER export blockade, suggests that presence of matrix proteins in BFA remnants is due to cycling via the ER and preferential ER export rather than their stable assembly in a matrix outside the ER. In summary, the Golgi apparatus appears capable of efficient self-assembly.

Interfacial zippering-up of coiled-coil protein filaments

2015 ◽  
Vol 17 (46) ◽  
pp. 31055-31060 ◽  
Author(s):  
Emiliana De Santis ◽  
Valeria Castelletto ◽  
Maxim G. Ryadnov
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Coiled Coil ◽  
Morphological Control

A de novo self-assembly topology for engineering protein nanostructures under morphological control is reported.

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.

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