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.

De novo design of α-helical proteins: basic research to medical applications

1996 ◽  
Vol 74 (2) ◽  
pp. 133-154 ◽  
Author(s):  
Robert S. Hodges
Keyword(s):  
Protein Folding ◽  
De Novo ◽  
Coiled Coil ◽  
Basic Research ◽  
De Novo Design ◽  
Coiled Coils ◽  
Medical Applications ◽  
Dimerization Domain ◽  
Recombinant Peptides ◽  
Helical Proteins

The two-stranded α-helical coiled-coil is a universal dimerization domain used by nature in a diverse group of proteins. The simplicity of the coiled-coil structure makes it an ideal model system to use in understanding the fundamentals of protein folding and stability and in testing the principles of de novo design. The issues that must be addressed in the de novo design of coiled-coils for use in research and medical applications are (i) controlling parallel versus antiparallel orientation of the polypeptide chains, (ii) controlling the number of helical strands in the assembly (iii) maximizing stability of homodimers or heterodimers in the shortest possible chain length that may require the engineering of covalent constraints, and (iv) the ability to have selective heterodimerization without homodimerization, which requires a balancing of selectivity versus affinity of the dimerization strands. Examples of our initial inroads in using this de novo design motif in various applications include: heterodimer technology for the detection and purification of recombinant peptides and proteins; a universal dimerization domain for biosensors; a two-stage targeting and delivery system; and coiled-coils as templates for combinatorial helical libraries for basic research and drug discovery and as synthetic carrier molecules. The universality of this dimerization motif in nature suggests an endless number of possibilities for its use in de novo design, limited only by the creativity of peptide–protein engineers.Key words: de novo design of proteins, α-helical coiled-coils, protein folding, protein stability, dimerization domain, dimerization motif.

scholarly journals Modification of a Single Atom Affects the Physical Properties of Double Fluorinated Fmoc-Phe Derivatives

2021 ◽  
Vol 22 (17) ◽  
pp. 9634
Author(s):  
Moran Aviv ◽  
Dana Cohen-Gerassi ◽  
Asuka A. Orr ◽  
Rajkumar Misra ◽  
Zohar A. Arnon ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physical Properties ◽  
Self Assembly ◽  
Deep Understanding ◽  
Building Blocks ◽  
The Self ◽  
Single Atom ◽  
Supramolecular Organization ◽  
Assembly Process ◽  
Wide Range

Supramolecular hydrogels formed by the self-assembly of amino-acid based gelators are receiving increasing attention from the fields of biomedicine and material science. Self-assembled systems exhibit well-ordered functional architectures and unique physicochemical properties. However, the control over the kinetics and mechanical properties of the end-products remains puzzling. A minimal alteration of the chemical environment could cause a significant impact. In this context, we report the effects of modifying the position of a single atom on the properties and kinetics of the self-assembly process. A combination of experimental and computational methods, used to investigate double-fluorinated Fmoc-Phe derivatives, Fmoc-3,4F-Phe and Fmoc-3,5F-Phe, reveals the unique effects of modifying the position of a single fluorine on the self-assembly process, and the physical properties of the product. The presence of significant physical and morphological differences between the two derivatives was verified by molecular-dynamics simulations. Analysis of the spontaneous phase-transition of both building blocks, as well as crystal X-ray diffraction to determine the molecular structure of Fmoc-3,4F-Phe, are in good agreement with known changes in the Phe fluorination pattern and highlight the effect of a single atom position on the self-assembly process. These findings prove that fluorination is an effective strategy to influence supramolecular organization on the nanoscale. Moreover, we believe that a deep understanding of the self-assembly process may provide fundamental insights that will facilitate the development of optimal amino-acid-based low-molecular-weight hydrogelators for a wide range of applications.

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.

Influence of the central metal ion in controlling the self-assembly and magnetic properties of 2D coordination polymers derived from [(NiL)2M]2+ nodes (M = Ni, Zn and Cd) (H2L = salen-type di-Schiff base) and dicyanamide spacers

2015 ◽  
Vol 44 (3) ◽  
pp. 1292-1302 ◽  
Author(s):  
Lakshmi Kanta Das ◽  
Carlos J. Gómez-García ◽  
Ashutosh Ghosh
Keyword(s):  
Magnetic Properties ◽  
Schiff Base ◽  
Coordination Polymers ◽  
Self Assembly ◽  
Significant Variation ◽  
Metal Ion ◽  
The Self ◽  
Central Metal

Three new 2D coordination polymers of different networks with significant variation in magnetic properties have been synthesized by changing the central metal in the trinuclear nodes.

scholarly journals Biophysical and biochemical properties of Deup1 self-assemblies: a potential driver for deuterosome formation during multiciliogenesis

Biology Open ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. bio056432 ◽  
Author(s):  
Shohei Yamamoto ◽  
Ryoichi Yabuki ◽  
Daiju Kitagawa
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Coiled Coil ◽  
Biochemical Properties ◽  
The Self ◽  
Centrosomal Protein ◽  
Biochemical Analyses ◽  
Stable Structures

ABSTRACTThe deuterosome is a non-membranous organelle involved in large-scale centriole amplification during multiciliogenesis. Deuterosomes are specifically assembled during the process of multiciliogenesis. However, the molecular mechanisms underlying deuterosome formation are poorly understood. In this study, we investigated the molecular properties of deuterosome protein 1 (Deup1), an essential protein involved in deuterosome assembly. We found that Deup1 has the ability to self-assemble into macromolecular condensates both in vitro and in cells. The Deup1-containing structures formed in multiciliogenesis and the Deup1 condensates self-assembled in vitro showed low turnover of Deup1, suggesting that Deup1 forms highly stable structures. Our biochemical analyses revealed that an increase of the concentration of Deup1 and a crowded molecular environment both facilitate Deup1 self-assembly. The self-assembly of Deup1 relies on its N-terminal region, which contains multiple coiled coil domains. Using an optogenetic approach, we demonstrated that self-assembly and the C-terminal half of Deup1 were sufficient to spatially compartmentalize centrosomal protein 152 (Cep152) and polo like kinase 4 (Plk4), master components for centriole biogenesis, in the cytoplasm. Collectively, the present data suggest that Deup1 forms the structural core of the deuterosome through self-assembly into stable macromolecular condensates.This article has an associated First Person interview with the first author of the paper.

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

Can metal ion complexation compete with the self-assembly processes of calix[4]arene amine derivatives?

2014 ◽  
Vol 43 (22) ◽  
pp. 8387
Author(s):  
Laura O'Toole ◽  
Bernadette S. Creaven ◽  
John McGinley
Keyword(s):  
Self Assembly ◽  
Metal Ion ◽  
The Self ◽  
Metal Ion Complexation ◽  
Ion Complexation

scholarly journals De novo design of isopeptide bond-tethered triple-stranded coiled coils with exceptional resistance to unfolding and proteolysis: implication for developing antiviral therapeutics

2015 ◽  
Vol 6 (11) ◽  
pp. 6505-6509 ◽  
Author(s):  
Chao Wang ◽  
Wenqing Lai ◽  
Fei Yu ◽  
Tianhong Zhang ◽  
Lu Lu ◽  
...  
Keyword(s):  
De Novo ◽  
Coiled Coil ◽  
De Novo Design ◽  
Coiled Coils ◽  
Isopeptide Bond ◽  
Hiv 1

Isopeptide bridge-tethered ultra-stable coiled-coil trimers have been de novo designed as structure-directing auxiliaries to guide HIV-1 gp41 NHR-peptide trimerization.

Fabrication of multichannel microtubules by the self-assembly of pyridine-based macrocyclic compounds and their use for heavy metal ion adsorption

2012 ◽  
Vol 24 (3) ◽  
pp. 165-174 ◽  
Author(s):  
Lidong Zhang ◽  
Xinhua Huang ◽  
Dong Eun Kang ◽  
Chang-Sik Ha ◽  
Hongsuk Suh ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Self Assembly ◽  
Metal Ion ◽  
The Self ◽  
Heavy Metal Ion ◽  
Ion Adsorption ◽  
Macrocyclic Compounds ◽  
Metal Ion Adsorption
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