Self-Assembling Protein Scaffold System for Easy in Vitro Coimmobilization of Biocatalytic Cascade Enzymes

ACS Catalysis ◽  
2018 ◽  
Vol 8 (6) ◽  
pp. 5611-5620 ◽  
Author(s):  
Guoqiang Zhang ◽  
Maureen B. Quin ◽  
Claudia Schmidt-Dannert
Keyword(s):  
Protein Scaffold ◽  
Self Assembling

scholarly journals Rational construction of compact de novo-designed biliverdin-binding proteins

2018 ◽  
Author(s):  
Molly M. Sheehan ◽  
Michael S. Magaraci ◽  
Ivan A. Kuznetsov ◽  
Joshua A. Mancini ◽  
Goutham Kodali ◽  
...  
Keyword(s):  
Protein Design ◽  
De Novo ◽  
Binding Pocket ◽  
Heptad Repeat ◽  
Hydrophobic Core ◽  
Protein Scaffold ◽  
Self Assembling ◽  
High Resolution Structure ◽  
Rational Construction

Abstract:We report the rational construction of a de novo-designed biliverdin-binding protein by first principles of protein design, informed by energy minimization modeling in Rosetta. The self-assembling tetrahelical bundles bind biliverdin IXa (BV) cofactor auto-catalytically in vitro, similar to photosensory proteins that bind BV (and related bilins, or linear tetrapyrroles) despite lacking sequence and structural homology to the natural counterparts. Upon identifying a suitable site for cofactor ligation to the protein scaffold, stepwise placement of residues stabilized BV within the hydrophobic core. Rosetta modeling was used in the absence of a high-resolution structure to define the structure-function of the binding pocket. Holoprotein formation indeed stabilized BV, resulting in increased far-red BV fluorescence. By removing segments extraneous to cofactor stabilization or bundle stability, the initial 15-kilodalton de novo-designed fluorescence-activating protein (“dFP”) was truncated without altering its optical properties, down to a miniature 10-kilodalton “mini,” in which the protein scaffold extends only a half-heptad repeat beyond the hypothetical position of the bilin D-ring. This work demonstrates how highly compact holoprotein fluorochromes can be rationally constructed using de novo protein design technology and natural cofactors.

Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

1985 ◽  
Vol 43 ◽  
pp. 522-523
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Tertiary Structure ◽  
Dna Complexes ◽  
Tertiary Structures ◽  
Self Assembling ◽  
Double Stranded Dna ◽  
Calf Thymus ◽  
Dna Organization ◽  
Condensed Dna ◽  
Dna Size

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

scholarly journals Newly Developed Self-Assembling Antioxidants as Potential Therapeutics for the Cancers

2021 ◽  
Vol 11 (2) ◽  
pp. 92 ◽  
Author(s):  
Babita Shashni ◽  
Yukio Nagasaki
Keyword(s):  
Cancer Survival ◽  
Self Assembling ◽  
Therapeutic Regime ◽  
Cancer Models ◽  
Secondary Messengers ◽  
Potential Therapeutics ◽  
Target Effects ◽  
Tempo Radical

Elevated reactive oxygen species (ROS) have been implicated as significant for cancer survival by functioning as oncogene activators and secondary messengers. Hence, the attenuation of ROS-signaling pathways in cancer by antioxidants seems a suitable therapeutic regime for targeting cancers. Low molecular weight (LMW) antioxidants such as 2,2,6,6-tetramethylpyperidine-1-oxyl (TEMPO), although they are catalytically effective in vitro, exerts off-target effects in vivo due to their size, thus, limiting their clinical use. Here, we discuss the superior impacts of our TEMPO radical-conjugated self-assembling antioxidant nanoparticle (RNP) compared to the LMW counterpart in terms of pharmacokinetics, therapeutic effect, and adverse effects in various cancer models.

Self Assembling Nanostructured Delivery Vehicles for Biochemically Reactive Pairs

1994 ◽  
Vol 351 ◽  
Author(s):  
Nir Kossovsky ◽  
A. Gelman ◽  
H.J. Hnatyszyn ◽  
E. Sponsler ◽  
G.-M. Chow
Keyword(s):  
Physical Properties ◽  
Self Assembly ◽  
Materials Science ◽  
Technology Development ◽  
Biological Behavior ◽  
X Ray Diffraction ◽  
Self Assembling ◽  
Transmission Electron ◽  
Carbon Ceramic

ABSTRACTIntrigued by the deceptive simplicity and beauty of macromolecular self-assembly, our laboratory began studying models of self-assembly using solids, glasses, and colloidal substrates. These studies have defined a fundamental new colloidal material for supporting members of a biochemically reactive pair.The technology, a molecular transportation assembly, is based on preformed carbon ceramic nanoparticles and self assembled calcium-phosphate dihydrate particles to which glassy carbohydrates are then applied as a nanometer thick surface coating. This carbohydrate coated core functions as a dehydroprotectant and stabilizes surface immobilized members of a biochemically reactive pair. The final product, therefore, consists of three layers. The core is comprised of the ceramic, the second layer is the dehydroprotectant carbohydrate adhesive, and the surface layer is the biochemically reactive molecule for which delivery is desired.We have characterized many of the physical properties of this system and have evaluated the utility of this delivery technology in vitro and in animal models. Physical characterization has included standard and high resolution transmission electron microscopy, electron and x-ray diffraction and ζ potential analysis. Functional assays of the ability of the system to act as a nanoscale dehydroprotecting delivery vehicle have been performed on viral antigens, hemoglobin, and insulin. By all measures at present, the favorable physical properties and biological behavior of the molecular transportation assembly point to an exciting new interdisciplinary area of technology development in materials science, chemistry and biology.

scholarly journals De novo design of self-assembling helical protein filaments

Science ◽  
2018 ◽  
Vol 362 (6415) ◽  
pp. 705-709 ◽  
Author(s):  
Hao Shen ◽  
Jorge A. Fallas ◽  
Eric Lynch ◽  
William Sheffler ◽  
Bradley Parry ◽  
...  
Keyword(s):  
De Novo ◽  
Computational Design ◽  
Building Blocks ◽  
Repeat Units ◽  
Self Assembling ◽  
Wide Range ◽  
Helical Protein ◽  
Monomeric Proteins

We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo–electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.

Instructive bio-inspired self-assembling peptide nanofiber enhance hepatocyte phenotype in vitro

Desalination ◽  
2006 ◽  
Vol 199 (1-3) ◽  
pp. 263-264 ◽  
Author(s):  
Elsa Genové ◽  
Paco Carrión ◽  
Salvador Borrós ◽  
C.E. Semino
Keyword(s):  
Self Assembling

BMP7-Based Functionalized Self-Assembling Peptides Protect Nucleus Pulposus-Derived Stem Cells From Apoptosis In Vitro

2016 ◽  
Vol 22 (19-20) ◽  
pp. 1218-1228 ◽  
Author(s):  
Xiao-Chuan Li ◽  
Yao-Hong Wu ◽  
Xue-Dong Bai ◽  
Wei Ji ◽  
Zi-Ming Guo ◽  
...  
Keyword(s):  
Stem Cells ◽  
Nucleus Pulposus ◽  
Self Assembling

scholarly journals The Fusion of Lipid and DNA Nanotechnology

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1001 ◽  
Author(s):  
Es Darley ◽  
Jasleen Kaur Daljit Singh ◽  
Natalie A. Surace ◽  
Shelley F. J. Wickham ◽  
Matthew A. B. Baker
Keyword(s):  
Membrane Proteins ◽  
Lipid Membranes ◽  
Dna Nanotechnology ◽  
Bilayer Membrane ◽  
Diverse Range ◽  
Impermeable Barrier ◽  
Self Assembling ◽  
Associated Proteins ◽  
Fundamental Biological Process

Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological process that is facilitated by a diverse range of membrane proteins, including ion-channels and pores. However, biological membranes and their associated proteins are challenging to experimentally characterize. These challenges have motivated recent advances in nanotechnology towards building and manipulating synthetic lipid systems. Liposomes—aqueous droplets enclosed by a bilayer membrane—can be synthesised in vitro and used as a synthetic model for the cell membrane. In DNA nanotechnology, DNA is used as programmable building material for self-assembling biocompatible nanostructures. DNA nanostructures can be functionalised with hydrophobic chemical modifications, which bind to or bridge lipid membranes. Here, we review approaches that combine techniques from lipid and DNA nanotechnology to engineer the topography, permeability, and surface interactions of membranes, and to direct the fusion and formation of liposomes. These approaches have been used to study the properties of membrane proteins, to build biosensors, and as a pathway towards assembling synthetic multicellular systems.

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