scholarly journals Direct interfacial Y731 oxidation in α2 by a photoβ2 subunit of E. coli class Ia ribonucleotide reductase

2015 ◽  
Vol 6 (8) ◽  
pp. 4519-4524 ◽  
Author(s):  
David Y. Song ◽  
Arturo A. Pizano ◽  
Patrick G. Holder ◽  
JoAnne Stubbe ◽  
Daniel G. Nocera
Keyword(s):  
Ribonucleotide Reductase ◽  
De Novo ◽  
Building Blocks ◽  
Biological Processes ◽  
E Coli ◽  
Proton Coupled Electron Transfer ◽  
Ribonucleotide Reductases ◽  
Wide Range ◽  
Dna Replication And Repair ◽  
Fundamental Mechanism

Proton-coupled electron transfer (PCET) is a fundamental mechanism important in a wide range of biological processes including the universal reaction catalysed by ribonucleotide reductases (RNRs) in making de novo, the building blocks required for DNA replication and repair.

scholarly journals The U28 ORF of human herpesvirus-7 does not encode a functional ribonucleotide reductase R1 subunit

1999 ◽  
Vol 80 (10) ◽  
pp. 2713-2718 ◽  
Author(s):  
Yunming Sun ◽  
Joe Conner
Keyword(s):  
Ribonucleotide Reductase ◽  
De Novo ◽  
Human Herpesvirus ◽  
Cloning And Expression ◽  
Subunit Interaction ◽  
Viral Dna ◽  
Sequence Comparisons ◽  
E Coli ◽  
Ribonucleotide Reductases ◽  
Functional Equivalent

Herpesvirus ribonucleotide reductases, essential for the de novo synthesis of viral DNA, are composed of two non-identical subunits, termed R1 and R2. The U28 ORF from human herpesvirus-7 has been classified, by sequence comparisons, as a homologue of the R1 subunit from ribonucleotide reductase but no R2 ORF is present. Detailed analysis of the U28 amino acid sequence indicated that a number of essential R1 catalytic residues are absent. Cloning and expression of the U28 protein in E. coli and its subsequent characterization in subunit interaction and enzyme activity assays confirmed that it is not a functional equivalent of a herpesvirus R1. In the absence of the R2 gene, we propose that the R1 ORF has evolved a distinct, as yet unidentified, function not only in human herpesvirus-7 but also in other human betaherpesviruses.

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.

Artificial protein assemblies with well-defined supramolecular protein nanostructures

2021 ◽  
Author(s):  
Suyeong Han ◽  
Yongwon Jung
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
Building Blocks ◽  
Protein Assembly ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Wide Range ◽  
Array Structures ◽  
Small Chemical ◽  
Artificial Protein

Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.

Specific inhibition of ribonucleotide reductases by peptides corresponding to the C-terminal of their second subunit

1991 ◽  
Vol 69 (1) ◽  
pp. 79-83 ◽  
Author(s):  
Gregory Cosentino ◽  
Pierre Lavallée ◽  
Sumanas Rakhit ◽  
Raymond Plante ◽  
Yvon Gaudette ◽  
...  
Keyword(s):  
Ribonucleotide Reductase ◽  
Synthetic Peptide ◽  
Herpes Virus ◽  
Small Subunit ◽  
Terminal Sequence ◽  
E Coli ◽  
Ribonucleotide Reductases ◽  
Human Enzyme ◽  
Bacterial Enzyme ◽  
Herpès Virus

Previous studies have shown that herpes virus ribonucleotide reductase can be inhibited by a synthetic nonapeptide whose sequence is identical to the C-terminal of the small subunit of the enzyme. This peptide is able to interfere with normal subunit association that takes place through the C-terminal of the small subunit. In this report, we illustrate that inhibition of ribonucleotide reductases by peptides corresponding to the C-terminal of subunit R2 is also observed for the enzyme isolated from Escherichia coli, hamster, and human cells. The nonapeptide corresponding to the bacterial C-terminal sequence was found to inhibit E. coli enzyme with an IC50 of 400 μM, while this peptide had no effect on mammalian ribonucleotide reductase. A corresponding synthetic peptide derived from the C-terminal of the small subunit of the human enzyme inhibited both human and hamster ribonucleotide reductases with IC50 values of 160 and 120 μM, respectively. However, this peptide had no inhibitory activity against the bacterial enzyme. Equivalent peptides derived from herpes virus ribonucleotide reductase had no effect on either the bacterial or mammalian enzymes. Thus, subunit association at the C-terminal of the small subunit appears to be a common feature of ribonucleotide reductases. In addition, the inhibitory phenomenon observed with peptides corresponding to the C-terminal appears not only to be universal, but also specific to the primary sequence of the enzyme.Key words: ribonucleotide reductase, inhibition, human, bacteria.

Deciphering the route to cyclic monoterpenes in Chrysomelina leaf beetles: source of new biocatalysts for industrial application?

2017 ◽  
Vol 72 (9-10) ◽  
pp. 417-427 ◽  
Author(s):  
Antje Burse ◽  
Wilhelm Boland
Keyword(s):  
De Novo ◽  
Sustainable Use ◽  
Building Blocks ◽  
Leaf Beetle ◽  
Industrial Applications ◽  
Metabolic Diversity ◽  
Leaf Beetles ◽  
Wide Range ◽  
Extreme Habitats ◽  
Plant Sources

AbstractThe drastic growth of the population on our planet requires the efficient and sustainable use of our natural resources. Enzymes are indispensable tools for a wide range of industries producing food, pharmaceuticals, pesticides, or biofuels. Because insects constitute one of the most species-rich classes of organisms colonizing almost every ecological niche on earth, they have developed extraordinary metabolic abilities to survive in various and sometimes extreme habitats. Despite this metabolic diversity, insect enzymes have only recently generated interest in industrial applications because only a few metabolic pathways have been sufficiently characterized. Here, we address the biosynthetic route to iridoids (cyclic monoterpenes), a group of secondary metabolites used by some members of the leaf beetle subtribe Chrysomelina as defensive compounds against their enemies. The ability to produce iridoids de novo has also convergently evolved in plants. From plant sources, numerous pharmacologically relevant structures have already been described. In addition, in plants, iridoids serve as building blocks for monoterpenoid indole alkaloids with broad therapeutic applications. As the commercial synthesis of iridoid-based drugs often relies on a semisynthetic approach involving biocatalysts, the discovery of enzymes from the insect iridoid route can account for a valuable resource and economic alternative to the previously used enzymes from the metabolism of plants. Hence, this review illustrates the recent discoveries made on the steps of the iridoid pathway in Chrysomelina leaf beetles. The findings are also placed in the context of the studied counterparts in plants and are further discussed regarding their use in technological approaches.

scholarly journals Transcriptome Analysis of Escherichia coli during dGTP Starvation

2016 ◽  
Vol 198 (11) ◽  
pp. 1631-1644 ◽  
Author(s):  
Mark Itsko ◽  
Roel M. Schaaper
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Stress Responses ◽  
De Novo ◽  
Replication Stress ◽  
Building Blocks ◽  
Content Type ◽  
Final Cause ◽  
E Coli ◽  
Genome Wide

ABSTRACTOur laboratory recently discovered thatEscherichia colicells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for thymineless death (TLD). Conditions for specific dGTP starvation can be achieved by depriving anE. colioptA1 gptstrain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses of actively growingoptA1 gptcells subjected to hypoxanthine deprivation for increasing periods. The data show that upon Hx withdrawal, theoptA1 gptstrain displays a diminished ability to derepress thede novopurine biosynthesis genes, likely due to internal guanine accumulation. The impairment in fully inducing thepurRregulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS response was observed, supporting the concept of replication stress as a final cause of death. No evidence was observed in the starved cells for the participation of other stress responses, including therpoS-mediated global stress response, reinforcing the lack of feedback of replication stress to the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient was observed for expression of genes located near the replication origin relative to those located toward the replication terminus.IMPORTANCEControl of the supply of the building blocks (deoxynucleoside triphosphates [dNTPs]) for DNA replication is important for ensuring genome integrity and cell viability. When cells are starved specifically for one of the four dNTPs, dGTP, the process of DNA replication is disturbed in a manner that can lead to eventual death. In the present study, we investigated the transcriptional changes in the bacteriumE. coliduring dGTP starvation. The results show increasing DNA replication stress with an increased time of starvation, as evidenced by induction of the bacterial SOS system, as well as a notable lack of induction of other stress responses that could have saved the cells from cell death by slowing down cell growth.

scholarly journals Beyond icosahedral symmetry in packings of proteins in spherical shells

2017 ◽  
Vol 114 (34) ◽  
pp. 9014-9019 ◽  
Author(s):  
Majid Mosayebi ◽  
Deborah K. Shoemark ◽  
Jordan M. Fletcher ◽  
Richard B. Sessions ◽  
Noah Linden ◽  
...  
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Multiple Scales ◽  
Building Blocks ◽  
Icosahedral Symmetry ◽  
Protein Cages ◽  
Natural Systems ◽  
Wide Range ◽  
Stable Arrangement ◽  
Symmetric Structures

The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.

scholarly journals Design of complicated all-α protein structures

2021 ◽  
Author(s):  
Koya Sakuma ◽  
Naohiro Kobayashi ◽  
Toshihiko Sugiki ◽  
Toshio Nagashima ◽  
Toshimichi Fujiwara ◽  
...  
Keyword(s):  
De Novo ◽  
Protein Structures ◽  
Building Blocks ◽  
Helical Structures ◽  
Helix Loop Helix ◽  
Naturally Occurring ◽  
Wide Range ◽  
Helical Protein ◽  
Helical Proteins ◽  
The Universe

A wide range of de novo protein structure designs have been achieved, but the complexity of naturally occurring protein structures is still far beyond these designs. To expand the diversity and complexity of de novo designed protein structures, we sought to develop a method for designing 'difficult-to-describe' α-helical protein structures composed of irregularly aligned α-helices, such as globins. Backbone structure libraries consisting of a myriad of α-helical structures with 5- or 6- helices were generated by combining 18 helix-loop-helix motifs and canonical α-helices, and five distinct topologies were selected for de novo design. The designs were found to be monomeric with high thermal stability in solution and fold into the target topologies with atomic accuracy. This study demonstrated that complicated α-helical proteins are created using typical building blocks. The method we developed would enable us to explore the universe of protein structures for designing novel functional proteins.

scholarly journals An evolutionary perspective on immunometabolism

Science ◽  
2019 ◽  
Vol 363 (6423) ◽  
pp. eaar3932 ◽  
Author(s):  
Andrew Wang ◽  
Harding H. Luan ◽  
Ruslan Medzhitov
Keyword(s):  
Cell Fate ◽  
Life History Theory ◽  
De Novo ◽  
Building Blocks ◽  
Biological Processes ◽  
Biological Functions ◽  
Cell Fate Decisions ◽  
Ecological Principles ◽  
Proliferation And Differentiation ◽  
Cell Quiescence

Metabolism is at the core of all biological functions. Anabolic metabolism uses building blocks that are either derived from nutrients or synthesized de novo to produce the biological infrastructure, whereas catabolic metabolism generates energy to fuel all biological processes. Distinct metabolic programs are required to support different biological functions. Thus, recent studies have revealed how signals regulating cell quiescence, proliferation, and differentiation also induce the appropriate metabolic programs. In particular, a wealth of new studies in the field of immunometabolism has unveiled many examples of the connection among metabolism, cell fate decisions, and organismal physiology. We discuss these findings under a unifying framework derived from the evolutionary and ecological principles of life history theory.

scholarly journals Lipase-Catalyzed Production of Sorbitol Laurate in a “2-in-1” Deep Eutectic System: Factors Affecting the Synthesis and Scalability

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2759
Author(s):  
André Delavault ◽  
Oleksandra Opochenska ◽  
Laura Laneque ◽  
Hannah Soergel ◽  
Claudia Muhle-Goll ◽  
...  
Keyword(s):  
De Novo ◽  
Choline Chloride ◽  
Building Blocks ◽  
Flash Chromatography ◽  
Phase System ◽  
Eutectic System ◽  
Two Phase ◽  
Factors Affecting ◽  
Ester Formation ◽  
Wide Range

Surfactants, such as glycolipids, are specialty compounds that can be encountered daily in cleaning agents, pharmaceuticals or even in food. Due to their wide range of applications and, more notably, their presence in hygiene products, the demand is continuously increasing worldwide. The established chemical synthesis of glycolipids presents several disadvantages, such as lack of specificity and selectivity. Moreover, the solubility of polyols, such as sugars or sugar alcohols, in organic solvents is rather low. The enzymatic synthesis of these compounds is, however, possible in nearly water-free media using inexpensive and renewable building blocks. Using lipases, ester formation can be achieved under mild conditions. We propose, herein, a “2-in-1” system that overcomes solubility problems, as a Deep Eutectic System (DES) made of sorbitol and choline chloride replaces either a purely organic or aqueous medium. For the first time, 16 commercially available lipase formulations were compared, and the factors affecting the conversion were investigated to optimize this process, owing to a newly developed High-Performance Liquid Chromatography-Evaporative Light Scattering Detector (HPLC-ELSD) method for quantification. Thus, using 50 g/L of lipase formulation Novozym 435® at 50 °C, the optimized synthesis of sorbitol laurate (SL) allowed to achieve 28% molar conversion of 0.5 M of vinyl laurate to its sugar alcohol monoester when the DES contained 5 wt.% water. After 48h, the de novo synthesized glycolipid was separated from the media by liquid–liquid extraction, purified by flash-chromatography and characterized thoroughly by one- and two-dimensional Nuclear Magnetic Resonance (NMR) experiments combined to Mass Spectrometry (MS). In completion, we provide initial proof of scalability for this process. Using a 2.5 L stirred tank reactor (STR) allowed a batch production reaching 25 g/L in a highly viscous two-phase system.

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