scholarly journals Coiled coil protein origami: from modular design principles towards biotechnological applications

2018 ◽  
Vol 47 (10) ◽  
pp. 3530-3542 ◽  
Author(s):  
Fabio Lapenta ◽  
Jana Aupič ◽  
Žiga Strmšek ◽  
Roman Jerala
Keyword(s):  
Modular Design ◽  
Coiled Coil ◽  
Design Principles ◽  
Biotechnological Applications ◽  
Current State

This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.

Future trends in diagnosis using laboratory-on-a-chip technologies

Parasitology ◽  
1999 ◽  
Vol 117 (7) ◽  
pp. 191-203 ◽  
Author(s):  
M. S. TALARY ◽  
J. P. H. BURT ◽  
R. PETHIG
Keyword(s):  
Gene Expression ◽  
Lower Cost ◽  
Building Blocks ◽  
Cancer Diagnostics ◽  
Future Trends ◽  
Biotechnological Applications ◽  
Environmental Testing ◽  
Current State ◽  
Microelectronic Fabrication ◽  
Wide Range

There has been an enormous growth in the development of biotechnological applications, where advances in the techniques of microelectronic fabrication and the technologies of miniaturization and integration in semiconductor industries are being applied to the production of Laboratory-on-a-Chip devices. The aim of this development is to create devices that will perform the same processes that are currently carried out in the laboratory in reduced timescales, at a lower cost, requiring less reagents, and with a greater resolution of detection and specificity. The expectations of this Laboratory-on-a-Chip revolution is that this technology will facilitate rapid advances in gene discovery, genetic mapping and gene expression with broader applications ranging from infectious diseases and cancer diagnostics to food quality and environmental testing. A review of the current state of development in this field reveals the scale of the ongoing revolution and serves to highlight the advances that can be perceived in the development of Laboratory-on-a-Chip technologies. Since miniaturization can be applied to such a wide range of laboratory processes, some of the sub-units that can be used as building blocks in these devices are described, with a brief description of some of the fabrication processes that can be used to create them.

scholarly journals Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures

2020 ◽  
Vol 21 (10) ◽  
pp. 3584 ◽  
Author(s):  
Won Min Park
Keyword(s):  
Modular Design ◽  
Coiled Coil ◽  
Molecular Complexes ◽  
Building Blocks ◽  
Structural Features ◽  
Coiled Coils ◽  
Design Strategies ◽  
Protein Motifs ◽  
Self Assembling ◽  
Current Design

Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.

DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences

2019 ◽  
Vol 35 (16) ◽  
pp. 2790-2795 ◽  
Author(s):  
Jan Ludwiczak ◽  
Aleksander Winski ◽  
Krzysztof Szczepaniak ◽  
Vikram Alva ◽  
Stanislaw Dunin-Horkawicz
Keyword(s):  
Coiled Coil ◽  
Protein Sequences ◽  
Coiled Coils ◽  
Supplementary Information ◽  
Biological Interactions ◽  
Structural Domains ◽  
Current State ◽  
Genome Wide ◽  
And Function ◽  
Higher Sensitivity

Abstract Motivation Coiled coils are protein structural domains that mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function. Results Here, we report DeepCoil, a new neural network-based tool for the detection of coiled-coil domains in protein sequences. In our benchmarks, DeepCoil significantly outperformed current state-of-the-art tools, such as PCOILS and Marcoil, both in the prediction of canonical and non-canonical coiled coils. Furthermore, in a scan of the human genome with DeepCoil, we detected many coiled-coil domains that remained undetected by other methods. This higher sensitivity of DeepCoil should make it a method of choice for accurate genome-wide detection of coiled-coil domains. Availability and implementation DeepCoil is written in Python and utilizes the Keras machine learning library. A web server is freely available at https://toolkit.tuebingen.mpg.de/#/tools/deepcoil and a standalone version can be downloaded at https://github.com/labstructbioinf/DeepCoil. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Cecilia R. Chambers ◽  
Wayne M. Patrick
Keyword(s):  
Nucleic Acid ◽  
Pyrococcus Furiosus ◽  
Bacteriophage T4 ◽  
Biotechnological Applications ◽  
Dna Ligases ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Current State ◽  
Methanothermobacter Thermautotrophicus

With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information onin vitroactivities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments). We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase fromPyrococcus furiosusand the RNA ligase fromMethanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.

A New Methodology for Ease-of-Disassembly in Product Design

2000 ◽  
Author(s):  
Devdas Shetty ◽  
Ken Rawolle ◽  
Claudio Campana
Keyword(s):  
Product Design ◽  
State Of The Art ◽  
Aerospace Industry ◽  
Integrated Design ◽  
Design Principles ◽  
Design For Disassembly ◽  
Design Processes ◽  
Current State ◽  
Current Product ◽  
Useful Life

Abstract As manufacturers are becoming responsible for their products when they reach the end of their operational lives, the dismantling of products has emerged as one of the serious part of this exercise. In situations involving integrated design principles, certain assembly procedures or joining techniques can make it very difficult to disassemble a product and to separate materials into non-contaminated groups. The strategy is to begin including design for disassembly guidelines in the current product design processes. Design for Disassembly (DFD) is a design philosophy that requires consideration to be given for a product or a part, even after it is in service. The inclusion of procedures for design for disassembly, recyclability and re-manufacture will save resources by prolonging the useful life of product. The paper initially examines the current state of the art in the area of Design for Disassembly and looks at the existing methodologies that are applicable to product design. A new methodology based on a combination of charts based on damage rating, tool rating, re-use rating and access-area rating is proposed. The methodology is compared with the existing methods and evaluated for various situations in aerospace industry.

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