scholarly journals Recent advances in user-friendly computational tools to engineer protein function

2020 ◽  
Author(s):  
Carlos Eduardo Sequeiros-Borja ◽  
Bartłomiej Surpeta ◽  
Jan Brezovsky
Keyword(s):  
Protein Engineering ◽  
Protein Design ◽  
Protein Function ◽  
Transport Processes ◽  
Allosteric Communication ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions ◽  
User Friendly ◽  
Ligand Transport ◽  
Further Development

Abstract Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein–protein and protein–nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.

scholarly journals POTATO: An automated pipeline for batch analysis of optical tweezers data

2021 ◽  
Author(s):  
Stefan Buck ◽  
Lukas Pekarek ◽  
Neva Caliskan
Keyword(s):  
Data Analysis ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Molecular Motors ◽  
Analysis Tool ◽  
Recent Developments ◽  
Protein Nucleic Acid ◽  
Programming Knowledge ◽  
Nucleic Acid Interactions ◽  
User Friendly

Optical tweezers is a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein-nucleic acid interactions and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (Practical Optical Tweezers Analysis TOol). POTATO automatically processes the high-frequency raw data generated by force-ramp experiments and identifies (un)folding events using predefined parameters. After segmentation of the force-distance trajectories at the identified (un)folding events, sections of the curve can be fitted independently to worm-like chain and freely-jointed chain models, and the work applied on the molecule can be calculated by numerical integration. Furthermore, the tool allows plotting of constant force data and fitting of the Gaussian distance distribution over time. All these features are wrapped in a user-friendly graphical interface (https://github.com/REMI-HIRI/POTATO), which allows researchers without programming knowledge to perform sophisticated data analysis.

NuProPlot: nucleic acid and protein interaction analysis and plotting program

2015 ◽  
Vol 71 (3) ◽  
pp. 667-674 ◽  
Author(s):  
Lagnajeet Pradhan ◽  
Hyun-Joo Nam
Keyword(s):  
Nucleic Acid ◽  
Interaction Analysis ◽  
Three Dimensional ◽  
Data Bank ◽  
Van Der Waals Interactions ◽  
Acid Complex ◽  
Protein Nucleic Acid ◽  
The Individual ◽  
Nucleic Acid Interactions ◽  
User Friendly

Growing numbers of protein and nucleic acid complex structures are being determined and deposited in the Protein Data Bank and the Nucleic Acid Database. With the increasing complexity of these structures, it is challenging to analyse and visualize the three-dimensional interactions. The currently available programs for such analysis and visualization are limited in their applications. They can only analyse a subset of protein–nucleic acid complexes and require multiple iterations before obtaining plots that are suitable for presentation. An interactive web-based program,NuProPlot(http://www.nuproplot.com), has been developed which can automatically identify hydrogen, electrostatic and van der Waals interactions between proteins and nucleic acids and generate a plot showing all of the interactions. Protein–DNA and protein–RNA interactions can be visualized in simple two-dimensional schematics. Interactive schematic drawing options allow selection of the plotted area and repositioning of the individual interactions for better legibility.NuProPlotis a fully automated and user-friendly program providing various custom options.NuProPlotrepresents a greatly improved option for analysis and presentation of protein–nucleic acid interactions.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

Use of difference boundary sedimentation velocity to investigate nonspecific protein-nucleic acid interactions

Biochemistry ◽  
1980 ◽  
Vol 19 (15) ◽  
pp. 3516-3522 ◽  
Author(s):  
Timothy M. Lohman ◽  
C. Glen Wensley ◽  
Jeffrey Cina ◽  
Richard R. Burgess ◽  
M. Thomas Record
Keyword(s):  
Nucleic Acid ◽  
Sedimentation Velocity ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

Protein—nucleic acid interactions Folding and binding Web alert

1998 ◽  
Vol 8 (1) ◽  
pp. 9-10 ◽  
Author(s):  
PhilipE Bourne ◽  
Judith Murray-Rust ◽  
JeremyH Lakey
Keyword(s):  
Nucleic Acid ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

Nonspecific Prion Protein–Nucleic Acid Interactions Lead to Different Aggregates and Cytotoxic Species

Biochemistry ◽  
2012 ◽  
Vol 51 (27) ◽  
pp. 5402-5413 ◽  
Author(s):  
Bruno Macedo ◽  
Thiago A. Millen ◽  
Carolina A. C. A. Braga ◽  
Mariana P. B. Gomes ◽  
Priscila S. Ferreira ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Prion Protein ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

scholarly journals Rational protein design for enhancing thermal stability of industrial enzymes

2020 ◽  
Vol 8 (1) ◽  
pp. 3-17
Author(s):  
Le Quang Anh Tuan
Keyword(s):  
High Temperature ◽  
Protein Engineering ◽  
Protein Design ◽  
Disulfide Bonds ◽  
Industrial Applications ◽  
Enzymatic Reactions ◽  
Industrial Enzymes ◽  
Effective Strategies ◽  
Environmental Treatment ◽  
Pharmaceutical Production

Enzymes possessing many excellent properties such as high selectivity, consuming less energy, and producing less side products or waste have been widely applied as biocatalysts in pharmaceutical production and many industries such as biofuel, biomaterials, biosensor, food, and environmental treatment. Although enzymes have shown its potential as biocatalysts for many industrial applications, natural enzymes were not originated for manufacturing process which requires harsh reaction conditions such as high temperature, alkaline pH, and organics solvents. It was reported that reduction of final conversion of several enzymatic reactions was declined at high temperature. Protein engineering to improve the enzymes’ thermostability is crucial to extend the use of the industrial enzymes and maximize effectiveness of the enzyme-based procesess. Various industrial enzymes with improved thermostability were produced through rational protein engineering using different strategies. This review is not aimed to cover all successful rational protein engineering studies. The review focuses on some effective strategies which have widely used to increase the thermostability of several industrial enzymes through introduction of disulfide bonds and introduction of proline.

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