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CCD²: design constructs for protein expression, the easy way.

Andrea Giovanni Murachelli¹, George Damaskos², Anastassis Perrakis¹

¹Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

Acta Crystallographica. Section D, Structural Biology

|August 3, 2021

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Creating protein constructs for research is simplified by CCD², a new software tool. It automates the design and primer generation for recombinant protein expression, saving researchers time and effort.

Area of Science:

Biochemistry
Molecular Biology
Bioinformatics

Background:

Protein structure and function studies often require numerous protein-truncation constructs.
Generating these constructs for recombinant expression is typically time-consuming and prone to errors.

Purpose of the Study:

To introduce CCD², a software tool designed to automate and simplify the creation of protein-expression constructs.
To streamline the process of designing and generating primers for recombinant protein production.

Main Methods:

CCD² aggregates essential data including sequence conservation, secondary structure predictions, domain identification, and disorder detection.
It integrates information on similar protein structures from the Protein Data Bank.
Users can define construct boundaries, and the software automatically generates primers for polymerase chain reaction (PCR).

Keywords:

CCD2 expression construct design meta server protein analysis protein expression

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Main Results:

CCD² automates the design of protein-expression constructs, reducing manual effort and potential errors.
The software facilitates the selection of construct boundaries and primer generation.
It provides construct property analysis and DNA vector maps for efficient laboratory management.

Conclusions:

CCD² is a valuable tool for laboratories involved in recombinant protein production.
It significantly aids researchers, particularly in structural biology, by automating a complex and laborious process.