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Protein Backbone Building

Protein Backbone Building

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Protein Backbone Building

CD Biosynsis provides professional backbone building services for synthetic biology researchers around the world to facilitate their cutting-edge research. Our aim is to obtain protein backbone configurations that satisfy a set of predefined requirements by the customers.

Introduction to Backbone Building

Backbone building is the preliminary step to designing a protein from scratch. The scientific community has adopted various methods to solve this problem. For symmetrical proteins, the method is necessary to ideally assemble secondary structural elements such as α-helices, β-chains, etc. that fall into the allowable area of the Ramachandran diagram, and then connect them with appropriate loops. If the target protein contains many structural elements, the spacing between these elements and the loop connecting them needs to be optimized. For symmetric proteins, backbone building can be optimized using a set of defined parameters. For proteins with irregular structures, backbone building follows a separate trend as the loops have to be designed separately with the assistance of PDB database. In this modern age of computer programming and algorithms, structure prediction programs can also be used to build the backbone structure.

Service Offering

CD Biosynsis provides de novo backbone design services involving backbone building and selection that best suit the target.

Figure 1. Schematic diagram of the backbone building process at CD Biosynsis.Figure 1. Schematic diagram of the backbone building process at CD Biosynsis.

  • Fragment-based—The most general and successful backbone generation method that relies on the assembly of preexisting fragments and can be applied to build any arbitrary protein fold.
  • Parametric design—Building arrangements of secondary structure elements using mathematical equations describing the overall fold.
  • Kinematic closure (KIC) —A robotics-inspired backbone conformational sampling method that was originally developed for loop prediction and has been recently extended for de novo design of loops and peptides.
  • SEWING—Aimed at building novel backbone tertiary structures by recombining continuous or discontinuous pieces of secondary structure from a nonredundant database of protein substructures.

Based on our advanced bioinformatics tools and computational approaches, CD Biosynsis provides backbone building services to help clients execute their projects. We start the design process based on the ideal target protein structure or topology, and then generate a compatible protein backbone for our customers.

If you are interested in our services, please contact us for more details.

References

  1. Marcos E & Silva D A. Essentials of de novo protein design: Methods and applications. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2018, 8(6): e1374.
  2. Gulati K & M Poluri K. An overview of computational and experimental methods for designing novel proteins. Recent patents on biotechnology, 2016, 10(3): 235-263.