Repeat Protein Design

A central question in protein design is the extent to which naturally existing proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed by multiple tandem copies of a modular unit are universal in nature and play key roles in biomolecular recognition, signal transduction, and other critical biological processes. As a first-class provider in the protein design services, Creative Biolabs offers advanced engineering services and multiple computational protein design methods for functional repeat proteins which have been modified for molecular recognition and modular scaffolding applications.

Repeat Proteins

Repeat proteins are essential for various biological programs ranging from cell adhesion to signaling to defense mechanisms. These proteins consist of proximal suites of usually different repeated amino acid sequences. In most cases, the repeated units cooperatively fold into either a toroid-shaped or a solenoid-shaped structure. Despite extremely diverse in sequence and structure, repeat proteins are characterized by short-ranged intra-repeat and inter-repeat interactions between residues neighbor in sequence. The inherent modularity of repeat proteins allows the combination of functionalities in a single domain, such as recognition motifs for peptides and nucleic acids, and can be exploited to generate biomaterials with tunable mechanical properties.

Rational Protein Design Services at Creative Biolabs

Proteins that carry patterns of repetitive sequences largely fold with well-defined motifs and thus can better message the sequence-structure information than most proteins. They mainly work as protein-protein interactors with binding interfaces that aren't conserved along with other family members but specific for each interacting pair. The repeat proteins have been widely used as scaffolds for protein design that are generally centered on the maximization of the stability of repeat arrays. At Creative Biolabs, we're dedicated to the state-of-the-art ideas of repeat protein design and has established the following methods for desired synthetic binding proteins.

• A modular approach to protein design
  

  Fig.1 Designing repeat proteins. (Parmeggiani, 2017)

  Repeat proteins have unique properties that make them attractive to design. Here, we consider that the goal of building repeat proteins is to create modular systems from which custom scaffolds could be engineered for many different applications. Modularity can be explored on two distinct levels, including sequence analysis and structure-based design. The aim is to create a variety of modules to produce custom shapes.

  • Design from sequence -- Analyzing sequences of native protein motifs
  • Structure-based design -- Designs using native structural templates; Template-free (de novo) design

• A computational approach to protein design
  

  Fig.2 Computational protocol for designing de novo repeat proteins. (Brunette, 2015)

  In repeat proteins, interactions of adjacent units describe the shape and the curvature of the overall structure. To investigate the scope of possible repeat protein structures, we have launched novel repeat protein backbone arrangements and designed sequences predictable to fold into these required structures. Notably, our designs are entire de novo and the engineered proteins aren’t based on naturally occurring repeat proteins. And since helix-loop-helix-loop is the basic repeating unit, we’re committed to forming this simplest unit, from which a large diversity of curvatures can be produced.

• A combinational approach to protein design
  

  Fig.3 Overview of repeat protein design protocol. (Parmeggiani, 2015)

  We developed a general computational approach for idealized repeat proteins that integrates available protein family-based sequence and structural information, with Rosetta (an object-oriented software suite for the simulation and design of macromolecules) de novo folding and design calculations. Compared to standard sequence consensus-based approaches, this approach increases the versatility and reduces the manual intervention required to achieve stable designs by automatically generating very low energy design models compatible with the sequence and structural information. Sets of sequences have been designed for six protein families, including:

  • Ankyrin
  • Tetratrico peptide repeat (TPR)

  • Armadillo
  • HEAT repeat protein

  • Leucine-rich repeats (LRR)
  • WD40

• Highlights
  • Designed repeat proteins with high thermal stabilities compared to the naturally occurring ones
  • The state-of-the-art computational design algorithms and standard programs
  • Better custom services, charge step by step, and 100% guaranteed results

Protein design strategies using repeat proteins as scaffolds have made impressive advances with hundreds of already on-going applications. Computational protein design has realized the goal of finding an energy-optimal amino acid sequence for a backbone structure. As a well-known partner in the biopharmaceutical field, Creative Biolabs has built a series of protein engineering services for repeat protein design. These designed molecules are well behaved to favor expression and folding that can perform further optimization of binding a specific target. If you’re interested in our techniques, please don’t hesitate to contact usor send us an inquiry.

References

1. Parmeggiani, F.; et al. Designing repeat proteins: a modular approach to protein design. Curr Opin Struct Biol. 2017, 45: 116-123.
2. Parmeggiani, F.; et al. A general computational approach for repeat protein design. J Mol Biol. 2015, 427(2): 563-575.
3. Brunette, T.J.; et al. Exploring the repeat protein universe through computational protein design. Nature. 2015, 528(7583): 580-584.

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