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Control of repeat-protein curvature by computational protein design.

Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D - Nat. Struct. Mol. Biol. (2015)

Bottom Line: Second, a set of junction modules that connect the different building blocks are designed.Finally, new proteins with custom-designed shapes are generated by appropriately combining building-block and junction modules.Crystal structures of the designs illustrate the power of the approach in controlling repeat-protein curvature.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Biochemistry, University of Washington, Seattle, Washington, USA. [2] Institute for Protein Design, University of Washington, Seattle, Washington, USA.

ABSTRACT
Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high-affinity protein reagents and therapeutics. Here we describe a general approach to control the shape of the binding surface on repeat-protein scaffolds and apply it to leucine-rich-repeat proteins. First, self-compatible building-block modules are designed that, when polymerized, generate surfaces with unique but constant curvatures. Second, a set of junction modules that connect the different building blocks are designed. Finally, new proteins with custom-designed shapes are generated by appropriately combining building-block and junction modules. Crystal structures of the designs illustrate the power of the approach in controlling repeat-protein curvature.

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(a) Overview of curvature-tunable scaffold design: idealized building block module design, junction module design, and general module assembly. (b) Module organization of natural LRR modules is represented by a network where nodes represent modules and edges transitions between modules. The size of nodes and the thickness of edges are proportional to the frequencies observed in the PDB. (c) Graphical representation of building block and junction modules. (d) Idealized building block module structures and sequences. The highly conserved residues are shown in sticks.
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Figure 1: (a) Overview of curvature-tunable scaffold design: idealized building block module design, junction module design, and general module assembly. (b) Module organization of natural LRR modules is represented by a network where nodes represent modules and edges transitions between modules. The size of nodes and the thickness of edges are proportional to the frequencies observed in the PDB. (c) Graphical representation of building block and junction modules. (d) Idealized building block module structures and sequences. The highly conserved residues are shown in sticks.

Mentions: Our design strategy has three steps (Fig. 1a). The first step is the design of a set of idealized self-compatible building block modules (BB1, BB2, …., BBn) from which a series of proteins of variable length BBin can be created directly by varying the number of building block repeats without any further engineering. These “homo-building block” proteins will have a constant curvature defined by the base building block module. The second step is the design of a set of junction modules (JNBBi→BBj) that connect building block module i to building block module j. A critical feature of the design at step one and two is that the interfaces between individual building blocks, as well as those between building blocks in junction modules, have sufficiently low energy that the orientation between all units depends only upon the identity of adjacent repeats and is independent of the longer-range context. This enables the third and final step -- general module assembly -- the combination of building blocks and junction modules to generate a protein with a desired overall curvature. While the overall strategy is applicable to any repeat protein, in this paper we focus on LRRs. We describe the computational design and experimental characterization for each step in the following sections.


Control of repeat-protein curvature by computational protein design.

Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D - Nat. Struct. Mol. Biol. (2015)

(a) Overview of curvature-tunable scaffold design: idealized building block module design, junction module design, and general module assembly. (b) Module organization of natural LRR modules is represented by a network where nodes represent modules and edges transitions between modules. The size of nodes and the thickness of edges are proportional to the frequencies observed in the PDB. (c) Graphical representation of building block and junction modules. (d) Idealized building block module structures and sequences. The highly conserved residues are shown in sticks.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4318719&req=5

Figure 1: (a) Overview of curvature-tunable scaffold design: idealized building block module design, junction module design, and general module assembly. (b) Module organization of natural LRR modules is represented by a network where nodes represent modules and edges transitions between modules. The size of nodes and the thickness of edges are proportional to the frequencies observed in the PDB. (c) Graphical representation of building block and junction modules. (d) Idealized building block module structures and sequences. The highly conserved residues are shown in sticks.
Mentions: Our design strategy has three steps (Fig. 1a). The first step is the design of a set of idealized self-compatible building block modules (BB1, BB2, …., BBn) from which a series of proteins of variable length BBin can be created directly by varying the number of building block repeats without any further engineering. These “homo-building block” proteins will have a constant curvature defined by the base building block module. The second step is the design of a set of junction modules (JNBBi→BBj) that connect building block module i to building block module j. A critical feature of the design at step one and two is that the interfaces between individual building blocks, as well as those between building blocks in junction modules, have sufficiently low energy that the orientation between all units depends only upon the identity of adjacent repeats and is independent of the longer-range context. This enables the third and final step -- general module assembly -- the combination of building blocks and junction modules to generate a protein with a desired overall curvature. While the overall strategy is applicable to any repeat protein, in this paper we focus on LRRs. We describe the computational design and experimental characterization for each step in the following sections.

Bottom Line: Second, a set of junction modules that connect the different building blocks are designed.Finally, new proteins with custom-designed shapes are generated by appropriately combining building-block and junction modules.Crystal structures of the designs illustrate the power of the approach in controlling repeat-protein curvature.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Biochemistry, University of Washington, Seattle, Washington, USA. [2] Institute for Protein Design, University of Washington, Seattle, Washington, USA.

ABSTRACT
Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high-affinity protein reagents and therapeutics. Here we describe a general approach to control the shape of the binding surface on repeat-protein scaffolds and apply it to leucine-rich-repeat proteins. First, self-compatible building-block modules are designed that, when polymerized, generate surfaces with unique but constant curvatures. Second, a set of junction modules that connect the different building blocks are designed. Finally, new proteins with custom-designed shapes are generated by appropriately combining building-block and junction modules. Crystal structures of the designs illustrate the power of the approach in controlling repeat-protein curvature.

Show MeSH