1,721,019 research outputs found
De Novo Design of Heterotrimeric Coiled Coils
No full textThe three-helix bundle is a common structural motif among natural proteins. It has been observed in numerous important proteins, such as fibrinogen, laminin, spectrin, dystrofin, hemagglutinin, and mannose binding proteins. The three-helix bundle is a simple structure in which three alpha-helices pack against each other, with a slight left-handed twist. Because of its simplicity relative to other structural motifs, the three-helix bundle can be conveniently used both to clarify the forces responsible for the protein folding and stability, and for the design of novel proteins. In this paper we describe the design, synthesis, and characterization of three peptides that self-assemble into antiparallel, heterotrimeric coiled coils. The experimental results, obtained from CD spectroscopy and ultracentrifugation equilibrium sedimentation, indicate that the mixture of the three peptides preferentially forms heterotrimers; moreover, these aggregates represent attractive systems for combinatorial design of libraries of pseudo C3 symmetric ligands or binding sites
Tertiary Templates for the Design of Diiron Proteins
No full textDiiron proteins represent a diverse class of structures involved in the binding and activation of oxygen. This review explores the simple structural features underlying the common metal-ion-binding and oxygen-binding properties of these proteins. The backbone geometries of their active sites are formed by four-helix bundles, which may be parameterized to within approximately 1 Å root mean square deviation. Such parametric models are excellent starting points for investigating how asymmetric deviations from an idealized geometry influence the functional properties of the metal ion centers. These idealized models also provide attractive frameworks for de novo protein design
Tertiary Templates for the Design of Diiron Proteins
No full textDiiron proteins represent a diverse class of structures involved in the binding and activation of oxygen. This review explores the simple structural features underlying the common metal-ion-binding and oxygen-binding properties of these proteins. The backbone geometries of their active sites are formed by four-helix bundles, which may be parameterized to within approximately 1 Å root mean square deviation. Such parametric models are excellent starting points for investigating how asymmetric deviations from an idealized geometry influence the functional properties of the metal ion centers. These idealized models also provide attractive frameworks for de novo protein design
Topology of Porphyrin Cofactors Covalently Linked to Synthetic Four-Helix Bundle: Towards the Design of Multicofactor Redox-Active Proteins
No full textTopology of Porphyrins Linked to De Novo Designed Four-Helix Bundles: Towards the Design and Synthesis of Multicofactor Redox Enzymes
No full textDe novo design of helical bundles as models for understanding protein folding and function
No full textDe novo protein design has proven to be a powerful tool for understanding protein folding, structure, and function. In this Account, we highlight aspects of our research on the design of dimeric, four-helix bundles. Dimeric, four-helix bundles are found throughout nature, and the history of their design in our laboratory illustrates our hierarchic approach to protein design. This approach has been successfully applied to create a completely native-like protein. Structural and mutational analysis allowed us to explore the determinants of native protein structure. These determinants were then applied to the design of a dinuclear metal-binding protein that can now serve as a model for this important class of proteins
Analysis and Design of Three Stranded Coiled Coils and Three-Helix Bundle
No full textThree-stranded coiledcoils and three-helix bundles are increasingly being identified in proteins. Design and engineering on the scaffolds of these motifs is a potential route towards combating associated viral infections as well as introducing novel functional sites
Design of a Synthetic Receptor for the Calmodulin-Binding Domain of Calcineurin
No full textThese paper reports the design of a helical hairpin peptide that binds specifically to the CaM-binding domain of calcineurin, a phosphatase involved in a number of signal transduction schemes
From Synthetic Coiled Coils to Functional Proteins: Automated Design of a Receptor for the Calmodulin-Binding Domain of Calcineurin
No full textA series of synthetic receptors capable of binding to the calmodulin-binding domain of calcineurin (CN393–414) was designed, synthesized and characterized. The design was accomplished by docking CN393–414 against a two-helix receptor, using an idealized three-stranded coiled coil as a starting geometry. The sequence of the receptor was chosen using a side-chain re-packing program, which employed a genetic algorithm to select potential binders from a total of 7.5 × 106 possible sequences. A total of 25 receptors were prepared, representing 13 sequences predicted by the algorithm as well as 12 related sequences that were not predicted. The receptors were characterized by CD spectroscopy, analytical ultracentrifugation, and binding assays. The receptors predicted by the algorithm bound CN393–414 with apparent dissociation constants ranging from 0.2 μM to >50 μM. Many of the receptors that were not predicted by the algorithm also bound to CN393–414. Methods to circumvent this problem and to improve the automated design of functional proteins are discussed
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