Design of a heme-binding four helix bundle

Choma, Christin T.; Åkerfeldt, Karin S.; Dutton, L.; Lear, J. D.; Nelson, Mark J.; Robertson, Dan E.; DeGrado, William

doi:10.1016/0162-0134(93)85094-o

Cited by 17 publications

(20 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…97,98 However, complete control of a cofactor's environment might be best effected through the de novo design [99][100][101][102] of proteins whose active sites are defined by the favorable free energy of folding of the polypeptide chain. There has also been much progress made in the de novo design of proteins that bind metalloporphyrins [92][93][94][95][103][104][105] and Zn-(II). 20,106 The structures of some simple porphyrin peptide complexes have been solved by NMR.…”

Section: From Structure To Function: Design Of Metalloproteinsmentioning

confidence: 99%

“…107,108 However, the structures of larger designed proteins with bound cofactors have not been solved, possibly because they have dynamically averaging structures. 41,104,109,110 As the principles and methods for de novo protein design have matured, it has recently become possible to design structurally defined models for metalloproteins. The diiron class of proteins, which are capable of performing a diverse range of functions yet contain a fourhelix bundle at the heart of the protein, provided an attractive target for these studies.…”

Section: From Structure To Function: Design Of Metalloproteinsmentioning

confidence: 99%

See 1 more Smart Citation

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

et al. 2000

View full text Add to dashboard Cite

De 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.Protein folding is an important and multifaceted scientific problem. 1-8 One facet of this problem involves the prediction of three-dimensional structure from amino acid sequence, an endeavor the importance of which has been highlighted by the recent release of gene sequences of many whole organisms. As the size of the protein structural database expands, it will be increasingly possible to assign amino acid sequences to a given structural family on the basis of the homology of their sequences with proteins of known structure. Another facet of the folding problem is the delineation of the kinetic mechanism by which an unfolded protein chain undergoes the transition from a random coil with an astronomical number of configurations to a uniquely folded structure. A final facet of the protein folding problem is to understand, at the atomic level, the detailed physicochemical features that kinetically and thermodynamically direct the formation of an unique, cooperatively folded, native structure. This latter endeavor is particularly important as it lays the groundwork for the design of novel inhibitors of natural proteins as well as the construction of novel proteins and related biopolymers not found in nature.De novo protein design is an approach to the protein folding problem that critically tests our understanding of all these facets of this problem. 9,10 This method involves the design of a sequence that is intended to fold into a predetermined three-dimensional structure without the sequence being patterned after any natural protein. Through an iterative process of design and rigorous characterization, the principles governing protein folding and function can be evaluated. Thus, "failures" highlight gaps in our understanding, whereas "successes" confirm the principles used in the design and often provide simple model systems to further

show abstract

Section: From Structure To Function: Design Of Metalloproteinsmentioning

confidence: 99%

Section: From Structure To Function: Design Of Metalloproteinsmentioning

confidence: 99%

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

et al. 2000

View full text Add to dashboard Cite

show abstract

“…Many peptides and proteins have been designed to bind heme. [34][35][36][37][38][39][40] The diversity of these designs-and the frequency of their success-suggests that a great variety of sequences containing histidine side chains can readily bind heme. Indeed, the inherent propensity of polypeptides to bind heme was observed in one of the first designs of a novel heme protein, when it was found that not only the designed sequence bound heme, but a control ''retro'' sequence synthesized backwards also bound the cofactor.…”

Section: Functional Proteins Occur Frequently In Unselected Librariesmentioning

confidence: 99%

“…Indeed, the inherent propensity of polypeptides to bind heme was observed in one of the first designs of a novel heme protein, when it was found that not only the designed sequence bound heme, but a control ''retro'' sequence synthesized backwards also bound the cofactor. 34 Peroxidase activity. Peptides and proteins that bind heme often display peroxidase activity.…”

Section: Functional Proteins Occur Frequently In Unselected Librariesmentioning

confidence: 99%

Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4‐helix bundle proteins

et al. 2009

View full text Add to dashboard Cite

To probe the potential for enzymatic activity in unevolved amino acid sequence space, we created a combinatorial library of de novo 4-helix bundle proteins. This collection of novel proteins can be considered an ''artificial superfamily'' of helical bundles. The superfamily of 102-residue proteins was designed using binary patterning of polar and nonpolar residues, and expressed in Escherichia coli from a library of synthetic genes. Sequences from the library were screened for a range of biological functions including heme binding and peroxidase, esterase, and lipase activities. Proteins exhibiting these functions were purified and characterized biochemically. The majority of de novo proteins from this superfamily bound the heme cofactor, and a sizable fraction of the proteins showed activity significantly above background for at least one of the tested enzymatic activities. Moreover, several of the designed 4-helix bundles proteins showed activity in all of the assays, thereby demonstrating the functional promiscuity of unevolved proteins. These studies reveal that de novo proteins-which have neither been designed for function, nor subjected to evolutionary pressure (either in vivo or in vitro)-can provide rudimentary activities and serve as a ''feedstock'' for evolution.

show abstract

“…Various approaches can be used to incorporate functions in the designed protein scaffolds (Smith and Hecht, 2011), and metal binding sites have been a particularly interesting target for this purpose because the biological chemistry of metals is extremely rich (Holm et al, 1996;Lu et al, 2009). For example, by engineering different cofactors like Zn 2+ (Handel et al, 1993), Fe 2+ /Fe 3+ (Kaplan and DeGrado, 2004), heme (Choma et al, 1994) and abiological chromophore (DPP) Zn (Fry et al, 2010) into the de novo designed four-helix bundles, functions like phenol oxidation, electron transfer, and nonlinear optical properties have been obtained.…”

Section: Introductionmentioning

confidence: 99%

Engineering a zinc binding site into the de novo designed protein DS119 with a βαβ structure

Zhu¹,

Liang²,

Lai³

2011

Protein Cell

View full text Add to dashboard Cite

Functional proteins designed de novo have potential application in chemical engineering, agriculture and healthcare. Metal binding sites are commonly used to incorporate functions. Based on a de novo designed protein DS119 with a βαβ structure, we have computationally engineered zinc binding sites into it using a home-made searching program. Seven out of the eight designed sequences tested were shown to bind Zn 2+ with micromolar affinity, and one of them bound Zn 2+ with 1:1 stoichiometry. This is the first time that metalloproteins with an α, β mixed structure have been designed from scratch.

show abstract

Design of a heme-binding four helix bundle

Cited by 17 publications

References 0 publications

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4‐helix bundle proteins

Engineering a zinc binding site into the de novo designed protein DS119 with a βαβ structure

Contact Info

Product

Resources

About