Synthetic protein–protein interaction domains created by shuffling Cys
            <sub>2</sub>
            His
            <sub>2</sub>
            zinc‐fingers

Giesecke, Astrid; Fang, Rui; Joung, J. Keith

doi:10.1038/msb4100053

Cited by 20 publications

(17 citation statements)

References 52 publications

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“…This current level of coverage enables predictions for most natural proteins via nearest neighbor decomposition, but also has implications regarding the fraction of natural C2H2-ZFs that are likely to bind DNA. In particular, some natural and engineered C2H2-ZFs bind protein or RNA instead of (or in addition to) DNA ( 69 – 71 ), and the ∼5% of human C2H2-ZFs that are not similar to any core sequence in our data set are the best candidates for such functionality. Further, in most cases, a single amino acid substitution in a DNA-binding position will not abolish DNA-binding activity, and thus it is likely that most human C2H2-ZF domains can bind DNA, though with varying levels of affinity and specificity.…”

Section: Discussionmentioning

confidence: 99%

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

Persikov

Wetzel

Rowland

et al. 2015

Nucleic Acids Research

101

104

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Cys2His2 zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain's well-defined DNA-recognition interface, and its successful use in the design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of >160 000 unique domain–DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain–DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.

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Section: Discussionmentioning

confidence: 99%

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

Persikov

Wetzel

Rowland

et al. 2015

Nucleic Acids Research

101

104

View full text Add to dashboard Cite

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“…In constructing protein interaction devices (Giesecke et al , 2006), the proteins must be well characterized to determine where changes, deletions, and replacements of domains can occur, as their 3D structure plays a large role in the nature of their interactions. Connecting protein interaction devices is not a trivial task.…”

Section: Biological Devicesmentioning

confidence: 99%

Synthetic biology: new engineering rules for an emerging discipline

Andrianantoandro

Basu

Karig

et al. 2006

Molecular Systems Biology

912

738

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Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

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“…It was further proposed that Hunchback has a concentrationdependent activity (35,36) through dimerization (37). This dimerization may be mediated by dimerization zinc-finger (DZF) domains in the Hunchback protein (38,39). Moreover, the second finger domain was shown to have a specific function for the repression of Kruppel but is not necessary for the repression of knirps (40).…”

Section: A Model With Dual Activity Of Hunchback Captures the Expressmentioning

confidence: 99%

Whole-Embryo Modeling of Early Segmentation in Drosophila Identifies Robust and Fragile Expression Domains

Bieler

Pozzorini

Naef

2011

Biophysical Journal

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Segmentation of the Drosophila melanogaster embryo results from the dynamic establishment of spatial mRNA and protein patterns. Here, we exploit recent temporal mRNA and protein expression measurements on the full surface of the blastoderm to calibrate a dynamical model of the gap gene network on the entire embryo cortex. We model the early mRNA and protein dynamics of the gap genes hunchback, Kruppel, giant, and knirps, taking as regulatory inputs the maternal Bicoid and Caudal gradients, plus the zygotic Tailless and Huckebein proteins. The model captures the expression patterns faithfully, and its predictions are assessed from gap gene mutants. The inferred network shows an architecture based on reciprocal repression between gap genes that can stably pattern the embryo on a realistic geometry but requires complex regulations such as those involving the Hunchback monomer and dimers. Sensitivity analysis identifies the posterior domain of giant as among the most fragile features of an otherwise robust network, and hints at redundant regulations by Bicoid and Hunchback, possibly reflecting recent evolutionary changes in the gap-gene network in insects.

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Synthetic protein–protein interaction domains created by shuffling Cys ₂ His ₂ zinc‐fingers

Cited by 20 publications

References 52 publications

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

Synthetic biology: new engineering rules for an emerging discipline

Whole-Embryo Modeling of Early Segmentation in Drosophila Identifies Robust and Fragile Expression Domains

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Synthetic protein–protein interaction domains created by shuffling Cys 2 His 2 zinc‐fingers

Cited by 20 publications

References 52 publications

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

Synthetic biology: new engineering rules for an emerging discipline

Whole-Embryo Modeling of Early Segmentation in Drosophila Identifies Robust and Fragile Expression Domains

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Synthetic protein–protein interaction domains created by shuffling Cys ₂ His ₂ zinc‐fingers