Engineering modular protein interaction switches by sequence overlap

Design of Protein Logic Gate System Operating on Lipid Membranes

Lipid membranes are becoming increasingly popular in synthetic biology due to their biophysical properties and crucial role in communication between different compartments. Several alluring protein-membrane sensors have already been developed, whereas protein logic gates designs on membrane-embedded proteins are very limited. Here we demonstrate the construction of a two-level protein-membrane logic gate with an OR-AND logic. The system consists of an engineered pH-dependent pore-forming protein listeriolysin O and its DARPin-based inhibitor, conjugated to a lipid vesicle membrane. The gate responds to low pH and removal of the inhibitor from the membrane either by switching to a reducing environment, protease cleavage, or any other signal depending on the conjugation chemistry used for inhibitor attachment to the membrane. This unique protein logic gate vesicle system advances generic sensing and actuator platforms used in synthetic biology and could be utilized in drug delivery.

Influence of Secondary-Structure Folding on the Mutually Exclusive Folding Process of GL5/I27 Protein: Evidence from Molecular Dynamics Simulations

Mutually exclusive folding proteins are a class of multidomain proteins in which the host domain remains folded while the guest domain is unfolded, and both domains achieve exchange of their folding status by a mutual exclusive folding (MEF) process. We carried out conventional and targeted molecular dynamics simulations for the mutually exclusive folding protein of GL5/I27 to address the MEF transition mechanisms. We constructed two starting models and two targeted models, i.e., the starting models GL5/I27-S and GL5/I27-ST in which the first model involves the host domain GL5 and the secondary-structure unfolded guest domain I27-S, while the second model involves the host domain GL5 and the secondary/tertiary-structure extending guest domain I27-ST, and the target models GL5-S/I27 and GL5-ST/I27 in which GL5-S and GL5-ST represent the secondary-structure unfolding and the secondary/tertiary-structure extending, respectively. We investigated four MEF transition processes from both starting models to both target models. Based on structural changes and the variations of the radius of gyration (R_g) and the fractions of native contacts (Q), the formation of the secondary structure of the I27-guest domain induces significant extending of the GL5-host domain; but the primary shrinking of the tertiary structure of the I27-guest domain causes insignificant extending of the GL5-host domain during the processes. The results indicate that only formation of the secondary structure in the I27-guest domain provides the main driving force for the mutually exclusive folding/unfolding between the I27-guest and GL5-host domains. A special structure as an intermediate with both host and guest domains being folded at the same time was found, which was suggested by the experiment. The analysis of hydrogen bonds and correlation motions supported the studied transition mechanism with the dynamical "tug-of-war" phenomenon.

Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression

Organisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves the de novo design of RNA modules enabling dynamic signal processing in live cells. This requires a scalable methodology for sensing, transmission, and actuation, which could be assembled into larger signaling networks. Here, we present a biochemical strategy to design RNA-mediated signal transduction cascades able to sense small molecules and small RNAs. We design switchable functional RNA domains by using strand-displacement techniques. We experimentally characterize the molecular mechanism underlying our synthetic RNA signaling cascades, show the ability to regulate gene expression with transduced RNA signals, and describe the signal processing response of our systems to periodic forcing in single live cells. The engineered systems integrate RNA–RNA interaction with available ribozyme and aptamer elements, providing new ways to engineer arbitrary complex gene circuits.

Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches

Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamplike embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ∼0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide an additional specificity check that increases the discrimination efficiency toward a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nanomachines.

Designing redox potential-controlled protein switches based on mutually exclusive proteins

Synthetic/artificial protein switches provide an efficient means of controlling protein functions using chemical signals and stimuli. Mutually exclusive proteins, in which only the host or guest domain can remain folded at a given time owing to conformational strain, have been used to engineer novel protein switches that can switch enzymatic functions on and off in response to ligand binding. To further explore the potential of mutually exclusive proteins as protein switches and sensors, we report here a new redox-based approach to engineer a mutually exclusive folding-based protein switch. By introducing a disulfide bond into the host domain of a mutually exclusive protein, we demonstrate that it is feasible to use redox potential to switch the host domain between its folded and unfolded conformations via the mutually exclusive folding mechanism, and thus switching the functionality of the host domain on and off. Our study opens a new and potentially general avenue that uses mutually exclusive proteins to design novel switches able to control the function of a variety of proteins.

Synthetic multicellularity

The ability to synthesize biological constructs on the scale of the organisms we observe unaided is probably one of the more outlandish, yet recurring, dreams humans have had since they began to modify genes. This review brings together recent developments in synthetic biology, cell and developmental biology, computation, and technological development to provide context and direction for the engineering of rudimentary, autonomous multicellular ensembles.

Evolutionary synthetic biology

Signaling networks process vast amounts of environmental information to generate specific cellular responses. As cellular environments change, signaling networks adapt accordingly. Here, I will discuss how the integration of synthetic biology and directed evolution approaches is shedding light on the molecular mechanisms that guide the evolution of signaling networks. In particular, I will review studies that demonstrate how different types of mutations, from the replacement of individual amino acids to the shuffling of modular domains, lead to markedly different evolutionary trajectories and consequently to diverse network rewiring. Moreover, I will argue that intrinsic evolutionary properties of signaling proteins, such as the robustness of wild type functions, the promiscuous nature of evolutionary intermediates, and the modular decoupling between binding and catalysis, play important roles in the evolution of signaling networks. Finally, I will argue that rapid advances in our ability to synthesize DNA will radically alter how we study signaling network evolution at the genome-wide level.

Ultrasensitive synthetic protein regulatory networks using mixed decoys

Cellular protein interaction networks exhibit sigmoidal input-output relationships with thresholds and steep responses (i.e., ultrasensitivity). Although cooperativity can be a source of ultrasensitivity, we examined whether the presence of "decoy" binding sites that are not coupled to activation could also lead to this effect. To systematically vary key parameters of the system, we designed a synthetic regulatory system consisting of an autoinhibited PDZ domain coupled to an activating SH3 domain binding site. In the absence of a decoy binding site, this system is non-ultrasensitive, as predicted by modeling of this system. Addition of a high-affinity decoy site adds a threshold, but the response is not ultrasensitive. We found that sigmoidal activation profiles can be generated utilizing multiple decoys with mixtures of high and low affinities, where high affinity decoys act to set the threshold and low affinity decoys ensure a sigmoidal response. Placing the synthetic decoy system in a mitotic spindle orientation cell culture system thresholds this physiological activity. Thus, simple combinations of non-activating binding sites can lead to complex regulatory responses in protein interaction networks.

Engineering and optimization of an allosteric biosensor protein for peroxisome proliferator-activated receptor γ ligands

The peroxisome proliferator-activated receptor gamma (PPARγ or PPARG) belongs to the nuclear receptor superfamily, and is a potential drug target for a variety of diseases. In this work, we constructed a series of bacterial biosensors for the identification of functional PPARγ ligands. These sensors entail modified Escherichia coli cells carrying a four-domain fusion protein, comprised of the PPARγ ligand binding domain (LBD), an engineered mini-intein domain, the E. coli maltose binding protein (MBD), and a thymidylate synthase (TS) reporter enzyme. E. coli cells expressing this protein exhibit hormone ligand-dependent growth phenotypes. Unlike our published estrogen (ER) and thyroid receptor (TR) biosensors, the canonical PPARγ biosensor cells displayed pronounced growth in the absence of ligand. They were able to distinguish agonists and antagonists, however, even in the absence of agonist. To improve ligand sensitivity of this sensor, we attempted to engineer and optimize linker peptides flanking the PPARγ LBD insertion point. Truncation of the original linkers led to decreased basal growth and significantly enhanced ligand sensitivity of the PPARγ sensor, while substitution of the native linkers with optimized G(4)S (Gly-Gly-Gly-Gly-Ser) linkers further increased the sensitivity. Our studies demonstrate that the properties of linkers, especially the C-terminal linker, greatly influence the efficiency and fidelity of the allosteric signal induced by ligand binding. Our work also suggests an approach to increase allosteric behavior in this multidomain sensor protein, without modification of the functional LBD.

Molecular simulations of mutually exclusive folding in a two-domain protein switch

A major challenge with testing designs of protein conformational switches is the need for experimental probes that can independently monitor their individual protein domains. One way to circumvent this issue is to use a molecular simulation approach in which each domain can be directly observed. Here we report what we believe to be the first molecular simulations of mutually exclusive folding in an engineered two-domain protein switch, providing a direct view of how folding of one protein drives unfolding of the other in a barnase-ubiquitin fusion protein. These simulations successfully capture the experimental effects of interdomain linker length and ligand binding on the extent of unfolding in the less stable domain. In addition, the effect of linker length on the potential for oligomerization, which eliminates switch activity, is in qualitative agreement with analytical ultracentrifugation experiments. We also perform what we believe to be the first study of protein unfolding via progressive localized compression. Finally, we are able to explore the kinetics of mutually exclusive folding by determining the effect of linker length on rates of unfolding and refolding of each protein domain. Our results demonstrate that molecular simulations can provide seemingly novel biological insights on the behavior of individual protein domains, thereby aiding in the rational design of bifunctional switches.

Converting a protein into a switch for biosensing and functional regulation

Proteins that switch conformations in response to a signaling event (e.g., ligand binding or chemical modification) present a unique solution to the design of reagent-free biosensors as well as molecules whose biological functions are regulated in useful ways. The principal roadblock in the path to develop such molecules is that the majority of natural proteins do not change conformation upon binding their cognate ligands or becoming chemically modified. Herein, we review recent protein engineering efforts to introduce switching properties into binding proteins. By co-opting natural allosteric coupling, joining proteins in creative ways and formulating altogether new switching mechanisms, researchers are learning how to coax conformational changes from proteins that previously had none. These studies are providing some answers to the challenging question: how can one convert a lock-and-key binding protein into a molecular switch?

Strategies for protein synthetic biology

Proteins are the most versatile among the various biological building blocks and a mature field of protein engineering has lead to many industrial and biomedical applications. But the strength of proteins—their versatility, dynamics and interactions—also complicates and hinders systems engineering. Therefore, the design of more sophisticated, multi-component protein systems appears to lag behind, in particular, when compared to the engineering of gene regulatory networks. Yet, synthetic biologists have started to tinker with the information flow through natural signaling networks or integrated protein switches. A successful strategy common to most of these experiments is their focus on modular interactions between protein domains or domains and peptide motifs. Such modular interaction swapping has rewired signaling in yeast, put mammalian cell morphology under the control of light, or increased the flux through a synthetic metabolic pathway. Based on this experience, we outline an engineering framework for the connection of reusable protein interaction devices into self-sufficient circuits. Such a framework should help to ‘refacture’ protein complexity into well-defined exchangeable devices for predictive engineering. We review the foundations and initial success stories of protein synthetic biology and discuss the challenges and promises on the way from protein- to protein systems design.

Engineering Ca2+/calmodulin-mediated modulation of protein translocation by overlapping binding and signaling peptide sequences

Protein translocation is used by cells to regulate protein activity in time and space. Synthetic systems have studied the effect of second messengers and exogenous chemicals on translocation, and have used translocation-based sensors to monitor unrelated pathways such as caspase activity. We have created a synthetic Ca2+-inducible protein using calmodulin binding peptides that selectively reveal nuclear localization and export signals in low Ca2+ (0 microM) and high Ca2+ (10 microM) environments, respectively. Experiments in live cells showed that our construct translocates between the nucleolus and plasma membrane with time constants of approximately 2 h. Further, a single amino acid mutation (Cys20Ala) in our construct prevented translocation to the plasma membrane and instead targeted it the mitochondria as predicted by bioinformatic analysis. Lastly, we studied the effect of cell line, Ca2+ concentration, chemical inhibitors, and cell morphology on translocation and found these conditions affected the rate, extent and direction of translocation. Our work demonstrates the feasibility of engineering Ca2+/calmodulin-mediated modulation of protein translocation and suggests that more natural analogs may exist.

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

PDZ domains (PDZs), the most common interaction domain proteins, play critical roles in many cellular processes. PDZs perform their job by binding specific protein partners. However, they are very promiscuous, binding to more than one protein, yet selective at the same time. We examined the binding related dynamics of various PDZs to have insight about their specificity and promiscuity. We used full atomic normal mode analysis and a modified coarse-grained elastic network model to compute the binding related dynamics. In the latter model, we introduced specificity for each single parameter constant and included the solvation effect implicitly. The modified model, referred to as specific-Gaussian Network Model (s-GNM), highlights some interesting differences in the conformational changes of PDZs upon binding to Class I or Class II type peptides. By clustering the residue fluctuation profiles of PDZs, we have shown: (i) binding selectivities can be discriminated from their dynamics, and (ii) the dynamics of different structural regions play critical roles for Class I and Class II specificity. s-GNM is further tested on a dual-specific PDZ which showed only Class I specificity when a point mutation exists on the betaA-betaB loop. We observe that the binding dynamics change consistently in the mutated and wild type structures. In addition, we found that the binding induced fluctuation profiles can be used to discriminate the binding selectivity of homolog structures. These results indicate that s-GNM can be a powerful method to study the changes in binding selectivities for mutant or homolog PDZs.

Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules

Generation of novel protein functions is a major goal in biotechnology and also a rigorous test for our understanding of the relationship between protein structure and function. Early examples of protein engineering focused on design and directed evolution within the constraints of the original protein architecture, exemplified by the highly successful fields of antibody and enzyme engineering. Recent studies show that protein engineering strategies which step away from these natural architectures, that is by manipulating the organization of domains and modules thus mimicking nonhomologous recombination, are highly effective in producing complex and sophisticated functions in terms of both molecular recognition and regulation.

Challenges in the computational design of proteins

Protein design has many applications not only in biotechnology but also in basic science. It uses our current knowledge in structural biology to predict, by computer simulations, an amino acid sequence that would produce a protein with targeted properties. As in other examples of synthetic biology, this approach allows the testing of many hypotheses in biology. The recent development of automated computational methods to design proteins has enabled proteins to be designed that are very different from any known ones. Moreover, some of those methods mostly rely on a physical description of atomic interactions, which allows the designed sequences not to be biased towards known proteins. In this paper, we will describe the use of energy functions in computational protein design, the use of atomic models to evaluate the free energy in the unfolded and folded states, the exploration and optimization of amino acid sequences, the problem of negative design and the design of biomolecular function. We will also consider its use together with the experimental techniques such as directed evolution. We will end by discussing the challenges ahead in computational protein design and some of their future applications.

Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors

Binding-induced biomolecular switches are used throughout nature and, increasingly, throughout biotechnology for the detection of chemical moieties and the subsequent transduction of this detection into useful outputs. Here we show that the thermodynamics of these switches are quantitatively described by a simple 3-state population-shift model, in which the equilibrium between a nonbinding, nonsignaling state and the binding-competent, signaling state is shifted toward the latter upon target binding. Because of this, their performance is determined by the tradeoff inherent to their switching thermodynamics; while a switching equilibrium constant favoring the nonbinding, nonsignaling, conformation ensures a larger signal change (more molecules are poised to respond), it also reduces affinity (binding must overcome a more unfavorable conformational free energy). We then derive and employ the relationship between switching thermodynamics and switch signaling to rationally tune the dynamic range and detection limit of a representative structure-switching biosensor, a molecular beacon, over 4 orders of magnitude. These findings demonstrate that the performance of biomolecular switches can be rationally tuned via mutations that alter their switching thermodynamics and suggest a mechanism by which the performance of naturally occurring switches may have evolved.

Designing switchable enzymes

The modulation of enzyme function is a key regulatory feature of biological systems. The ability to engineer synthetic enzymes that can be controlled by any arbitrary signal would enable a wide array of sensing applications and therapeutics and provide us with powerful tools for the basic study of biology. Here several recent advances in the engineering of switchable enzymes through domain fusion are discussed.

Synthetic gene networks: the next wave in biotechnology?

Engineering novel, reusable gene networks to provide greater control over cellular processes is one of the goals of the emerging discipline of synthetic biology. This article reviews the landmark literature pertaining to the development of synthetic gene networks, the engineering framework used to design and characterize them and the technological developments on the horizon that could potentially advance the field in new directions. As gene network engineering enters its second decade, an attempt is also made to outline the challenges in advancing this nascent field, especially with regard to the practical limitations of component reusability and reliability and the opportunities that present themselves in the development of novel gene expression controllers and single-cell biosensors.

Harnessing nature's toolbox: regulatory elements for synthetic biology

Synthetic biologists seek to engineer complex biological systems composed of modular elements. Achieving higher complexity in engineered biological organisms will require manipulating numerous systems of biological regulation: transcription; RNA interactions; protein signalling; and metabolic fluxes, among others. Exploiting the natural modularity at each level of biological regulation will promote the development of standardized tools for designing biological systems.

A Ca2+-sensing molecular switch based on alternate frame protein folding

Existing strategies for creating biosensors mainly rely on large conformational changes to transduce a binding event to an output signal. Most molecules, however, do not exhibit large-scale structural changes upon substrate binding. Here, we present a general approach (alternate frame folding, or AFF) for engineering allosteric control into ligand binding proteins. AFF can in principle be applied to any protein to establish a binding-induced conformational change, even if none exists in the natural molecule. The AFF design duplicates a portion of the amino acid sequence, creating an additional "frame" of folding. One frame corresponds to the wild-type sequence, and folding produces the normal structure. Folding in the second frame yields a circularly permuted protein. Because the two native structures compete for a shared sequence, they fold in a mutually exclusive fashion. Binding energy is used to drive the conformational change from one fold to the other. We demonstrate the approach by converting the protein calbindin D(9k) into a molecular switch that senses Ca2+. The structures of Ca2+-free and Ca2+-bound calbindin are nearly identical. Nevertheless, the AFF mechanism engineers a robust conformational change that we detect using two covalently attached fluorescent groups. Biological fluorophores can also be employed to create a genetically encoded sensor. AFF should be broadly applicable to create sensors for a variety of small molecules.

Light-activated DNA binding in a designed allosteric protein

An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that the rigidity and defined geometry of an alpha-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed 12 fusions between the naturally photoactive LOV2 domain from Avena sativa phototropin 1 and the Escherichia coli trp repressor. When illuminated, one of the fusions selectively binds operator DNA and protects it from nuclease digestion. The ready success of our rational design strategy suggests that the helical "allosteric lever arm" is a general scheme for coupling the function of two proteins.

The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency

Enterohaemorrhagic Escherichia coli attaches to the intestine through actin pedestals that are formed when the bacterium injects its protein EspF(U) (also known as TccP) into host cells. EspF(U) potently activates the host WASP (Wiskott-Aldrich syndrome protein) family of actin-nucleating factors, which are normally activated by the GTPase CDC42, among other signalling molecules. Apart from its amino-terminal type III secretion signal, EspF(U) consists of five-and-a-half 47-amino-acid repeats. Here we show that a 17-residue motif within this EspF(U) repeat is sufficient for interaction with N-WASP (also known as WASL). Unlike most pathogen proteins that interface with the cytoskeletal machinery, this motif does not mimic natural upstream activators: instead of mimicking an activated state of CDC42, EspF(U) mimics an autoinhibitory element found within N-WASP. Thus, EspF(U) activates N-WASP by competitively disrupting the autoinhibited state. By mimicking an internal regulatory element and not the natural activator, EspF(U) selectively activates only a precise subset of CDC42-activated processes. Although one repeat is able to stimulate actin polymerization, we show that multiple-repeat fragments have notably increased potency. The activities of these EspF(U) fragments correlate with their ability to coordinate activation of at least two N-WASP proteins. Thus, this pathogen has used a simple autoinhibitory fragment as a component to build a highly effective actin polymerization machine.