Jonathan J. Silberg

A transposase strategy for creating libraries of circularly permuted proteins

A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.

Thermodynamic prediction of protein neutrality

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. Our theory also predicts that a protein can gain extra robustness to the first few substitutions by increasing its thermodynamic stability. We validate our theory with simulations on lattice protein models and by showing that it quantitatively predicts previously published experimental measurements on subtilisin and our own measurements on variants of TEM1 beta-lactamase. Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications.

Library analysis of SCHEMA-guided protein recombination

The computational algorithm SCHEMA was developed to estimate the disruption caused when amino acid residues that interact in the three‐dimensional structure of a protein are inherited from different parents upon recombination. To evaluate how well SCHEMA predicts disruption, we have shuffled the distantly‐related β‐lactamases PSE‐4 and TEM‐1 at 13 sites to create a library of 214 (16,384) chimeras and examined which ones retain lactamase function. Sequencing the genes from ampicillin‐selected clones revealed that the percentage of functional clones decreased exponentially with increasing calculated disruption (E = the number of residue–residue contacts that are broken upon recombination). We also found that chimeras with low E have a higher probability of maintaining lactamase function than chimeras with the same effective level of mutation but chosen at random from the library. Thus, the simple distance metric used by SCHEMA to identify interactions and compute E allows one to predict which chimera sequences are most likely to retain their function. This approach can be used to evaluate crossover sites for recombination and to create highly mosaic, folded chimeras.

Biochar and Microbial Signaling: Production Conditions Determine Effects on Microbial Communication

Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m(2)/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m(2)/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.

Effect of thiocyanate on ampa receptor mediated responses in excised patches and hippocampal slices

The binding affinity of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors for [3H]AMPA is increased 10-30-fold by the chaotropic anion thiocyanate. The present experiments tested if thiocyanate alters AMPA receptor mediated current fluxes and if any such effects are reflected in the waveform of synaptic responses. Currents were measured after a step application of glutamate or AMPA to patches excised from pyramidal cells of hippocampal slice cultures. Application of 1 mM AMPA produced responses with an average peak amplitude of 86 pA at -50 mV and a 10-90% rise time of 1.7 +/- 0.1 ms; the responses desensitized to a steady-state level below 10% of the peak current with a time constant of 11.1 +/- 0.7 ms. Glutamate in presence of D-amino-phosphonopentanoate produced similar responses which were inhibited by 6-cyano-7-nitro-quinoxaline-dione and enhanced by aniracetam or cyclothiazide and thus are characteristic for AMPA receptors. Thiocyanate accelerated the decay of AMPA responses two-fold and reduced the peak current by 30-50% with an EC50 of 3.2 mM which is comparable to its EC50 for enhancing binding. Effects on the desensitization of glutamate induced responses were much smaller and only evident at the highest thiocyanate concentration; no effect was seen on response amplitude. Binding and physiological effects can be adequately explained by assuming that thiocyanate enhances conversion from the sensitive to the desensitized state of the receptor and reduces ligand dissociation from the desensitized state. Synaptic responses were measured in disinhibited hippocampal slices. Perfusion with 20 mM sodium thiocyanate increased the slope of the field excitatory postsynaptic potential by 44.9 +/- 4.2% and reduced its decay time by 10.4 +/- 4.3%. The former effect appears to result at least in part from an increase in transmitter release since it was accompanied by a decrease in paired-pulse facilitation and was reduced in magnitude after enhancing transmitter release. The decrease in the decay time constant points to an effect of thiocyanate on AMPA receptors in situ which is similar to that seen in excised patches. These results demonstrate that an increase in binding affinity may be indicative of reduced rather than enhanced current flow through AMPA receptors. In addition, the results provide further evidence that the kinetics of the AMPA receptor channel contribute significantly to at least the decay phase of fast excitatory synaptic responses.

In Vivo Fluorescent Detection of Fe-S Clusters Coordinated by Human GRX2

A major challenge to studying Fe-S cluster biosynthesis in higher eukaryotes is the lack of simple tools for imaging metallocluster binding to proteins. We describe the first fluorescent approach for in vivo detection of 2Fe2S clusters that is based upon the complementation of Venus fluorescent protein fragments via human glutaredoxin 2 (GRX2) coordination of a 2Fe2S cluster. We show that Escherichia coli and mammalian cells expressing Venus fragments fused to GRX2 exhibit greater fluorescence than cells expressing fragments fused to a C37A mutant that cannot coordinate a metallocluster. In addition, we find that maximal fluorescence in the cytosol of mammalian cells requires the iron-sulfur cluster assembly proteins ISCU and NFS1. These findings provide evidence that glutaredoxins can dimerize within mammalian cells through coordination of a 2Fe2S cluster as observed with purified recombinant proteins.

The human escort protein Hep binds to the ATPase domain of mitochondrial hsp70 and regulates ATP hydrolysis.

Hsp70 escort proteins (Hep) have been implicated as essential for maintaining the function of yeast mitochondrial hsp70 molecular chaperones (mtHsp70), but the role that escort proteins play in regulating mammalian chaperone folding and function has not been established. We present evidence that human mtHsp70 exhibits limited solubility due to aggregation mediated by its ATPase domain and show that human Hep directly enhances chaperone solubility through interactions with this domain. In the absence of Hep, mtHsp70 was insoluble when expressed in Escherichia coli, as was its isolated ATPase domain and a chimera having this domain fused to the peptide-binding domain of HscA, a soluble monomeric chaperone. In contrast, these proteins all exhibited increased solubility when expressed in the presence of Hep. In vitro studies further revealed that purified Hep regulates the interaction of mtHsp70 with nucleotides. Full-length mtHsp70 exhibited slow intrinsic ATP hydrolysis activity (6.8 ± 0.2 × 10-4 s-1) at 25 °C, which was stimulated up to 49-fold by Hep. Hep also stimulated the activity of the isolated ATPase domain, albeit to a lower maximal extent (11.5-fold). In addition, gel-filtration studies showed that formation of chaperone-escort protein complexes inhibited mtHsp70 self-association, and they revealed that Hep binding to full-length mtHsp70 and its isolated ATPase domain is strongest in the absence of nucleotides. These findings provide evidence that metazoan escort proteins regulate the catalytic activity and solubility of their cognate chaperones, and they indicate that both forms of regulation arise from interactions with the mtHsp70 ATPase domain.

Differences in the refractory properties of two distinct inhibitory circuitries in field CA1 of the hippocampus

Extracellular reflections of IPSPs were examined in two distinct circuitries in field CA1 of the hippocampus. Stimulation in the stratum radiatum in the presence of AMPA receptor antagonists elicited positive potentials in the same stratum that were eliminated by picrotoxin, a blocker of GABAA receptors. Laminar profile analysis revealed that the response was maximal in the stratum radiatum at a point well distal to the pyramidal cell body layer and had a negative reflection in the stratum oriens. These field IPSPs presumably mediate the feedforward inhibition normally activated by the Schaffer-commissural projections to field CA1. Stimulation of the alveus produced an antidromic response followed by a much slower positive potential in recordings collected in the pyramidal cell layer. The latter response was suppressed by AMPA receptor antagonists or picrotoxin, as expected for disynaptic, recurrent (feedback) inhibition. The laminar profile for the feedback field IPSPs had its maximum near the pyramidal cell layer and its negative dipole in the stratum radiatum. Feedforward IPSPs were inhibited by about 50% if they were preceded within 200 ms by a priming pulse while feedback IPSPs were reduced by less than 20% under comparable conditions. The refractory effect was minimally dependent on stimulation intensity but was strongly affected by an antagonist of GABAB receptors. Attempts to modify IPSPs in the s. radiatum with long trains of low frequency stimulation or with theta-burst stimulation were not successful, suggesting that GABAergic synapses do not have the plasticities found in their glutamatergic counterparts. These results indicate that interneurons contacted by the extrinsic afferents of hippocampus form GABAergic synapses that differ in terms of spatial location and functional properties from the synapses generated by interneurons innervated by the recurrent collaterals of the pyramidal cells. The findings also suggest that repetitive afferent activity, while reducing the influence of dendritic IPSPs on excitatory input, will leave feedback suppression of cell spiking largely intact.

SCHEMA-Guided Protein Recombination

Publisher Summary This chapter examines the different aspects of SCHEMA-guided protein recombination. SCHEMA is a scoring function that predicts which elements in homologous proteins can be swapped without disturbing the integrity of the structure. Using the structural coordinates of the parent proteins, SCHEMA identifies pairs of residues that are interacting, and determines the number of interactions that are broken when a chimeric protein inherits portions of its sequence from different parents. The SCHEMA disruption of a chimeric sequence made by recombining sequence elements from homologous proteins is presented. The best methods available for creating the libraries identified by SCHEMA as enriched in folded chimeras are sequence-independent site directed chimeragenesis and chemical synthesis. These techniques can recombine parents with any level of sequence identity at multiple sites and easily create libraries encoding thousands of chimeras. It is observed that when the parents do not exhibit sufficient identity at the desired crossover locations, synonymous mutations can often be introduced to allow recombination at that site. It is found that SCHEMA only calculates the disruption arising from recombination, not from mutation.

Tunable protease-activatable virus nanonodes.

We explored the unique signal integration properties of the self-assembling 60-mer protein capsid of adeno-associated virus (AAV), a clinically proven human gene therapy vector, by engineering proteolytic regulation of virus–receptor interactions such that processing of the capsid by proteases is required for infection. We find the transfer function of our engineered protease-activatable viruses (PAVs), relating the degree of proteolysis (input) to PAV activity (output), is highly nonlinear, likely due to increased polyvalency. By exploiting this dynamic polyvalency, in combination with the self-assembly properties of the virus capsid, we show that mosaic PAVs can be constructed that operate under a digital AND gate regime, where two different protease inputs are required for virus activation. These results show viruses can be engineered as signal-integrating nanoscale nodes whose functional properties are regulated by multiple proteolytic signals with easily tunable and predictable response surfaces, a promising development toward advanced control of gene delivery.