An important strategy in the construction of biomimetic membranes and devices is to use natural proteins as the functional components for incorporation in a polymeric or nanocomposite matrix. Toward this goal, an important step is to immobilize proteins with high efficiency and precision without disrupting the protein function. Here, we developed a dual-functional tag containing histidine and the non-natural amino acid azidohomoalanine (AHA). AHA is metabolically incorporated into the protein, taking advantage of the Met-tRNA and Met-tRNA synthetase. Histidine in the tag can facilitate metal-affinity purification, whereas AHA can react with an alkyne-functionalized probe or surface via well-established click chemistry. We tested the performance of the tag using two model proteins, green fluorescence protein and an enzyme pyrophosphatase. We found that the addition of the tag and the incorporation of AHA did not significantly impair the properties of these proteins, and the histidine–AHA tag can facilitate protein purification, immobilization, and labeling.Topics: Bacteria; Cell and Molecular biology; Enzyme kinetics; Proteins;

ATP-dependent degradation plays a critical role in the quality control and recycling of proteins in cells. However, complete degradation of membrane proteins by ATP-dependent proteases in bacteria is not well-studied. We discovered that the degradation of a multidomain and multispan integral membrane protein AcrB could be facilitated by the introduction of a ssrA-tag at the C-terminus of the protein sequence and demonstrated that the cytoplasmic unfoldase-protease complex ClpXP was involved in the degradation. This is the first report to our knowledge to reveal that the ClpXP complex is capable of degrading integral membrane proteins. The chaperone SspB also played a role in the degradation. Using purified proteins, we demonstrated that the addition of the ssrA-tag did not drastically affect the structure of AcrB, and the degradation of detergent solubilized AcrB by purified ClpXP could be observed in vitro.

A popular thermal-stability assay developed especially for the study of membrane proteins uses a thiol-specific probe, 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). The fluorescence emission of CPM surges when it forms a covalent bond with the side chain of a free Cys, which becomes more readily accessible upon protein thermal denaturation. Interestingly, the melting temperatures of membrane proteins determined using the CPM assay in literature are closely clustered in the temperature range 45–55 °C. A thorough understanding of the mechanism behind the observed signal change is critical for the accurate interpretation of the protein unfolding. Here we used two α-helical membrane proteins, AqpZ and AcrB, as model systems to investigate the nature of the fluorescence surge in the CPM assay. We found that the transition temperatures measured using circular-dichroism (CD) spectroscopy and the CPM assay were significantly different. To eliminate potential artifact that might arise from the presence of detergent, we monitored the unfolding of two soluble proteins. We found that, contrary to current understanding, the presence of a sulfhydryl group was not a prerequisite for the CPM thermal-stability assay. The observed fluorescence increase is probably caused by binding of the fluorophore to hydrophobic patches exposed upon protein unfolding.

The majority of membrane proteins function as oligomers. However, it remains largely unclear how the oligomer stability of protein complexes correlates with their function. Understanding the relationship between oligomer stability and activity is essential to protein research and to virtually all cellular processes that depend on the function of protein complexes. Proteins make lasting or transient interactions as they perform their functions. Obligate oligomeric proteins exist and function exclusively at a specific oligomeric state. Although oligomerization is clearly critical for such proteins to function, a direct correlation between oligomer affinity and biological activity has not yet been reported. Here, we used an obligate trimeric membrane transporter protein, AcrB, as a model to investigate the correlation between its relative trimer affinity and efflux activity. AcrB is a component of the major multidrug efflux system in Escherichia coli. We created six AcrB constructs with mutations at the transmembrane intersubunit interface, and we determined their activities using both a drug susceptibility assay and an ethidium bromide accumulation assay. The relative trimer affinities of these mutants in detergent micelles were obtained using blue native polyacrylamide gel electrophoresis. A correlation between the relative trimer affinity and substrate efflux activity was observed, in which a threshold trimer stability was required to maintain efflux activity. The trimer affinity of the wild-type protein was approximately 3 kcal/mol more stable than the threshold value. Once the threshold was reached, an additional increase of stability in the range observed had no observable effect on protein activity.

Multidrug efflux pumps play important roles in bacteria drug resistance. A major multidrug efflux system in Gram-negative bacteria is composed of the inner membrane transporter AcrB, outer membrane protein channel TolC, and membrane fusion protein AcrA. These three proteins form a large complex that spans both layers of cell membranes and the periplasmic space. AcrB exists and functions as a homotrimer. To identify residues at the trimer interface that play important roles in AcrB function, we conducted site directed mutagenesis and discovered a key residue, R780. Although R780K was partially functional, all other R780 mutants tested were completely nonfunctional. Replacement of R780 by other residues disrupted trimer association. However, a decrease of trimer stability was not the lone cause for the observed loss of activity, because the activity loss could not be restored by strengthening trimer interaction. Using both heat and chemical denaturation methods, we found that the mutation decreased protein stability. Finally, we identified a repressor mutation, M774K, through random mutagenesis. It restored the activity of AcrBR780A to a level close to that of the wild-type protein. To examine the mechanism of activity restoration, we monitored denaturation of AcrBR780A/M774K and found that the repressor mutation improved protein stability. These results suggest that R780 is critical for AcrB stability. When R780 was replaced by Ala, the protein retained the overall structure, still trimerized in the cell membrane, and interacted with AcrA. However, local structural rearrangement might have occurred and lead to the decrease of protein stability and loss of substrate efflux activity.

Biocompatible hydrogels have great potentials in biomedical and biotechnological applications. In the current study, we reported a new naturally occurring protein motif that formed a transparent hydrogel when heated to 90 °C at a concentration as low as 0.4 mg/mL. The protein motif is the C-terminal soluble domain of an Escherichia coli inner membrane protein YajC (YajC-CT). We investigated the conformational change and self-assembly of the protein that lead to the formation of hydrogels using multiple methods. Atomic force microscopy studies of dilute gel samples revealed the presence of β-sheet-rich fibrils that were 2 to 3 nm in height and micrometers in length, which appeared to originate from homogeneous particles. On the basis of these observations, we proposed a three-step pathway of YajC-CT gelation. Hydrogels formed at different pH contained slightly different fibril structures. To our knowledge, this is the smallest hydrogel-forming globular protein module that has been characterized in detail. It may be useful as a model system in the elucidation of the mechanisms of protein fibrillation and gelation processes.

Glycopeptide antibiotics are widely used in the treatment of infections caused by Gram-positive bacteria. They inhibit the biosynthesis of the bacterial cell wall through binding to the d-alanyl-d-alanine (d-Ala-d-Ala) terminal peptide of the peptidoglycan precursor. Taking advantage of this highly specific interaction, we developed a direct fluorescence polarization based method for the detection of glycopeptide antibiotics. Briefly, we labeled the acetylated tripeptide Ac-l-Lys-d-Ala-d-Ala-OH with a fluorophore to create a peptide probe. Using three glycopeptide antibiotics, vancomycin, teicoplanin, and telavancin, as model compounds, we demonstrated that the fluorescence polarization of the peptide probe increased upon binding to antibiotics in a concentration dependent manner. The dissociation constants (Kd) between the peptide probes and the antibiotics were consistent with those reported between free d-Ala-d-Ala and the antibiotics in the literature. The assay is highly reproducible and selective toward glycopeptide antibiotics. Its detection limit and work concentration range are 0.5 μM and 0.5−4 μM for vancomycin, 0.25 μM and 0.25−2 μM for teicoplanin, and 1 μM and 1−8 μM for telavancin. Furthermore, we compared our assay in parallel with a commercial fluorescence polarization immunoassay (FPIA) kit in detecting teicoplanin spiked in human blood samples. The accuracy and precision of the two methods are comparable. We expect our assay to be useful in both research and clinical laboratories.

Due to the complexity and diversity of protein structures, site-specific protein immobilization has always been challenging. On the contrary, DNA immobilization is straightforward with well established chemical methods. Single-strand DNA binding protein (SSB) binds tightly to single-stranded DNA (ssDNA). Herein, we investigated the feasibility of using SSB as a fusion tag to facilitate site-specific and reversible immobilization of target proteins. As a model system, we constructed a fusion protein by joining a superfolder green fluorescent protein (sfGFP) with SSB. The fluorescence emission and ssDNA binding affinity of the fusion protein were compared separately with those of the individual modules. Both modules fully retained their properties in the fusion construct. Next, we covalently attached ssDNA (dT37) to a supporting matrix through either amine or thiol functionalization. The attached ssDNA mediated reversible sfGFP-SSB immobilization. The immobilized protein could be released through changes of conditions including pH, concentration of divalent cations, and the presence of the complementary dA35 oligonucleotide.

While a rich collection of bacterium-like regulating proteins has been identified in the archaeal genome, few of them have been studied at the molecular level. In this study, we characterized the ligand and DNA binding properties of a putative regulator ST1710 from the archaeon Sulfolobus tokodaii. ST1710 is homologous to the multiple-antibiotic resistance repressor (MarR) family bacterial regulators. The protein consists of a ligand binding site, partially overlapping with a winged helix−turn−helix DNA binding site. We characterized the interactions between ST1710 and three ligands, salicylate, carbonyl cyanide m-chlorophenylhydrazone (CCCP), and ethidium, which bind to bacterial MarRs. The binding affinities of the ligands for ST1710 were comparable to their affinities for the bacterial MarRs. The ligand binding was temperature sensitive and caused conformational changes in ST1710. To investigate the effect of ligand binding on the interaction between ST1710 and DNA, we fluorescently labeled a 47mer dsDNA (ST1) containing a putative ST1710 recognition site and determined the dissociation constant between ST1 and ST1710 using the fluorescence polarization method. The binding affinity almost doubled from 10 °C (Kd = 618 ± 34 nM) to 30 °C (Kd = 334 ± 15 nM), and again from 30 to 50 °C (Kd = 189 ± 9 nM). This result suggests that under the natural living condition (80 °C) of S. tokodaii, the binding affinity might increase even further. The presence of CCCP and salicylate suppressed ST1710−ST1 interaction, indicating that ST1710 functioned as a repressor.

A putative dehalogenase, l-HADST, from the thermophile Sulfolobus tokodaii, was cloned and expressed in Escherichia coli. The recombinant enzyme catalyzes the stereospecific dehalogenation of l-2-haloacids with similar levels of activity as its homolog from mesophiles. l-HADST remains fully active after being incubated for 4 h at 70 °C and tolerates extreme pH conditions ranging from 4 to 10. Furthermore, it can be purified conveniently without the usage of any chromatography method. The high expression yield and easy purification procedure make the recombinant dehalogenase an excellent candidate for biotechnological applications.

Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg2+-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn2+-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn2+ at 2.1 Å resolution. The active site contains two catalytic Mn2+ binding sites, each half-occupied, reconciling the previously observed 1:1 Mn2+:enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295–298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme.

AcrB and its homologues are major players in the efflux of anti-microbials out of Gram-negative bacteria. The structural and functional unit of AcrB is a homo-trimer. The assembly process of obligate membrane protein oligomers, including AcrB, remains elusive. It is not clear if an individual subunit folds into a monomeric form first followed by association (three-stage pathway) or if association occurs simultaneously with subunit folding (two-stage pathway). To answer this question, we investigated the feasibility of creating a folded monomeric AcrB mutant. The existence of well-folded monomers in the cell membrane would be an evidence of a three-stage pathway. A monomeric AcrB mutant, AcrBΔloop, was created through the truncation of a protruding loop that appeared to contribute to the stability of an AcrB trimer. AcrBΔloop expressed at a level similar to that of wild-type AcrB. The secondary structure content and tertiary conformation of AcrBΔloop were very similar to those of wild-type AcrB. However, when expressed in an acrB-deficient strain, AcrBΔloop failed to complement its defect in drug efflux. Results from blue native polyacrylamide gel electrophoresis and chemical cross-linking experiments suggested that AcrBΔloop existed as a monomer. The expression of this monomeric mutant in a wild-type Escherichia coli strain did not have a significant dominant-negative effect, suggesting that the mutant could not effectively co-assemble with genomic AcrB. AcrBΔloop is the first monomeric mutant reported for the intrinsically trimeric AcrB. The structural characterization results of this mutant suggest that the oligomerization of AcrB occurs through a three-stage pathway involving folded monomers.Download high-res image (137KB)Download full-size image

The interaction between protein and DNA is usually regulated by a third species, an effector, which can be either a protein or a small molecule. Convenient methods capable of detecting protein–DNA interaction and its regulation are highly desirable research tools. In the current study, we developed a method to directly “visualize” the interaction between a protein–DNA pair and its effector through the coupling with gold nanoparticles (AuNPs). As a proof-of-concept experiment, we constructed a model system based on the interaction between the lac repressor (protein) and operator (DNA) and its interplay with the lac operon inducer isopropyl β-d-1-thiogalactopyranoside (IPTG, which inhibits the interaction between the lac repressor and operator). We coated AuNPs with the lac operator sequences and mixed them with the lac repressor. Because the lac repressor homotetramer contains two DNA binding modules, it bridged the particles and caused them to aggregate. We demonstrated that the assembly of DNA-modified AuNPs correlated with the presence of the corresponding protein and effector in a concentration-dependent manner. This AuNP-based platform has the potential to be generalized in the creation of reporter and detection systems for other interacting protein–DNA pairs and their effectors.

Many membrane proteins exist and function as oligomers, but how monomers oligomerize in the cell membrane remains poorly understood. AcrB is an obligate homo-trimer. We previously found that the folding of individual subunit precedes oligomerization. Following folding, individual AcrB subunits must locate and interact with each other in order to dimerize and eventually trimerize. It has been unclear if AcrB trimerization is a spontaneous process following the “chance encounter and random assembling” mechanism. In other words, it is currently unknown whether monomeric subunits diffuse freely to “search” for each other after they are co-translationally inserted and folded into the cell membrane. Using four sets of experiments exploiting AcrB variants with different fusion tags, disulfide trapping, and activity measurement, here we showed that AcrB variants co-expressed in the same Escherichia coli cell did co-assemble into hybrid trimers in vivo. However, the level of co-assembly measured experimentally was not consistent with calculations derived from random assembling. The potential role of the polysome structure during protein translation and the resultant clustering effect were discussed as a potential explanation for the observed bias in AcrB subunit assembling in vivo. Our results provide new insights into the dynamic assembling and equilibration process of obligate homo-oligomeric membrane proteins in the cell membrane.Download high-res image (372KB)Download full-size imageHighlights► How monomers oligomerize in the cell membrane is poorly understood. ► AcrB trimerization involves well-folded monomers. ► AcrB trimerization is not entirely random. When co-expressed, subunits from different gene sources co-assemble. ► When co-expressed, subunits from the same gene source assemble preferentially.