Polarized ATR-FTIR Spectroscopy of the Membrane-Embedded Domains of the Particulate Methane Monooxygenase

Dissemination of antibiotic resistance genes is regulated by iron oxides: Insight into the influence on bacterial transformation

The transportation of antibiotic resistance genes (ARGs) in manure-soil-plant continuums poses risks to human health. Horizontal gene transfer, particularly for bacterial transformation, is an important way for ARG dissemination. As crucial components in soils, iron oxides impacted the fates of various abiotic and biotic contaminants due to their active properties. However, whether they can influence the transformation of ARGs is unknown, which waits to be figured out to boost the assessment and control of ARG spread risks. In this study, we have investigated the effects of goethite, hematite, and magnetite (0-250 mg/L, with sizes < 100 nm and > 100 nm) on the transfer of ampicillin resistance genes to Escherichia coli cells. At lower iron oxide concentrations, the transformation of ARGs was first facilitated (transformation frequency reached up to 3.38-fold higher), but the facilitating effects gradually weakened and eventually disappeared as concentrations further increased. Particle size and iron oxide type were not the universal determinants controlling the transformation. At lower concentrations, iron oxides interacted with proteins and phospholipids in E. coli envelope structures, and induced the overgeneration of intracellular reactive oxygen species. Consequently, they led to pore formation and permeability enhancement on the cell membrane, thus promoting the transformation. The facilitation was also associated with the carrier-like effect of iron oxides for antibiotic resistance plasmids. At higher concentrations, the weakened facilitations were attributed to the aggregation of iron oxides. In this study, we highlight the crucial roles of the concentrations (contents) of iron oxides on the dissemination of ARGs in soils; this study may serve as a reference for ARG pollution control in future agricultural production.

Influence of tryptic hydrolysis on the enzymatic function of the membrane-bound form of particulate methane monooxygenase from Methylosinus trichosporium OB3b

Particulate methane monooxygenase (pMMO) is a membrane protein embedded in the intracytoplasmic membrane of methane-oxidizing bacteria. Structural analysis of pMMO showed the existence of a hydrophilic region exposed outside of the bacterial membrane. To obtain information regarding the role of this hydrophilic region in the enzymatic function of pMMO, trypsin proteolysis of the membrane-bound form of pMMO from Methylosinus trichosporium OB3b was performed at 4 °C. The polypeptides produced by this hydrolysis were analyzed by polyacrylamide gel electrophoresis and MALDI-TOF/TOF. Furthermore, the influence of this tryptic digestion on the methane hydroxylation and propene epoxidation enzymatic activities of pMMO was investigated. Among the three subunits of pMMO, PmoB and PmoC were hydrolyzed by trypsin, but PmoA was not. With 10 mg L^-1 trypsin, both terminal regions or the C-terminal region of PmoC polypeptide was selectively hydrolyzed. Furthermore, the stability of pMMO was decreased by this digestion. These results indicate that PmoC plays a role in maintaining the stability of pMMO in vitro. On the other hand, the digestion of PmoB with 100 mg L^-1 trypsin produced several polypeptides, indicating that trypsin digestion occurs at several sites of the hydrophilic region of PmoB. Hydrolysis led to a decrease in pMMO activity towards methane hydroxylation and propene epoxidation. These results indicate that the hydrophilic region of PmoB is critically important for the enzymatic function of pMMO, which is consistent with the models of the functional mechanism of pMMO proposed so far.

Proton detection for signal enhancement in solid-state NMR experiments on mobile species in membrane proteins

Direct proton detection is becoming an increasingly popular method for enhancing sensitivity in solid-state nuclear magnetic resonance spectroscopy. Generally, these experiments require extensive deuteration of the protein, fast magic angle spinning (MAS), or a combination of both. Here, we implement direct proton detection to selectively observe the mobile entities in fully-protonated membrane proteins at moderate MAS frequencies. We demonstrate this method on two proteins that exhibit different motional regimes. Myelin basic protein is an intrinsically-disordered, peripherally membrane-associated protein that is highly flexible, whereas Anabaena sensory rhodopsin is composed of seven rigid transmembrane α-helices connected by mobile loop regions. In both cases, we observe narrow proton linewidths and, on average, a 10× increase in sensitivity in 2D insensitive nuclear enhancement of polarization transfer-based HSQC experiments when proton detection is compared to carbon detection. We further show that our proton-detected experiments can be easily extended to three dimensions and used to build complete amino acid systems, including sidechain protons, and obtain inter-residue correlations. Additionally, we detect signals which do not correspond to amino acids, but rather to lipids and/or carbohydrates which interact strongly with membrane proteins.

Characterization of a membrane-active peptide from the Bordetella pertussis CyaA toxin

Bordetella pertussis, the pathogenic bacteria responsible for whooping cough, secretes several virulence factors, among which is the adenylate cyclase toxin (CyaA) that plays a crucial role in the early stages of human respiratory tract colonization. CyaA invades target cells by translocating its catalytic domain directly across the plasma membrane and overproduces cAMP, leading to cell death. The molecular process leading to the translocation of the catalytic domain remains largely unknown. We have previously shown that the catalytic domain per se, AC384, encompassing residues 1-384 of CyaA, did not interact with lipid bilayer, whereas a longer polypeptide, AC489, spanning residues 1-489, binds to membranes and permeabilizes vesicles. Moreover, deletion of residues 375-485 within CyaA abrogated the translocation of the catalytic domain into target cells. Here, we further identified within this region a peptidic segment that exhibits membrane interaction properties. A synthetic peptide, P454, corresponding to this sequence (residues 454-485 of CyaA) was characterized by various biophysical approaches. We found that P454 (i) binds to membranes containing anionic lipids, (ii) adopts an α-helical structure oriented in plane with respect to the lipid bilayer, and (iii) permeabilizes vesicles. We propose that the region encompassing the helix 454-485 of CyaA may insert into target cell membrane and induce a local destabilization of the lipid bilayer, thus favoring the translocation of the catalytic domain across the plasma membrane.

Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy

Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques.

Molecular interactions of proteins and peptides at interfaces studied by sum frequency generation vibrational spectroscopy

Interfacial peptides and proteins are critical in many biological processes and thus are of interest to various research fields. To study these processes, surface sensitive techniques are required to completely describe different interfacial interactions intrinsic to many complicated processes. Sum frequency generation (SFG) spectroscopy has been developed into a powerful tool to investigate these interactions and mechanisms of a variety of interfacial peptides and proteins. It has been shown that SFG has intrinsic surface sensitivity and the ability to acquire conformation, orientation, and ordering information about these systems. This paper reviews recent studies on peptide/protein-substrate interactions, peptide/protein-membrane interactions, and protein complexes at interfaces and demonstrates the ability of SFG on unveiling the molecular pictures of complicated interfacial biological processes.

Proton-detected solid-state NMR reveals intramembrane polar networks in a seven-helical transmembrane protein proteorhodopsin

We used high-resolution proton-detected multidimensional NMR to study the solvent-exposed parts of a seven-helical integral membrane proton pump, proteorhodopsin (PR). PR samples were prepared by growing the apoprotein on fully deuterated medium and reintroducing protons to solvent-accessible sites through exchange with protonated buffer. This preparation leads to NMR spectra with proton resolution down to ca. 0.2 ppm at fast spinning (28 kHz) in a protein back-exchanged at a level of 40%. Novel three-dimensional proton-detected chemical shift correlation spectroscopy allowed for the identification and resonance assignment of the solvent-exposed parts of the protein. Most of the observed residues are located at the membrane interface, but there are notable exceptions, particularly in helix G, where most of the residues are susceptible to H/D exchange. This helix contains Schiff base-forming Lys231, and many conserved polar residues in the extracellular half, such as Asn220, Tyr223, Asn224, Asp227, and Asn230. We proposed earlier that high mobility of the F-G loop may transiently expose a hydrophilic cavity in the extracellular half of the protein, similar to the one found in xanthorhodopsin. Solvent accessibility of helix G is in line with this hypothesis, implying that such a cavity may be a part of the proton-conducting pathway lined by this helix.

Investigating the surface properties of Escherichia coli under glucose controlled conditions and its effect on aggregation

Bacteria exist as aggregates or in biofilms to help with adaptation and protection from environmental stresses. The hypothesis that is tested in this paper is that the relative presence of glucose in the media, at the beginning of the growth phase, influences the surface chemistry of the cell, which as a consequence reduces the tendency for the cells to interact and form aggregates. In this study, we used Escherichia coli (E. coli) MG1655 as a model organism and measured the change in the surface chemistry of cells harvested at different growth phases, which had been cultured in Luria-Bertani media with and without the addition of glucose, using potentiometric titration and infrared spectroscopy. Cells, cultivated with the additional supplement of glucose at the beginning of the growth phase, displayed a higher concentration of bacterial surface functional groups and a variation in outer membrane proteins. As a consequence, the tendency for cell-to-cell attachment was significantly reduced. Our findings therefore revealed that glucose limits aggregation in E. coli MG1655 by altering the concentration of functional groups from macromolecules present on the bacterial surface.

Sensitivity and resolution in proton solid-state NMR at intermediate deuteration levels: quantitative linewidth characterization and applications to correlation spectroscopy

We present a systematic study of proton linewidths in rigid solids as a function of sample spinning frequency and proton density, with the latter controlled by the ratio of protonated and perdeuterated model compounds. We find that the linewidth correlates more closely with the overall proton density (rho(H)) than the size of local clusters of (1)H spins. At relatively high magic-angle spinning (MAS) rates, the linewidth depends linearly upon the inverse MAS rate. In the limit of infinite spinning rate and/or zero proton concentration, the linewidth extrapolates to a non-zero value, owing to contributions from scalar couplings, chemical shift dispersion, and B(0) field inhomogeneity. The slope of this line depends on the overall concentration of unexchangeable protons in the sample and the spinning rate. At up to 30% protonation levels ( approximately 2 (1)H/100A(3)), proton detection experiments are demonstrated to have a substantial (2- to 3-fold) sensitivity gain over corresponding (13)C-detected experiments. Within this range, the absolute sensitivity increases with protonation level; the optimal compromise between sensitivity and resolution is in the range of 20-30% protonation. We illustrate the use of dilute protons for polarization transfer to and from low-gamma spins within 5A, and to be utilized as both magnetization source and detection spins. The intermediate protonation regime enhances relaxation properties, which we expect will enable new types of (1)H correlation pulse sequences to be implemented with improved resolution and sensitivity.

The quest for the particulate methane monooxygenase active site

Particulate methane monooxygenase is a copper-containing, membrane-bound metalloenzyme that converts methane to methanol in Nature. How pMMO accomplishes this difficult reaction under ambient conditions is one of the major unsolved problems in bioinorganic chemistry. Despite considerable research efforts in the past 20 years, the active site of the enzyme remains unknown. We recently solved the first crystal structure of pMMO to 2.8 è resolution, revealing the overall structure, oligomerization state, subunit ratio, and composition and location of the metal centers. Almost none of the key structural features were predicted. In this Perspective, we review the state of knowledge before and after the structure determination, emphasizing elucidation of the pMMO active site.