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Early in the SARS-CoV-2 pandemic, convalescent plasma (CP) therapy was proposed as a treatment for severely ill patients. We conducted a CP treatment protocol under the Mayo Clinic Extended Access Program at University Hospital Brooklyn (UHB). Potential donors were screened with a lateral flow assay (LFA) for IgM and IgG antibodies against the SARS-CoV-2 S1 receptor-binding domain (RBD). Volunteers that were LFA positive were tested with an ELISA to measure IgG titers against the RBD. Subjects with titers of at least 1:1024 were selected to donate. Most donors with positive LFA had acceptable titers and were eligible to donate. Out of 171 volunteers, only 65 tested positive in the LFA (38.0%), and 55 (32.2%) had titers of at least 1:1024. Before our donation program started, 31 CP units were procured from the New York Blood Center (NYBC). Among the 31 CP units that were obtained from the NYBC, 25 units (80.6%) were positive in the LFA but only 12 units (38.7%) had titers of at least 1:1024. CP was administered to 28 hospitalized COVID-19 patients. Patients who received low titer CP, high titer CP and patients who did not receive CP were followed for 45 days after presentation. Severe adverse events were not associated with CP transfusion. Death was a less frequent outcome for patients that received high titer CP (>1:1024) 38.6% mortality, than patients that received low titer CP (≤1:1024) 77.8% mortality.

The reliability of single antigen bead (SAB) assays and their use in predicting a negative cell based cross match (CBXM) is essential in the era of expanded organ sharing. A wide range of accuracy (80-95%) in predicting negative CBXM has been reported. We hypothesized that in SAB assays an antibody against an HLA eplet that was common among a number of different HLA alleles would be distributed among all of the shared eplet positive SABs. This would reduce binding to the donor specific SAB resulting in an under-estimate of antibody strength. We tested this proposal in adsorption studies using, instead of lymphocytes, a novel reagent, single-SAB (sSAB). Properties of SAB assays were examined that provided a basis for conducting adsorption - elution experiments with the sSABs. We found that incubation of sera with sA*02:01 or sB*42:01 not only depleted reactivity to these alleles but also depleted reactivity to beads that shared the reactive eplet. Anti-eplet strength from SAB data (sum of the MFI of eplet positive SABs (MFI-s) was compared with CBXM out comes in two case studies and with 99 proficiency testing sera. In these validation studies, an MFI-s above 11,000 was associated with a positive FCXM. This approach was placed into clinical practice for listing unacceptable antigens that shared a common eplet. CDCXMs (n = 3261) and FCXMs (n = 1012) were performed on patients listed in UNOS for deceased donor kidneys. All CDCXMs were negative and all FCXMs except one were negative. We conclude that summation of eplet strength provides a highly reliable method of predicting prospective negative CBXMs resulting in substantial savings of time and effort. Based on shared eplet summation data, CMS/NYSDOH has accepted our bead based XM (BBXM) method (aka, virtual XM) performed prior to transplant as fulfilling the regulation that XM results be available before kidney transplantation.

Native lipids in cell-membrane support crucial functions like intercell communication via their ability to deform into curved membrane structures. Cell membrane mimicking Giant unilamellar vesicles (GUV) is imperative in understanding native lipid's role in membrane transformation however remains challenging to assemble. We construct two giant vesicle models mimicking bacterial inner-membrane (IM) and outer-membrane (OM) under physiological conditions using single-step gel-assisted lipid swelling. IM vesicles composed of native bacterial lipids undergo small-scale membrane remodeling into bud and short-nanotube structures. In contrast, OM vesicles asymmetrically assembled from Lipopolysaccharide (LPS) and bacterial lipids underwent global membrane deformation under controlled osmotic stress. Remarkably, highly-curved structures mimicking cell-membrane architectures, including daughter vesicle networks interconnected by necks and nano-tubes ranging from micro to nanoscale, are generated in OM vesicles at osmotic stress comparable to that applied in IM vesicles. Further, we provide a quantitative description of the membrane structures by experimentally determining membrane elastic parameters, i.e., neck curvature and bending rigidity. We can conclude that a larger spontaneous curvature estimated from the neck curvature and softer membranes in OM vesicles is responsible for large-scale deformation compared to IM vesicles. Our findings will help comprehend the shape dynamics of complex native bacterial lipid membranes.

Controlled design of giant unilamellar vesicles under defined conditions has vast applications in the field of membrane and synthetic biology. Here, we bio-engineer bacterial-membrane mimicking models of controlled size under defined salt conditions over a range of pH. A complex bacterial lipid extract is used for construction of physiologically relevant Gram-negative membrane mimicking vesicles whereas a ternary mixture of charged lipids (DOPG, cardiolipin and lysyl-PG) is used for building Gram-positive bacterial-membrane vesicles. Furthermore, we construct stable multi-compartment biomimicking vesicles using the gel-assisted swelling method. Importantly, we validate the bio-application of the bacterial vesicle models by quantifying diffusion of chemically synthetic amphoteric antibiotics. The transport rate is pH-responsive and depends on the lipid composition, based on which a permeation model is proposed. The permeability properties of antimicrobial peptides reveal pH dependent pore-forming activity in the model vesicles. Finally, we demonstrate the functionality of the vesicles by quantifying the uptake of membrane-impermeable molecules facilitated by embedded pore-forming proteins. We suggest that the bacterial vesicle models developed here can be used to understand fundamental biological processes like the peptide assembly mechanism or bacterial cell division and will have a multitude of applications in the bottom-up assembly of a protocell., Giant vesicle functional models mimicking a bacterial membrane under physiological conditions are constructed.

The pore-forming structures of an anionic human antimicrobial peptide dermcidin (DCD) in a membrane environment has not been demonstrated previously. Using single-channel electrical recordings, we characterized the structural and functional properties of the DCD peptide channel in lipid membranes. We show that a 48-residue, 8 nm long anionic DCD-1L peptide is folded in the right conformation in sodium dodecyl sulfate (SDS) that spontaneously inserts into lipid bilayers to form well-defined channels. However, the DCD-1L peptides are not properly folded in n-dodecyl-β-d-maltoside (DDM), resulting in unstable channels suggesting the significance of specific detergent in stable channel formation. Furthermore, a 25-residue cationic DCD SSL-25 peptide formed channels both in SDS and DDM micelles as the length of the peptide matches with the thickness of the membrane. Finally, we quantified the permeation of small molecules through the DCD channels in liposome assays. Accordingly, we propose a molecular model demonstrating the structural self-assembly of the DCD channels in the membrane. We suggest that an understanding of the mechanism of action of DCD peptides at single-channel resolution will lead to developing peptide-based therapeutics.

The outer cell wall of the Gram-negative bacteria is a crucial barrier for antibiotics to reach their target. Here, we show that the chemical stability of the widely used antibiotic ampicillin is a major factor in the permeation across OmpF to reach the target in the periplasm. Using planar lipid bilayers we investigated the interactions and permeation of OmpF with ampicillin, its basic pH–induced primary degradation product (penicilloic acid), and the chemically more stable benzylpenicillin. We found that the solute-induced ion current fluctuation is 10 times higher with penicilloic acid than with ampicillin. Furthermore, we also found that ampicillin can easily permeate through OmpF, at an ampicillin gradient of 10 μm and a conductance of G(amp) ≅ 3.8 fS, with a flux rate of roughly 237 molecules/s of ampicillin at V(m) = 10 mV. The structurally related benzylpenicillin yields a lower conductance of G(amp) ≅ 2 fS, corresponding to a flux rate of ≈120 molecules/s. In contrast, the similar sized penicilloic acid was nearly unable to permeate through OmpF. MD calculations show that, besides their charge difference, the main differences between ampicillin and penicilloic acid are the shape of the molecules, and the strength and direction of the dipole vector. Our results show that OmpF can impose selective permeation on similar sized molecules based on their structure and their dipolar properties.

Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A–F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.

Integral membrane proteins known as porins are the major pathway by which hydrophilic antibiotics cross the outer membrane of Gram-negative bacteria. Single point mutations in porins can decrease the permeability of an antibiotic, either by reduction of channel size or modification of electrostatics in the channel, and thereby confer clinical resistance. Here, we investigate four mutant OmpC proteins from four different clinical isolates of Escherichia coli obtained sequentially from a single patient during a course of antimicrobial chemotherapy. OmpC porin from the first isolate (OmpC20) undergoes three consecutive and additive substitutions giving rise to OmpC26, OmpC28, and finally OmpC33. The permeability of two zwitterionic carbapenems, imipenem and meropenem, measured using liposome permeation assays and single channel electrophysiology differs significantly between OmpC20 and OmpC33. Molecular dynamic simulations show that the antibiotics must pass through the constriction zone of porins with a specific orientation, where the antibiotic dipole is aligned along the electric field inside the porin. We identify that changes in the vector of the electric field in the mutated porin, OmpC33, create an additional barrier by "trapping" the antibiotic in an unfavorable orientation in the constriction zone that suffers steric hindrance for the reorientation needed for its onward translocation. Identification and understanding the underlying molecular details of such a barrier to translocation will aid in the design of new antibiotics with improved permeation properties in Gram-negative bacteria.

In general, the method of choice to characterize the conductance properties of channel-forming bacterial porins is electrophysiology. Here, the classical method is to reconstitute single porins into planar lipid bilayers to derive functional information from the observed channel conductance. In addition to an estimated pore size, ion selectivity or transport properties in general are of importance. For the latter, measuring the ion current fluctuation can provide some information about the mode of transport of charged molecules penetrating the proteins. For instance, increasing the external voltage modifies the residence time in the channel: charged molecules with the ability to permeate through channels will travel faster whereas non-permeating molecules get pushed to the constriction zone with enhanced residence time. Here, we are interested in the ability of antibiotics to permeate channels and compare different techniques to reveal fast events.

Transport of molecules through biological membranes is a fundamental process in biology, facilitated by selective channels and general pores. The architecture of some outer membrane pores in Gram-negative bacteria, common to other eukaryotic pores, suggests them as prototypes of electrostatically regulated nanosieve devices. In this study, we sensed the internal electrostatics of the two most abundant outer membrane channels of Escherichia coli, using norfloxacin as a dipolar probe in single molecule electrophysiology. The voltage dependence of the association rate constant of norfloxacin interacting with these nanochannels follows an exponential trend, unexpected for neutral molecules. We combined electrophysiology, channel mutagenesis, and enhanced sampling molecular dynamics simulations to explain this molecular mechanism. Voltage and temperature dependent ion current measurements allowed us to quantify the transversal electric field inside the channel as well as the distance where the applied potential drops. Finally, we proposed a general model for transport of polar molecules through these electrostatic nanosieves. Our model helps to further understand the basis for permeability in Gram-negative pathogens, contributing to fill in the innovation gap that has limited the discovery of effective antibiotics in the last 20 years.

Multi-drug resistant (MDR) bacteria are an increasingly serious threat to global public health. In the last decades, many studies showed that general outer membrane porins (OMPs) from Gram-negative bacteria represent the major route for antibiotics to translocate through the outer membrane.To explore the molecular rules for efficient drug transport and therefore cell killing, molecule-protein interaction is analyzed at single molecule level via electrophysiology. We incorporated OMPs into planar bilayer and single-channel currents were measured by an automated planar lipid bilayer station (Orbit 16, Nanion). The role of OMPs in the molecule-protein interactions can be characterized by the interaction kinetics. Here, we show by using 11 clinical relevant antibiotics and Omp35, Omp36 porins from Enterobacter aerogenes, that Omp35 has generally higher antibiotic-porin interaction than Omp36. Interestingly, E. aerogenes preferentially expresses Omp36 in human hosts. These in vitro results also correlate well with in vivo data collected from bacterial viability assays.On the other side, we studied the effect of magnesium on the antibiotic-porin interactions in order to approach physiological conditions. Since fluoroquinolones antibiotics have relatively heavy dipole, they can be used as probes to detect the electrostatic properties at the constriction zone of the porin channels. We found that the addition of magnesium strengthened the interaction between norfloxacin antibiotics and Omp36. The results indicate that the electrostatic properties of the constriction zone are altered and show a more efficient route to transport the norfloxacin.In conclusion, the porin properties can be better understood when considering the host environment. Improved understanding of antibiotic-porin interaction kinetics and the correlated antibiotic translocation based cell killing would facilitate the understanding on porin specificity thus the design of new antibiotics that can more efficiently reach high intracellular concentration.

The role of major porin OmpPst1 of Providencia stuartii in antibiotic susceptibility for two carbapenems is investigated by combining high-resolution conductance measurements, liposome swelling, and microbiological assays. Reconstitution of a single OmpPst1 into a planar lipid bilayer and measuring the ion current, in the presence of imipenem, revealed a concentration-dependent decrease in conductance, whereas meropenem produced well-resolved short ion current blockages. Liposome swelling assays suggested a small flux of imipenem in contrast to a rapid permeation of meropenem. The lower antibiotic susceptibility of P. stuartii to imipenem compared to meropenem correlated well with the decreased level of permeation of the former through the OmpPst1 channel.

Decreased drug accumulation is a common cause of antibiotic resistance in microorganisms. However, there are few reliable general techniques capable of quantifying drug uptake through bacterial membranes. We present a semiquantitative optofluidic assay for studying the uptake of autofluorescent drug molecules in single liposomes. We studied the effect of the Escherichia coli outer membrane channel OmpF on the accumulation of the fluoroquinolone antibiotic, norfloxacin, in proteoliposomes. Measurements were performed at pH 5 and pH 7, corresponding to two different charge states of norfloxacin that bacteria are likely to encounter in the human gastrointestinal tract. At both pH values, the porins significantly enhance drug permeation across the proteoliposome membranes. At pH 5, where norfloxacin permeability across pure phospholipid membranes is low, the porins increase drug permeability by 50-fold on average. We estimate a flux of about 10 norfloxacin molecules per second per OmpF trimer in the presence of a 1 mM concentration gradient of norfloxacin. We also performed single channel electrophysiology measurements and found that the application of transmembrane voltages causes an electric field driven uptake in addition to concentration driven diffusion. We use our results to propose a physical mechanism for the pH mediated change in bacterial susceptibility to fluoroquinolone antibiotics.

Bacterial porins are water-filled β-barrel channels that allow translocation of solutes across the outer membrane. They feature a constriction zone, contributed by the plunging of extracellular loop 3 (L3) into the channel lumen. Porins are generally in the open state, but undergo gating in response to external voltages. To date the underlying mechanism is unclear. Here we report results from molecular dynamics simulations on the two porins of Providenica stuartii, Omp-Pst1 and Omp-Pst2, which display distinct voltage sensitivities. Voltage gating was observed in Omp-Pst2, where the binding of cations in-between L3 and the barrel wall results in exposing a conserved aromatic residue in the channel lumen, thereby halting ion permeation. Comparison of Omp-Pst1 and Omp-Pst2 structures and trajectories suggests that their sensitivity to voltage is encoded in the hydrogen-bonding network anchoring L3 onto the barrel wall, as we observed that it is the strength of this network that governs the probability of cations binding behind L3. That Omp-Pst2 gating is observed only when ions flow against the electrostatic potential gradient of the channel furthermore suggests a possible role for this porin in the regulation of charge distribution across the outer membrane and bacterial homeostasis., Author Summary Porins are the main conduits for hydrophilic nutrients and ions uptake into the periplasm of Gram-negative bacteria. Their translocation permeability is determined by the amino-acid distribution on their extracellular loop L3. Bacterial porin channels have long been known to undergo step-wise gating, under the application of a transmembrane potential. Yet the exact molecular mechanism by which gating is achieved and the exact relevance of this evolved characteristic remain elusive. In the present study, we report on electrophysiology experiments and molecular dynamics simulations on the two general-diffusion porins of Providencia stuartii, Omp-Pst1 and Omp-Pst2. Our results show that gating in Omp-Pst2 occurs as the result of L3 displacement, which follows from the binding of cations in acidic niches between L3 and the barrel wall and effects in exposing the side chain of a highly conserved aromatic residue at the tip of L3 in the channel lumen. That Omp-Pst2 displays asymmetric voltage sensitivity and that the likelihood of gating is increased when cations transit from the extracellular to the intracellular side suggests voltage-gating underlies a regulatory role in bacterial homeostasis. Rational antibiotic-design strategies based on the maximization of antibiotic penetration and accumulation at their target sites, should take this role into account.

For an antibiotic to be effective, it needs to cross the outer membrane barrier and reach the target inside the cell. Hydrophilic antibiotics, e.g. β-lactams, use porin channels to cross the outer membrane and accumulate in the periplasm. Experimental determination of antibiotic interactions with porin is performed by using electrophysiology on a single channel level by noise analysis or single event analysis methods. We report a novel framework for analyzing the ion-current noise, taking into account the corrections due to the analogous filter and the sampling procedure, with the goal of extending the time resolution to a range previously inaccessible by event analysis or by conventional noise analysis. The new method allows one to analyse fast binding events and/or the case when the single channel is not completely blocked by the substrate. We demonstrate the power of this approach by using as an example the interactions of meropenem, an antibiotic of the carbapenem family, with the OmpF porin that is considered to be one of the main pathways for antibiotics to enter Escherichia coli. The presence of meropenem in OmpF is detected by ion current blockages, and the on and off rates are estimated from the concentration dependence of the average ion current and of its power spectral density. The obtained average residence time of the antibiotic inside the channel is in the range of a few microseconds, i.e. more than 50 times smaller than the inverse cut-off frequency of the analogous filter.

The role of the outer-membrane channel from a mycolic acid containing Gram-positive bacteria Nocardia farcinica, which forms a hydrophilic pathway across the cell wall, was characterized. Single channel electrophysiology measurements and liposome swelling assays revealed the permeation of hydrophilic solutes including sugars, amino acids and antibiotics. The cation selective N. farcinica channel exhibited strong interaction with the positively charged antibiotics; amikacin and kanamycin, and surprisingly also with the negatively charged ertapenem. Voltage dependent kinetics of amikacin and kanamycin interactions were studied to distinguish binding from translocation. Moreover, the importance of charged residues inside the channel was investigated using mutational studies that revealed rate limiting interactions during the permeation.

Penetration through the outer cell wall is the first step for an antibiotic to reach the target site inside the bacteria. In this study, the role of major porin- OmpPst1 of Providencia stuartii is investigated in its susceptibility for two carbapenem antibiotics imipenem and meropenem. Electrophysiology measurements revealed kinetic parameters of antibiotic binding to the channel. Activity of antibiotics against bacterium determined by microbiological assays correlates with the results obtained from liposome swelling assay and planar lipid bilayer measurements. In addition, the effect of divalent and trivalent cations on antibiotic affinity to the channel is investigated. To follow the exact translocation pathway, molecular modeling provides atomistic details on the interaction of specific side chains of the two antibiotics with the channel residues and the position of affinity sites. Further, mutation of these specific sites in the channel and recording ion current fluctuation in presence of antibiotics reveal the rate limiting interaction for its translocation. Here, we have concluded on the relation between permeation of the antibiotics and resistance acquired by Providencia stuartii. Moreover, employing a multidisciplinary approach from MD simulations to protein engineering helps to get a molecular picture. This information further might give insights for rational drug design, for effective uptake of antibiotics through porins- check point of the cell.References:1. Bajaj H, et al. (2012) Biochemistry, 51, 10244-9.2. Tran QT, et al. (2010) J Biol Chem, 285, 32273-81.

The emergence and dissemination of coordinated resistance mechanism (MDR) underline the importance to understand the rate limiting steps in antibiotic action. Here OmpF porin from E. coli is used as an example to demonstrate what limits the penetration of carbapenems. Bacteriological kinetic killing assays, temperature dependent ion conductance measurements, and all-atom computer simulations were combined to study interaction and translocation of clinically relevant β-lactam antibiotics through wild type OmpF and two mutants D113A and D121A, where the key residues at the constriction region have been substituted. Expression of these various OmpF mutants in an otherwise porin-null bacterial strain revealed an increase of bacterial susceptibility for the mutants. High-resolution conductance measurements and modulating the temperature indicates lower energy barriers for mutant porin correlating with the microbiological assays. All atom modeling provided a most probable pathway able to identify the relevant side-chain interactions. This combined approach allows identifying rate limiting interaction and suggests possible modification to enhance antibiotic penetration.References:1. Hajjar E, et al. Bridging timescales and length scales: from macroscopic flux to molecular mechanism of antibiotic diffusion through porins. Biophys J. 2010, 98, 569-75.2. Singh PR, et al. Antibiotic permeation across the OmpF channel: modulation of the affinity site in the presence of magnesium. J Phys Chem B. 2012, 116, 4433-8.

The outer membrane of Gram-negative bacteria such as Escherichia coli acts as a selective permeable barrier between cell and external environment. Water filled outer membrane proteins called as porins were identified for exchange of hydrophilic solutes and hydrophilic antibiotics. One of the most abundant outer membrane porins in E. coli is OmpC and many studies revealed that down-regulation or mutation of this porin shows reduced accumulation of antibacterials in bacterial cells [1]. Fluoroquinolones, used since 1980, are the most common treatment for urinary tract infection caused by E. coli and today this treatment is ineffective in more than half of the patients globally due to widespread resistance. So far the influx kinetics of fluoroquinolones with OmpC has been characterized on free standing lipid bilayers formed on a glass substrate [2]. In particular, detailed analysis of antibiotic interaction with a single OmpC channel using electrophysiology can provide a kinetic description. Here we have investigated two fluoroquinolones, Ciprofloxacin and Enrofloxacin, using an advanced molecular dynamics technique, i.e., metadynamics [3,4]. These free energy calculations help to identify the most favorable paths and activation energies required for molecules to translocate through the OmpC channel. Furthermore, we have also investigated the translocation of the same molecules in the presence of different salts to understand the altered translocation kinetics [5]. Moreover, the identification of favorable interactions networks is important to determine the most prominent residues required for translocation.[1] H. Lou et al., PloS one 6, e25825 (2011).[2] K. R. Mahendran et al., J. Biomol. Screen. 15, 302 (2010).[3] A. Kumar et al., J. Phys.: Condens. Matter 22, 454125 (2010).[4] T. Mach et al., J. Am. Chem. Soc. 130, 13301 (2008).[5] S. Kojima et al., J. Biol. Chem. 289, 26464 (2014).