Why do the outer membrane proteins OmpF from E. coli and OprP from P. aeruginosa prefer trimers? Simulation studies

Distribution of AC Electric Field-Induced Transmembrane Voltage in Escherichia coli Cell Wall Layers

On the basis of Gram-negative bacterium Escherichia coli models previously published in the literature, the transmembrane voltage induced by the application of an alternating current (AC) electric field on a bacterial suspension is calculated using COMSOL Multiphysics software, in the range 1-20 MHz, for longitudinal and transverse field orientations. The voltages developed on each of the three layers of the cell wall are then calculated using an electrical equivalent circuit. This study shows that the overall voltage on the cell wall, whose order of magnitude is a few tens of µV, is mainly distributed on inner and outer layers, while a near-zero voltage is found on the periplasm, due to its much higher electrical conductivity compared with the other layers. Although the outer membrane electrical conductivity taken in the model is a thousand times higher than that of the inner membrane, the voltage there is about half of that on the inner membrane, due to capacitive effects. It follows that the expression of protein complexes anchored in the inner membrane could potentially be disrupted, inducing in particular a possible perturbation of biological processes related to cellular respiration and proton cycle, and leading to growth inhibition as a consequence. Protein complexes anchored in the outer membrane or constituting a bridge between the three layers of the cell wall, such as some porins, may also undergo the same action, which would add another growth inhibition factor, as a result of deficiency in porin filtration function when the external environment contains biocides. Bioelectromagnetics. 2020;41:279-288 © 2020 Bioelectromagnetics Society.

Exploring the binding modes of cordycepin to human adenosine deaminase 1 (ADA1) compared to adenosine and 2'-deoxyadenosine

Cordycepin (3'-deoxyadenosine, abbreviated as COR) from Cordyceps shows a wide range of pharmacological activities, including antioxidant and anticancer effects, therefore representing a potential alternative medicine. However, COR has a short half-life in the human body, where it is metabolized by adenosine deaminase 1 (ADA1). ADA1 helps regulate adenosine levels by deaminating excess adenosine (ADE) and its derivatives, such as 2'-deoxyadenosine (DEO). Understanding binding mechanisms of ADA1 with COR in comparison with its other substrates will play a vital role in improving the bioactivity and lifetime of COR for commercial medicinal use. Recently, the first structure of human ADA1 in complex with DEO was solved. We therefore employed molecular dynamics (MD) simulations to predict structures and dynamics of ADA1 complexing with ADE, DEO, and COR in comparison to a ligand-free (LF) structure. Our data reveal that a large and highly water-exposed binding pocket of ADA1 is responsible for ligand translocation and reorientation. Two possible binding locations (site1 and site2) are identified. The binding affinities of the ligands are ADE > COR > DEO. Furthermore, the movements of two loop regions at the binding pocket entrance, residues 183-193 and 215-230, contribute to gating activity.

Dynamics of OmpF Trimer Formation in the Bacterial Outer Membrane of Escherichia coli

The self-assembly of outer membrane protein F (OmpF) in the outer membrane of Escherichia coli Gram-negative bacteria was studied using multiscale molecular dynamics simulations. To accommodate the long time scale required for protein assembly, coarse-grained parametrization of E. coli outer membrane lipids was first developed. The OmpF monomers formed stable dimers at specific protein-protein interactions sites irrespective of the lipid membrane environment. The dimer intermediate was asymmetric but provided a template to form a symmetric trimer. Superposition analysis of the self-assembled trimer with the X-ray crystal structure of the trimer available in the protein data bank showed excellent agreement with global root-mean-square deviation of less than 2.2 Å. The free energy change associated with dimer formation was -26 ± 1 kcal mol^-1, and for a dimer to bind to a monomer and to form a trimer yielded -56 ± 4 kcal mol^-1. Based on thermodynamic data, an alternate path to trimer formation via interaction of two dimers is also presented.

Effect of natural polymorphism on structure and function of the Yersinia pestis outer membrane porin F (OmpF protein): a computational study

The Yersinia pestis outer membrane porin F (OmpF) is a transmembrane protein located in the outer membrane of this Gram-negative bacterium which is the causative agent of plague, where it plays a significant role in controlling the selective permeability of the membrane. The amino acid sequences of OmpF proteins from 48 Y. pestis strains representing all currently available phylogenetic groups of this Gram-negative bacterium were recently deduced. Comparison of these amino acid sequences revealed that the OmpF can be present in four isoforms, the pestis-pestis type, and the pestis-microtus types I, II, and III. OmpF of the most recent pestis-pestis type has an alanine residue at the position 148, where all the pestis-microtus types have threonine there (T148A polymorphism). The variability of different pestis-microtus types is caused by an additional polymorphism at the 193rd position, where the OmpFs of the pestis-microtus type II and type III have isoleucine-glycine (IG⁺₁₉₃) or isoleucine-glycine-isoleucine-glycine (IGIG⁺₁₉₃) insertions, respectively (IG⁺₁₉₃ and IGIG⁺₁₉₃ polymorphism). To investigate potential effects of these sequence polymorphisms on the structural properties of the OmpF protein, we conducted multi-level computational analysis of its isoforms. Analysis of the I-TASSER-generated 3D-models revealed that the Yersinia OmpF is very similar to other non-specific enterobacterial porins. The T148A polymorphism affected a loop located in the external vestibule of the OmpF channel, whereas IG⁺₁₉₃ and IGIG⁺₁₉₃ polymorphisms affected one of its β-strands. Our analysis also suggested that polymorphism has moderate effect on the predicted local intrinsic disorder predisposition of OmpF, but might have some functional implementations.

In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality

Diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (OMP) family in Gram-negative bacteria. Differences in pore size and amino acid composition contribute to the specificity. Structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. Entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, specificity and biological niche adaptation. The high mutation rate in their surface-exposed loops is likely an important mechanism for host immune system evasion. Multiple sequence alignments for each subclass revealed conserved residue positions that are involved in substrate recognition and specificity. An analysis of monomeric protein channels revealed particular sequence patterns of amino acids that were observed in other classes at multimeric interfaces. This adds to the emerging evidence that all members of the family exist in a multimeric state. Our findings are important for understanding the role of members of this family in a wide range of bacterial processes, including bacterial food uptake, survival and adaptation mechanisms.