Browsing by Author "Prajapati, Jigneshkumar Dahyabhai"

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Atomistic modeling of two-dimensional electronic spectra and excited-state dynamics for a light harvesting 2 complex
(ACS, 2015-01) Prajapati, Jigneshkumar Dahyabhai
The Light Harvesting 2 (LH2) complex is a vital part of the photosystem of purple bacteria. It is responsible for the absorption of light and transport of the resulting excitations to the reaction center in a highly efficient manner. A general description of the chromophores and the interaction with their local environment is crucial to understand this highly efficient energy transport. Here we include this interaction in an atomistic way using mixed quantum-classical (molecular dynamics) simulations of spectra. In particular, we present the first atomistic simulation of nonlinear optical spectra for LH2 and use it to study the energy transport within the complex. We show that the frequency distributions of the pigments strongly depend on their positions with respect to the protein scaffold and dynamics of their local environment. Furthermore, we show that although the pigments are closely packed the transition frequencies of neighboring pigments are essentially uncorrelated. We present the simulated linear absorption spectra for the LH2 complex and provide a detailed explanation of the states responsible for the observed two-band structure. Finally, we discuss the energy transfer within the complex by analyzing population transfer calculations and 2D spectra for different waiting times. We conclude that the energy transfer from the B800 ring to the B850 ring is mediated by intermediate states that are delocalized over both rings, allowing for a stepwise downhill energy transport.
Atomistic simulation of molecules interacting with biological nanopores: from current understanding to future directions
(ACS, 2022-05) Prajapati, Jigneshkumar Dahyabhai
Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute–protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.
Biophysical insight into the substrate permeation through the major outer membrane channels of acinetobacter baumannii
(Cell Press, 2017-02) Prajapati, Jigneshkumar Dahyabhai
Among other mechanisms the cause for Multidrug Resistant (MDR) bacteria is their reduced permeability for antibiotics in particular in Gram-negative bacteria such as Acinetobacter baumanii. Owing to the low permeability (100 fold less compared to that of E. coli) and genetic plasticity to adopt to the external environment accompanied with robust efflux pumps aids these bugs in limiting the intracellular active concentration of the antibiotic to minimum. Here we characterize transport of small water soluble molecules across channels in the outer membrane (OM) of A. baumanii. We use Single Channel Electrophysiology as a main tool for the biophysical characterization of the majorly expressed channels from A. baumanii. Combining our study with high resolution X- ray crystallography and molecular dynamics simulations, we provide insight into the OM of A. baumanii.
BPS2025 - MUON approach for ribosome simulations: Illustration of deacyl-tRNA release from E site
(Cell Press, 2025-02) Prajapati, Jigneshkumar Dahyabhai
A grand challenge in atomistic simulations is achieving large-scale conformation changes and observing multiple binding and unbinding events in a large molecular machine, such as the ribosome. These dynamics typically unfold at timescales ranging from milliseconds to seconds, which are impractical to achieve with current simulation methods and supercomputing capabilities. Here, we introduce a coarse-grained technique, termed MUON, a novel multi-rigid body simulation approach which employs a constrained dynamics algorithm. This innovative approach allows for the modelling of molecular machines as numerous independent rigid bodies or as interconnected chains of rigid bodies linked by flexible connections. We harness the capabilities of constrained algorithms to temperate accelerate the simulation, thereby facilitating the exploration of slow transitions, such as association or dissociation of macromolecules within molecular complexes, over a reduced timescale. We successfully simulated the dissociation of deacylated tRNA from the E site of the Escherichia coli ribosome—a process that typically occurs on the timescale of seconds—while utilizing minimal computational resources and achieving results in a reduced timeframe. Our study captured 100 tRNA dissociation events from each of the last three recognized stages of the translocation cycle (INT2, INT3, and POST) in a manner that is biologically relevant. The derivation of kinetic and thermodynamic parameters, along with the elucidation of transition pathways, has provided profound insights into the unbinding mechanism of deacylated tRNA.
Changes in salt concentration modify the translocation of neutral molecules through a δcyma nanopore in a non-monotonic manner
(ACS, 2022-04) Prajapati, Jigneshkumar Dahyabhai
The voltage-dependent transport through biological and artificial nanopores is being used in many applications such as DNA or protein sequencing and sensing. The primary approach to determine the transport has been to measure the temporal ion current fluctuations caused by solutes when applying external voltages. Crossing the nanoscale confinement in the presence of an applied electric field primarily relies on two factors, i.e., the electrophoretic drag and electroosmosis. The electroosmotic flow (EOF) is a voltage-dependent ion-associated flow of solvent molecules, i.e., usually water, and depends on many factors, such as pH, temperature, pore diameter, and also the concentration of ions. The exact interplay between these factors is so far poorly understood. In this joint experimental and computational study, we have investigated the dependence of the EOF on the concentration of the buffer salt by probing the transport of α-cyclodextrin molecules through the ΔCymA channel. For five different KCl concentrations in the range between 0.125 and 2 M, we performed applied-field molecular dynamics simulations and analyzed the ionic flow and the EOF across the ΔCymA pore. To our surprise, the concentration-dependent net ionic flux changes non-monotonically and nonlinearly and the EOF is seen to follow the same pattern. On the basis of these findings, we were able to correlate the concentration-dependent EOF with experimental kinetic constants for the translocation of α-cyclodextrin through the ΔCymA nanopore. Overall, the results further improve our understanding of the EOF-mediated transport through nanopores and show that the EOF needs to seriously be taken into consideration when analyzing the permeation of (neutral) substrates through nanopores.
Characterization of ciprofloxacin permeation pathways across the Porin OmpC using metadynamics and a string method
(ACS, 2017-08) Prajapati, Jigneshkumar Dahyabhai
The rapid spreading of antimicrobial resistance in Gram-negative bacteria has become a major threat for humans as well as animals. As one of the main factors involved, the permeability of the outer membrane has attracted a great deal of attention recently. However, the knowledge regarding the translocation mechanisms for most available antibiotics is so far rather limited. Here, a theoretical study concerning the diffusion route of ciprofloxacin across the outer membrane porin OmpC from E. coli is presented. To this end, we establish a protocol to characterize meaningful permeation pathways by combining metadynamics with the zero-temperature string method. It was found that the lowest-energy pathway requires a reorientation of ciprofloxacin in the extracellular side of the porin before reaching the constriction region with its carboxyl group ahead. Several affinity sites have been identified, and their metastability has been evaluated using unbiased simulations. Such a detailed understanding is potentially very helpful in guiding the development of next generation antibiotics.
Computational modeling of ion transport in bulk and through a nanopore using the drude polarizable force field
(ACS, 2020-06) Prajapati, Jigneshkumar Dahyabhai
In the past two decades, molecular dynamics simulations have become the method of choice for elucidating the transport mechanisms of ions through various membrane channels. Often, these simulations heavily rely on classical nonpolarizable force fields (FFs), which lack electronic polarizability in the treatment of the electrostatics. The recent advancements in the Drude polarizable FF lead to a complete set of parameters for water, ions, protein, and lipids, allowing for a more realistic modeling of membrane proteins. However, the quality of these Drude FFs remains untested for such systems. Here, we examine the quality of this FF set in two ways, i.e., (i) in simple ionic aqueous solution simulations and (ii) in more complex membrane channel simulations. First, the aqueous solutions of KCl, NaCl, MgCl2, and CaCl2 salts are simulated using the polarizable Drude and the nonpolarizable CHARMM36 FFs. The bulk conductivity has been estimated for both FF sets using applied-field simulations for several concentrations and temperatures in the case of all investigated salts and compared to experimental findings. An excellent improvement in the ability of the Drude FF to reproduce the experimental bulk conductivities for KCl, NaCl, and MgCl2 solutions can be observed but not in the case of CaCl2. Moreover, the outer membrane channel OmpC from the bacterium Escherichia coli has been employed to examine the ability of the polarizable and nonpolarizable FFs to reproduce ion transport-related quantities known from experiment. Unbiased and applied-field simulations have been performed in the presence of KCl using both FF sets. Unlike for the bulk systems of aqueous salt solutions, it has been found that the Drude FF is not accurate in modeling KCl transport properties across the OmpC porin.
Conformational dynamics of loop L3 in OMPF: implications toward antibiotic translocation and voltage gating
(ACS, 2022-12) Prajapati, Jigneshkumar Dahyabhai
In the present work, we delineate the molecular mechanism of a bulky antibiotic permeating through a bacterial channel and uncover the role of conformational dynamics of the constriction loop in this process. Using the temperature accelerated sliced sampling approach, we shed light onto the dynamics of the L3 loop, in particular the F118 to S125 segment, at the constriction regions of the OmpF porin. We complement the findings with single channel electrophysiology experiments and applied-field simulations, and we demonstrate the role of hydrogen-bond stabilization in the conformational dynamics of the L3 loop. A molecular mechanism of permeation is put forward wherein charged antibiotics perturb the network of stabilizing hydrogen-bond interactions and induce conformational changes in the L3 segment, thereby aiding the accommodation and permeation of bulky antibiotic molecules across the constriction region. We complement the findings with single channel electrophysiology experiments and demonstrate the importance of the hydrogen-bond stabilization in the conformational dynamics of the L3 loop. The generality of the present observations and experimental results regarding the L3 dynamics enables us to identify this L3 segment as the source of gating. We propose a mechanism of OmpF gating that is in agreement with previous experimental data that showed the noninfluence of cysteine double mutants that tethered the L3 tip to the barrel wall on the OmpF gating behavior. The presence of similar loop stabilization networks in porins of other clinically relevant pathogens suggests that the conformational dynamics of the constriction loop is possibly of general importance in the context of antibiotic permeation through porins.
Cryo-EM reveals remodeling of a tandem riboswitch at 2.9 Å resolution
(2025) Prajapati, Jigneshkumar Dahyabhai
Riboswitches are non-coding RNA sequences that control cellular processes through ligand binding. Conformational heterogeneity is fundamental to riboswitch functionality, yet this same attribute makes structural characterization of these mRNA elements challenging. Here, we use a combination of molecular dynamics and cryo-electron microscopy to expound the flexible nature of the glycine riboswitch tandem aptamers and characterize diMerent structural populations. We find that Mg2+ partially stabilizes the fully folded state, resulting in one-third of the particles adopting a unique “walking man” conformation, consisting of a rigidified core and two dynamic helices, and two-thirds adopting distinct, partially folded states. Glycine interactions double the relative population of fully folded particles by stabilizing a conserved inter-aptamer Hoogsteen base pair, enabling our capture of a 2.9 Å structure for this RNA-only system. The population data show that glycine and Mg2+ operate synergistically: glycine enhances Mg2+ occupancy, while Mg2+ drives glycine specificity. Our findings indicate that cryo-electron microscopy oMers a promising avenue to characterize RNA folding ensembles.
Cyclodextrin interaction with specific channel CymA from K. Oxytoca
(Cell Press, 2015-01) Prajapati, Jigneshkumar Dahyabhai
The outer membrane acts as a selective uptake barrier in Gram negative bacteria. It contains protein channels (porins) which provide an entry pathway for hydrophilic molecules like small nutrient molecules and β-lactam antibiotics. However the CymA channel is known to take up cyclodextrin molecules giving bacteria the ability to survive on cyclodextrins. Hence understanding uptake of these molecules via porins is vital to comprehend the transport mechanism across the cell membrane. Electrophysiology forms a promising approach to study the permeation of molecules across outer membrane and thereby understanding molecular interactions with the channel. Here we present cyclodextrin interaction studies of CymA from K. oxytoca using single channel electrophysiology. Detailed single channel analysis revealed inherent asymmetric gating characteristics of the channel. Analysis of the ion current reduction through CymA in presence of cyclodextrin led revealed kinetic parameters of substrate binding. To further elucidate the affinity sites of substrate to the channel, mutation of certain channel residues has been performed. An altered channel gating behaviour is observed. To obtain an atomistic view we complement our studies with all-atom molecular dynamics simulation to study the various conductance states of the channel in the absence of cyclodextrin and to get molecular insight into the uptake of cyclodextrins as well.
DFTB/MM molecular dynamics simulations of the FMO light-harvesting complex
(ACS, 2020-09) Prajapati, Jigneshkumar Dahyabhai
Because of the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated with a combined quantum–classical description. To this end, Born−Oppenheimer molecular dynamics simulations have been employed in a quantum mechanics/molecular mechanics (QM/MM) fashion for the ground state followed by excitation energy calculations again in a QM/MM scheme for the Fenna−Matthews−Olson (FMO) complex. The self-consistent-charge density functional tight-binding (DFTB) method electrostatically coupled to a classical description of the environment was applied to perform the ground-state dynamics. Subsequently, long-range-corrected time-dependent DFTB calculations were performed to determine the excitation energy fluctuations of the individual bacteriochlorophyll a molecules. The spectral densities obtained using this approach show an excellent agreement with experimental findings. In addition, the fluctuating site energies and couplings were used to estimate the exciton transfer dynamics.
Dynamic interaction of fluoroquinolones with magnesium ions monitored using bacterial outer membrane nanopores
(RSC, 2020-08) Prajapati, Jigneshkumar Dahyabhai
Divalent ions are known to have a severe effect on the translocation of several antibiotic molecules into (pathogenic) bacteria. In the present study we have investigated the effect of divalent ions on the permeability of norfloxacin across the major outer membrane channels from E. coli (OmpF and OmpC) and E. aerogenes (Omp35 and Omp36) at the single channel level. To understand the rate limiting steps in permeation, we reconstituted single porins into planar lipid bilayers and analyzed the ion current fluctuations caused in the presence of norfloxacin. Moreover, to obtain an atomistic view, we complemented the experiments with millisecond-long free energy calculations based on temperature-accelerated Brownian dynamics simulations to identify the most probable permeation pathways of the antibiotics through the respective pores. Both, the experimental analysis and the computational modelling, suggest that norfloxacin is able to permeate through the larger porins, i.e., OmpF, OmpC, and Omp35, whereas it only binds to the slightly narrower porin Omp36. Moreover, divalent ions can bind to negatively charged residues inside the porin, reversing the ion selectivity of the pore. In addition, the divalent ions can chelate with the fluoroquinolone molecules and alter their physicochemical properties. The results suggest that the conjugation with either pores or molecules must break when the antibiotic molecules pass the lumen of the porin, with the conjugation to the antibiotic being more stable than that to the respective pore. In general, the permeation or binding process of fluoroquinolones in porins occurs irrespective of the presence of divalent ions, but the presence of divalent ions can vary the kinetics significantly. Thus, a detailed investigation of the interplay of divalent ions with antibiotics and pores is of key importance in developing new antimicrobial drugs.
Dynamic interaction of norfloxacin to magnesium monitored by bacterial outer membrane nanopores
(2020-05) Prajapati, Jigneshkumar Dahyabhai
The effect of divalent ions on the permeability of norfloxacin across the major outer membrane channels from E. coli (OmpF, OmpC) and E. aerogenes (Omp35, Omp36) has been investigated at the single channel level. To understand the rate limiting steps in permeation, we reconstituted single porin into planar lipid bilayers and analyzed the ion current fluctuations caused in the presence of norfloxacin. To obtain an atomistic view, we complemented the experiments with millisecond-long free energy calculations based on temperature-accelerated Brownian dynamics simulations to identify the most probable permeation pathways of the antibiotics through the respective pore. Both, experimental analysis and computational modelling, suggest that norfloxacin is able to permeate through the larger porins, i.e., OmpF, OmpC, and Omp35, whereas it only binds to the slightly narrower porin Omp36. Moreover, divalent ions can bind to negatively charged residues inside the porin, reversing the ion selectivity of the pore. In addition, the divalent ions can chelate with the fluoroquinolones and alter their physicochemical properties. The results suggest that the conjugation must break with either one of them when the antibiotics molecules bypass the lumen of the porin, with the conjugation to the antibiotic being more stable than that to the pore. In general, the permeation or binding process of fluoroquinolone in porins occurs irrespective of the presence of divalent ions, but the presences of divalent ions can vary the kinetics significantly.
Effect of electroosmotic flow on the transport of α-cyclodextrin through the channel CymA
(Elsevier, 2017-02) Prajapati, Jigneshkumar Dahyabhai
CymA, an outer membrane channel of Klebsiella oxytoca, allows the passive diffusion of the bulky molecule α-cyclodextrin (α-CD, M.W. 972.8 Da) to the periplasm of the bacterium [1]. In single channel electrophysiology experiments, the flow of the uncharged α-CD was found asymmetric with respect to the applied voltage and ionic salts used. The net water current associated with the ion movement, i.e., the so-called electroosmotic flow (EOF), is induced by the ionic selectivity of the pore. This effects has been found to be a major factor behind the modified interactions of the α-CD molecule with the channel [2]. To get atomistic insight into the EOF on α-CD permeation, we have performed ∼40 μs free energy calculations in presence of three different ionic conditions, i.e., in the absence of ions, in the presence of 1 M KCl and of 1 M MgCl2, using well-tempered matadynamics simulations [3] applying an external field of 0 V, +1 V and −1 V. No major changes in the free energy landscapes were observed in the absence of ions at both polarities of the voltage. This finding indicates the absence of an electrophoretic effect on the neutral α-CD molecule and of an EOF mediated effect due to the absence ions. However, using an electric field together 1 M KCl salt, we observed significant free energy changes in the transport of the α-CD consistent with net EOF at both voltage polarities. Moreover, using 1 M MgCl2 salt, we demonstrate an alteration of the pore selectivity from cationic to anionic. Thereby, the direction of the resulting EOF at a particular voltage polarity and its effect on the α-CD permeation is inverted. These results highlight the role of the EOF in the transport of α-CD through the nanometer-sized CymA channel.
Electro-osmotic driven kinetics of cyclodextrin through the cyma channel
(Cell Press, 2016-02) Prajapati, Jigneshkumar Dahyabhai
Trans membrane voltage is applied to understand the permeation of uncharged molecules into and across nano pores in Electrophysiology. The permeating molecule blocks the ion flow causing ion current fluctuations. However the fluctuation density is dependent on the magnitude and direction of the applied voltage. This dependency may be assumed due to electro-osmotic (EOF) flow, electrically driven ion – associated water flow. Here we investigate the contribution of the electro-osmotic flow (EOF) as a potential cause for an external voltage driven substrate permeation. As an example, we quantified the permeation of α-cyclodextrin through the cyclodextrin-specific channel-forming porin CymA from the Gram-negative bacterium Klebsiella oxytoca. To further elucidate these effects, substrate interaction studies were performed at various external voltages in presence of three different electrolyte solutions: KCl, NaCl and MgCl2. To demonstrate the significance of the EOF at an atomistic level, the net water flux was calculated and its effect on the binding affinity of substrates was studied by employing extensive molecular dynamics simulations.
Enrofloxacin permeation pathways across the porin OmpC
(ACS, 2018-01) Prajapati, Jigneshkumar Dahyabhai
In Gram-negative bacteria, the lack or quenching of antibiotic translocation across the outer membrane is one of the main factors for acquiring antibiotic resistance. An atomic-level comprehension of the key features governing the transport of drugs by outer-membrane protein channels would be very helpful in developing the next generation of antibiotics. In a previous study [J. D. Prajapati et al. J. Chem. Theory Comput. 2017, 13, 4553], we characterized the diffusion pathway of a ciprofloxacin molecule through the outer membrane porin OmpC of Escherichia coli by combining metadynamics and a zero-temperature string method. Here, we evaluate the diffusion route through the OmpC porin for a similar fluoroquinolone, that is, the enrofloxacin molecule, using the previously developed protocol. As a result, it was found that the lowest-energy pathway was similar to that for ciprofloxacin; namely, a reorientation was required on the extracellular side with the carboxyl group ahead before enrofloxacin reached the constriction region. In turn, the free-energy basins for both antibiotics are located at similar positions in the space defined by selected reaction coordinates, and their affinity sites share a wide number of porin residues. However, there are some important deviations due to the chemical differences of these two drugs. On the one hand, a slower diffusion process is expected for enrofloxacin, as the permeation pathway exhibits higher overall energy barriers, mainly in the constriction region. On the other hand, enrofloxacin needs to replace some polar interactions in its affinity sites with nonpolar ones. This study demonstrates how minor chemical modifications can qualitatively affect the translocation mechanism of an antibiotic molecule.
Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations
(Elsevier, 2018-11) Prajapati, Jigneshkumar Dahyabhai
Although a multitude of theoretical studies exist on light-harvesting complex 2 (LH2), less is known about the light-harvesting complex 3 (LH3) of similar ring-like structure. In a comparative study of three system, i.e., the LH2 protein-pigment aggregate of the purple bacterium Rhodospirillum molischianum as well as for the LH2 and LH3 complexes of Rhodoblastus acidophilus the similarities and the differences in the excitonic system were analyzed. To this end, the systems have been studied in a multi-scale approach that combines molecular dynamics simulations with quantum chemistry calculations and quantum dynamics. Along the ground-state molecular dynamics trajectories, the excited energy gaps were determined in a quantum mechanics/molecular mechanics hybrid fashion. Based on the simulations, spectral densities, absorption spectra and exciton dynamics have been determined. After correcting for some shortcoming in the absorption spectra, the exciton dynamics within and between the ring systems have been determined and discussed.
Exploration of free energy surfaces across a membrane channel using metadynamics and umbrella sampling
(ACS, 2020-03) Prajapati, Jigneshkumar Dahyabhai
To reach their site of action, it is essential for antibiotic molecules to cross the bacterial outer membrane. The progress of enhanced sampling techniques in molecular dynamics simulations enables us to understand these translocations at an atomic level. To this end, calculations of free energy surfaces for these permeation processes are of key importance. Herein, we investigate the translocation of a variety of anionic solutes through the outer membrane pore OprO of the Gram-negative bacterium Pseudomonas aeruginosa using the metadynamics and umbrella sampling techniques at the all-atom level. Free energy calculations have been performed employing these two distinct methods in order to illustrate the difference in computed free energies, if any. The investigated solutes range from a single atomic chloride ion over a multiatomic monophosphate ion to a more bulky fosmidomycin antibiotic. The role of complexity of the permeating solutes in estimating accurate free energy profiles is demonstrated by performing extensive convergence analysis. For simple monatomic ions, good agreement between the well-tempered metadynamics and the umbrella sampling approaches is achieved, while for the permeation of the monophosphate ion differences start to appear. In the case of larger molecules such as fosmidomycin it is a tough challenge to achieve converged free energy profiles. This issue is mainly due to neglecting orthogonal degrees of freedom during the free energy calculations. Nevertheless, the freely driven metadynamics approach leads to clearly advantageous results. Additionally, atomistic insights of the translocation mechanisms of all three solutes are discussed.
Exploring the energy landscape of riboswitches using collective variables based on tertiary contacts
(Elsevier, 2022-09) Prajapati, Jigneshkumar Dahyabhai
Messenger RNA regulatory elements, such as riboswitches, can display a high degree of flexibility. By characterizing their energy landscapes, and corresponding distributions of 3D configurations, structure–function relationships can be elucidated. Molecular dynamics simulation with enhanced sampling is an important strategy used to computationally access free energy landscapes characterizing the accessible 3D conformations of RNAs. While tertiary contacts are thought to play important roles in RNA dynamics, it is difficult, in explicit solvent, to sample the formation and breakage of tertiary contacts, such as helix-helix interactions, pseudoknot interactions, and junction interactions, while maintaining intact secondary structure elements. To this end, we extend previously developed collective variables and metadynamics efforts, to establish a simple metadynamics protocol, which utilizes only one collective variable, based on multiple tertiary contacts, to characterize the underlying free energy landscape of any RNA molecule. We develop a modified collective variable, the tertiary contacts distance (), which can probe the formation and breakage of all or selectively chosen tertiary contacts of the RNA. The SAM-I riboswitch in the presence of three ionic and substrate conditions was investigated and validated against the structure ensemble previously generated using SAXS experiments. This efficient and easy to implement all-atom MD simulation based approach incorporating metadynamics to study RNA conformational dynamics can also be transferred to any other type of biomolecule.
How to enter a bacterium: bacterial porins and the permeation of antibiotics
(ACS, 2021-03) Prajapati, Jigneshkumar Dahyabhai
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure–function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.