2,684 research outputs found
The mechanism of an electrostatic nanofilter: overcoming entropy with electrostatics
No full textGeneral porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. These biological nanopores have been designed to protect the interior of the bacterial cell from leakage of toxic compounds while selectively allowing the entry of the molecules needed for cell growth and function. The mechanism of transport through porins is of utmost and direct interest for drug discovery, extending toward nanotechnology applications for blue energy, separations, and sequencing. Here we present a theoretical framework for analysing the filter of general porins in relation to translocating molecules with the aid of enhanced molecular simulations quantitatively. Using different electrostatic probes in the form of a series of related molecules, we describe the nature of this filter and how to finely tune permeability by exploiting electrostatic interactions between the pore and the translocating molecule. Eventually, we show how enhanced simulations constitute today a valid tool for characterising the mechanism and quantifying energetically the transport of molecules through nanopores
Macroscopic electric field inside water-filled biological nanopores
No full textMulti-drug resistance bacteria are a challenging problem of contemporary medicine. This is particularly critical for Gram-negative bacteria, where antibiotics are hindered by the outer membrane to reach internal targets. Here more polar antibiotics make use of nanometric water-filled channels to permeate inside. We present in this work a computational all-atom approach, using water as a probe, for the calculation of the macroscopic electric field inside water-filled channels. The method allows one to compare not only different systems but also the same system under different conditions, such as pH and ion concentration. This provides a detailed picture of electrostatics in biological nanopores shedding more light on how the charged residues of proteins determine the electric field inside, and also how medium can tune it. These details are central to unveil the filtering mechanism behind the permeation of small polar molecules through nanometric water-filled channel
Sensing Single Molecule Penetration into Nanopores: Pushing the Time Resolution to the Diffusion Limit
No full textTo quantify small molecule penetration into and eventually permeation through nanopores, we applied an improved excess-noise analysis of the ion current fluctuation caused by entering molecules. The kinetic parameters of substrate entry and exit are derived from a two-state Markov model, analyzing the substrate concentration dependence of the average ion current and its variance. Including filter corrections allows one to detect the transition rates beyond the cutoff frequency, fc, of the instrumental ion-current filter. As an application of the method, we performed an analysis of the single-channel ion current of Meropenem, an antibiotic of the carbapenem family, interacting with OmpF, the major general outer membrane channel of Escherichia coli bacteria. At 40 °C we detected the residence time of Meropenem inside OmpF of about 500 ns - more than 2 orders of magnitude smaller than fc-1 and close to the diffusion limit of few hundred nanoseconds. We also have established theoretical limit conditions under which the substrate-induced channel blockages can be detected and suggest that submicrosecond-scale gating kinetic parameters are accessible with existing experimental equipment
How the physical properties of bacterial porins match environmental conditions
No full textTransmembrane beta-barrel proteins are key systems for transport phenomena in biology. Based on their broad substrate specificity, they represent good candidates for present and future technological applications, such as DNA/RNA and protein sequencing, sensing of biomedical analytes, and production of blue energy. For a better understanding of the process at the molecular level, we applied parallel tempering simulations in the WTE ensemble to compare two beta-barrel porins from Escherichia coli, OmpF and OmpC. Our analysis showed a different behavior of the two highly homologous porins, where subtle amino acid substitutions can modulate critical properties of mass transport. Interestingly, the differences can be mapped to the respective environmental conditions under which the two porins are expressed. Apart from reporting on the advantages of the enhanced sampling methods in assessing the molecular properties of nanopores, our comparative analysis provided new and key results to better understand biological function and technical applications. Eventually, we showed how results from molecular simulations align well with experimental single-channel measurements, thus demonstrating the mature evolution of numerical methodologies for predicting properties in this field crucial for future biomedical applications
Promising Perspectives on the Use of Fullerenes as Efficient Containers for Beryllium Atoms
No full textThe possibility of using fullerenes as containers for toxic beryllium atoms is studied by a multi-scale approach in which first-principles and classical molecular dynamics simulations are combined. By studying the energetics, electronic and spectroscopic properties of Be-fullerene systems and by simulating their interaction at finite temperature in vacuo and in representative biological environments it is concluded that: i) Be endohedral complexes can be obtained by implanting Be atoms at energies >2.3 eV that is consistent with laser implantation technologies; ii) it is in principle possible to distinguish stable endohedral complexes from metastable exohedral ones by optical absorption, suggesting that optical spectroscopy can be a valuable a non-destructive technique to assist the synthesis and the control of implanted films iii) the Be-endohedral complexes are long-lived and thermodynamically stable and can confine beryllium both in vacuo and in aqueous solution; iv) Be@C60 complexes are likely unable to penetrate the selectivity filters of a prototypical protein showing that fullerene prevents undesired interactions with biomolecules and toxicity effects of Be2+ related to replacement of the Ca2+. Overall, these results provide an assessment on the possibility to encapsulate Be atoms into fullerenes by ion implantation to synthesize inert and highly stable and safe molecular containers for toxic beryllium radionuclides. Great opportunities are expected for the realization and application of Be-C60 complexes to nanotechnology and nanomedicine with particularly appealing perspectives in the field of neutron capture therapy of cancer
Glucose transport via the pseudomonad porin OprB: implications for the design of Trojan Horse anti-infectives
No full textDeciphering the transport through outer-membrane porins is crucial to understand how anti-infectives enter Gram-negative bacteria and perform their function. Here we elucidated the transport mechanism of substrates through the Pseudomonads sugar-specific porin OprB by means of multiscale modeling. We used molecular dynamics simulations to quantify the energetics of transport and thus a diffusion model to quantify the macroscopic flux of molecules through OprB. Our results show that Trp171 and several glutamate residues in the constriction region are key for the transport of glucose, the preferred natural substrate, through OprB. The unveiled transport mechanism suggests that 2-acetamido-1,2-dideoxynojirimycin (DNJ-NAc), an anti-infective structurally similar to glucose, can enter the cell via OprB. We quantified its energetics and macroscopic flux through OprB providing a comparative analysis with the natural substrate. Thus this pore can be considered as a promising gateway for exploiting the Trojan Horse strategy in pathogenic bacteria
Internal electric field of Gram- unspecific porins directs the choreography of antibiotic translocation
No full textNew Perspectives for Neutron Capture Radiation Therapy with 7Be. The Chemistry and Biochemistry Gap
No full textThe research on new radiopharmaceuticals for therapy of cancer is evolving rapidly. Thanks to novel technologies and new selective and less toxic compounds, we move towards personalized molecular medicine. The neutron capture radiation therapy (NCT) can be potentially much safer and can offer a better spatial and temporal control than the radioisotope therapy. Still, there are not many options in NCT: the 10B isotope has been almost exclusively used for decades, and only recently, 157Gd has attracted some interest. Here, we want to draw attention to a new nuclide, 7Be, recently suggested for the NCT, and discuss perspective of Be2+ confinement in aqueous solutions and targeted delivery to cancerous tissues
7Be and 22Na radionuclides for a new therapy for cancer
No full text10B isotopes have been almost exclusively used in the neutron-capture radiation therapy (NCT) of cancer for decades. We have identified two other nuclides suitable for radiotherapy, which have ca. ten times larger cross section of absorption for neutrons and emit heavy charged particles. This would provide several key advantages for potential NCT, such as the possibility to use a lower nuclide concentration in the target tissues or a lower neutron irradiation flux. By detecting the characteristic γ radiation from the spontaneous decay of the radionuclides, one can image their biodistribution. These advantages could open up new possibilities for NCT applications as a safer and more efficient cancer therapy
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