A kinetic model for molecular diffusion through pores. 2016

Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
Department of Physics, University of Cagliari, Italy.

The number of pathogens developing multiple drug resistance is ever increasing. The impact on healthcare systems is huge and the need for novel antibiotics as well a new way to develop them is urgent, especially against Gram-negative bacteria. The first defense of these bacteria is the outer membrane, where unspecific protein channels (porins) modulate nutrients passive diffusion. Also polar antibiotics enter through this path and down-regulation and/or mutation of porins are very common in drug resistant strains. Our inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features enabling better penetration through porins. Molecular dynamics simulations offer an extraordinary tool in the study of the dynamics of biological systems; however, one of the major drawbacks of this method is that its use is currently restricted to study time scales of the order of microsecond. Enhanced sampling methods like Metadynamics have been recently used to investigate the diffusion of antibiotics through bacterial porins. The main limitation is that dynamical properties cannot be estimated because of the different potential that the systems under study are experiencing. Recently, the scope of Metadynamics has been extended. By applying an a posteriori analysis one can obtain rates of transitions and rate-limiting steps of the process under study, directly comparable with kinetic data extracted from electrophysiology experiments. In this work, we apply this method to the study of the permeability of Escherichia coli's OmpF with respect to Meropenem, finding good agreement with the residence time obtained analyzing experimental current noise. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

UI MeSH Term Description Entries
D007473 Ion Channels Gated, ion-selective glycoproteins that traverse membranes. The stimulus for ION CHANNEL GATING can be due to a variety of stimuli such as LIGANDS, a TRANSMEMBRANE POTENTIAL DIFFERENCE, mechanical deformation or through INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS. Membrane Channels,Ion Channel,Ionic Channel,Ionic Channels,Membrane Channel,Channel, Ion,Channel, Ionic,Channel, Membrane,Channels, Ion,Channels, Ionic,Channels, Membrane
D008051 Lipid Bilayers Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes. Bilayers, Lipid,Bilayer, Lipid,Lipid Bilayer
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D002462 Cell Membrane The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells. Plasma Membrane,Cytoplasmic Membrane,Cell Membranes,Cytoplasmic Membranes,Membrane, Cell,Membrane, Cytoplasmic,Membrane, Plasma,Membranes, Cell,Membranes, Cytoplasmic,Membranes, Plasma,Plasma Membranes
D002463 Cell Membrane Permeability A quality of cell membranes which permits the passage of solvents and solutes into and out of cells. Permeability, Cell Membrane
D004058 Diffusion The tendency of a gas or solute to pass from a point of higher pressure or concentration to a point of lower pressure or concentration and to distribute itself throughout the available space. Diffusion, especially FACILITATED DIFFUSION, is a major mechanism of BIOLOGICAL TRANSPORT. Diffusions
D006090 Gram-Negative Bacteria Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method. Gram Negative Bacteria
D000900 Anti-Bacterial Agents Substances that inhibit the growth or reproduction of BACTERIA. Anti-Bacterial Agent,Anti-Bacterial Compound,Anti-Mycobacterial Agent,Antibacterial Agent,Antibiotics,Antimycobacterial Agent,Bacteriocidal Agent,Bacteriocide,Anti-Bacterial Compounds,Anti-Mycobacterial Agents,Antibacterial Agents,Antibiotic,Antimycobacterial Agents,Bacteriocidal Agents,Bacteriocides,Agent, Anti-Bacterial,Agent, Anti-Mycobacterial,Agent, Antibacterial,Agent, Antimycobacterial,Agent, Bacteriocidal,Agents, Anti-Bacterial,Agents, Anti-Mycobacterial,Agents, Antibacterial,Agents, Antimycobacterial,Agents, Bacteriocidal,Anti Bacterial Agent,Anti Bacterial Agents,Anti Bacterial Compound,Anti Bacterial Compounds,Anti Mycobacterial Agent,Anti Mycobacterial Agents,Compound, Anti-Bacterial,Compounds, Anti-Bacterial

Related Publications

Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
September 2013, The Journal of chemical physics,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
October 2017, The journal of physical chemistry. B,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
December 1976, Biochimica et biophysica acta,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
January 1987, The Journal of experimental zoology. Supplement : published under auspices of the American Society of Zoologists and the Division of Comparative Physiology and Biochemistry,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
August 1972, Journal of theoretical biology,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
August 2008, Journal of the American Chemical Society,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
April 2002, Analytical chemistry,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
May 1978, Journal of theoretical biology,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
January 1978, Biofizika,
Tommaso D'Agostino, and Samuele Salis, and Matteo Ceccarelli
November 2023, Heliyon,
Copied contents to your clipboard!