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Kovacs T, Nagy P, Panyi G, Szente L, Varga Z, Zakany F. Cyclodextrins: Only Pharmaceutical Excipients or Full-Fledged Drug Candidates? Pharmaceutics 2022; 14:pharmaceutics14122559. [PMID: 36559052 PMCID: PMC9788615 DOI: 10.3390/pharmaceutics14122559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Cyclodextrins, representing a versatile family of cyclic oligosaccharides, have extensive pharmaceutical applications due to their unique truncated cone-shaped structure with a hydrophilic outer surface and a hydrophobic cavity, which enables them to form non-covalent host-guest inclusion complexes in pharmaceutical formulations to enhance the solubility, stability and bioavailability of numerous drug molecules. As a result, cyclodextrins are mostly considered as inert carriers during their medical application, while their ability to interact not only with small molecules but also with lipids and proteins is largely neglected. By forming inclusion complexes with cholesterol, cyclodextrins deplete cholesterol from cellular membranes and thereby influence protein function indirectly through alterations in biophysical properties and lateral heterogeneity of bilayers. In this review, we summarize the general chemical principles of direct cyclodextrin-protein interactions and highlight, through relevant examples, how these interactions can modify protein functions in vivo, which, despite their huge potential, have been completely unexploited in therapy so far. Finally, we give a brief overview of disorders such as Niemann-Pick type C disease, atherosclerosis, Alzheimer's and Parkinson's disease, in which cyclodextrins already have or could have the potential to be active therapeutic agents due to their cholesterol-complexing or direct protein-targeting properties.
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Affiliation(s)
- Tamas Kovacs
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lajos Szente
- CycloLab Cyclodextrin R & D Laboratory Ltd., H-1097 Budapest, Hungary
| | - Zoltan Varga
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Florina Zakany
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
- Correspondence:
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2
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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3
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Willems K, Ruić D, L R Lucas F, Barman U, Verellen N, Hofkens J, Maglia G, Van Dorpe P. Accurate modeling of a biological nanopore with an extended continuum framework. NANOSCALE 2020; 12:16775-16795. [PMID: 32780087 DOI: 10.1039/d0nr03114c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.
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Affiliation(s)
- Kherim Willems
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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4
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Wilson J, Sarthak K, Si W, Gao L, Aksimentiev A. Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model. ACS Sens 2019; 4:634-644. [PMID: 30821441 DOI: 10.1021/acssensors.8b01375] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly benefit from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes, and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA, and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field.
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Affiliation(s)
| | | | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, 210096, China
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5
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Simakov NA, Kurnikova MG. Membrane Position Dependency of the pK a and Conductivity of the Protein Ion Channel. J Membr Biol 2018; 251:393-404. [PMID: 29340712 DOI: 10.1007/s00232-018-0013-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
The dependency of current-voltage characteristics of the α-hemolysin channel on the channel position within the membrane was studied using Poisson-Nernst-Planck theory of ion conductivity with soft repulsion between mobile ions and protein atoms (SP-PNP). The presence of the membrane environment also influences the protonation state of the residues at the boundary of the water-lipid interface. In this work, we predict that Asp and Lys residues at the protein rim change their protonation state upon penetration to the lipid environment. Free energies of protein insertion in the membrane for different penetration depths were estimated using the Poisson-Boltzmann/solvent-accessible surface area (PB/SASA) model. The results show that rectification and reversal potentials are very sensitive to the relative position of channel in the membrane, which in turn contributes to alternative protonation states of lipid-penetrating ionizable groups. The prediction of channel position based on the matching of calculated rectification with experimentally determined rectification is in good agreement with recent neutron reflection experiments. Based on the results, we conclude that α-hemolysin membrane position is determined by a combination of factors and not only by the pattern of the surface hydrophobicity as is typically assumed.
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Affiliation(s)
- Nikolay A Simakov
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.
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6
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Bargiello TA, Oh S, Tang Q, Bargiello NK, Dowd TL, Kwon T. Gating of Connexin Channels by transjunctional-voltage: Conformations and models of open and closed states. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:22-39. [PMID: 28476631 DOI: 10.1016/j.bbamem.2017.04.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 11/18/2022]
Abstract
Voltage is an important physiologic regulator of channels formed by the connexin gene family. Connexins are unique among ion channels in that both plasma membrane inserted hemichannels (undocked hemichannels) and intercellular channels (aggregates of which form gap junctions) have important physiological roles. The hemichannel is the fundamental unit of gap junction voltage-gating. Each hemichannel displays two distinct voltage-gating mechanisms that are primarily sensitive to a voltage gradient formed along the length of the channel pore (the transjunctional voltage) rather than sensitivity to the absolute membrane potential (Vm or Vi-o). These transjunctional voltage dependent processes have been termed Vj- or fast-gating and loop- or slow-gating. Understanding the mechanism of voltage-gating, defined as the sequence of voltage-driven transitions that connect open and closed states, first and foremost requires atomic resolution models of the end states. Although ion channels formed by connexins were among the first to be characterized structurally by electron microscopy and x-ray diffraction in the early 1980's, subsequent progress has been slow. Much of the current understanding of the structure-function relations of connexin channels is based on two crystal structures of Cx26 gap junction channels. Refinement of crystal structure by all-atom molecular dynamics and incorporation of charge changing protein modifications has resulted in an atomic model of the open state that arguably corresponds to the physiologic open state. Obtaining validated atomic models of voltage-dependent closed states is more challenging, as there are currently no methods to solve protein structure while a stable voltage gradient is applied across the length of an oriented channel. It is widely believed that the best approach to solve the atomic structure of a voltage-gated closed ion channel is to apply different but complementary experimental and computational methods and to use the resulting information to derive a consensus atomic structure that is then subjected to rigorous validation. In this paper, we summarize our efforts to obtain and validate atomic models of the open and voltage-driven closed states of undocked connexin hemichannels. This article is part of a Special Issue entitled: Gap Junction Proteins edited by Jean Claude Herve.
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Affiliation(s)
- Thaddeus A Bargiello
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, United States.
| | - Seunghoon Oh
- Department of Physiology, College of Medicine, Dankook University, Cheonan, Republic of Korea
| | - Qingxiu Tang
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Nicholas K Bargiello
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Terry L Dowd
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210, United States
| | - Taekyung Kwon
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, United States
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7
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Guo Y, Jian F, Kang X. Nanopore sensor for copper ion detection using a polyamine decorated β-cyclodextrin as the recognition element. RSC Adv 2017. [DOI: 10.1039/c7ra00454k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A novel and simple nanopore sensing method has been developed for the detection of CuII ions using polyamine decorated cyclodextrin as the recognition element.
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Affiliation(s)
- Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
| | - Feifei Jian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
| | - Xiaofeng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
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8
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Pohorille A, Wilson MA, Wei C. Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels. J Phys Chem B 2016; 121:3607-3619. [PMID: 27936743 DOI: 10.1021/acs.jpcb.6b09598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We examine the validity and utility of the electrodiffusion (ED) equation, i.e., the generalized Nernst-Planck equation, to characterize, in combination with molecular dynamics, the electrophysiological behavior of simple ion channels. As models, we consider three systems-two naturally occurring channels formed by α-helical bundles of peptaibols, trichotoxin, and alamethicin, and a synthetic, hexameric channel, formed by a peptide that contains only leucine and serine. All these channels mediate transport of potassium and chloride ions. Starting with equilibrium properties, such as the potential of mean force experienced by an ion traversing the channel and diffusivity, obtained from molecular dynamics simulations, the ED equation can be used to determine the full current-voltage dependence with modest or no additional effort. The potential of mean force can be obtained not only from equilibrium simulations, but also, with comparable accuracy, from nonequilibrium simulations at a single voltage. The main assumptions underlying the ED equation appear to hold well for the channels and voltages studied here. To expand the utility of the ED equation, we examine what are the necessary and sufficient conditions for Ohmic and nonrectifying behavior and relate deviations from this behavior to the shape of the ionic potential of mean force.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,SETI Institute , 189 N Bernardo Ave #200, Mountain View, California 94043, United States
| | - Chenyu Wei
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
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9
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Liu QY, Zuo F, Chong YY, Zhao ZG, Kwon Y, Chen JX, Kim CK. Molecular simulation of liquid crystal sensor based on competitive inclusion effect. J INCL PHENOM MACRO 2016. [DOI: 10.1007/s10847-016-0678-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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10
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Campos EJ, McVey CE, Astier Y. Stochastic Detection of MPSA-Gold Nanoparticles Using a α-Hemolysin Nanopore Equipped with a Noncovalent Molecular Adaptor. Anal Chem 2016; 88:6214-22. [PMID: 27238076 DOI: 10.1021/acs.analchem.5b03558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the first study of a novel, more sensitive method for the characterization of nanoparticles (NPs). This approach combines detection via a protein nanopore with modification of its interaction behavior using a molecular adaptor. We identify different populations of 3-mercapto-1-propanesulfonate (MPSA)-modified-gold NPs using the biological nanopores α-hemolysin (αHL) and its M113N mutant equipped with a noncovalently bound γ-cyclodextrin molecule as a stochastic sensor. Identification takes place on the basis of the extent of current blockades and residence times. Here, we demonstrate that noncovalently attached adaptors can be used to change the sensing properties of αHL nanopores, allowing the detection and characterization of different populations of MPSA NPs. This is an advance in sensitivity and diversity of NP sensing, as well as a promising and reliable technology to characterize NPs by using protein nanopores.
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Affiliation(s)
- Elisa J Campos
- Single Molecule Processes Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
| | - Colin E McVey
- Structural Virology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
| | - Yann Astier
- Single Molecule Processes Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
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11
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Solano CJF, Pothula KR, Prajapati JD, De Biase PM, Noskov SY, Kleinekathöfer U. BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms. J Chem Theory Comput 2016; 12:2401-17. [DOI: 10.1021/acs.jctc.5b01196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos J. F. Solano
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Karunakar R. Pothula
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Jigneshkumar D. Prajapati
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Pablo M. De Biase
- Centre
for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ulrich Kleinekathöfer
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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12
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Eddy MT, Andreas L, Teijido O, Su Y, Clark L, Noskov SY, Wagner G, Rostovtseva TK, Griffin RG. Magic angle spinning nuclear magnetic resonance characterization of voltage-dependent anion channel gating in two-dimensional lipid crystalline bilayers. Biochemistry 2015; 54:994-1005. [PMID: 25545271 PMCID: PMC4318587 DOI: 10.1021/bi501260r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The N-terminus of the voltage-dependent
anion channel (VDAC) has
been proposed to contain the mechanistically important gating helices
that modulate channel opening and closing. In this study, we utilize
magic angle spinning nuclear magnetic resonance (MAS NMR) to determine
the location and structure of the N-terminus for functional channels
in lipid bilayers by measuring long-range 13C–13C distances between residues in the N-terminus and other
domains of VDAC reconstituted into DMPC lipid bilayers. Our structural
studies show that the distance between A14 Cβ in
the N-terminal helix and S193 Cβ is ∼4–6
Å. Furthermore, VDAC phosphorylation by a mitochondrial kinase
at residue S193 has been claimed to delay mitochondrial cell death
by causing a conformational change that closes the channel, and a
VDAC-Ser193Glu mutant has been reported to show properties very similar
to those of phosphorylated VDAC in a cellular context. We expressed
VDAC-S193E and reconstituted it into DMPC lipid bilayers. Two-dimensional 13C–13C correlation experiments showed chemical
shift perturbations for residues located in the N-terminus, indicating
possible structural perturbations to that region. However, electrophysiological
data recorded on VDAC-S193E showed that channel characteristics were
identical to those of wild type samples, indicating that phosphorylation
of S193 does not directly affect channel gating. The combination of
NMR and electrophysiological results allows us to discuss the validity
of proposed gating models.
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Affiliation(s)
- Matthew T Eddy
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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13
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Gurnev PA, Nestorovich EM. Channel-forming bacterial toxins in biosensing and macromolecule delivery. Toxins (Basel) 2014; 6:2483-540. [PMID: 25153255 PMCID: PMC4147595 DOI: 10.3390/toxins6082483] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022] Open
Abstract
To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.
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Affiliation(s)
- Philip A Gurnev
- Physics Department, University of Massachusetts, Amherst, MA 01003, USA.
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14
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Weiser BP, Salari R, Eckenhoff RG, Brannigan G. Computational investigation of cholesterol binding sites on mitochondrial VDAC. J Phys Chem B 2014; 118:9852-60. [PMID: 25080204 PMCID: PMC4141696 DOI: 10.1021/jp504516a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
mitochondrial voltage-dependent anion channel (VDAC) allows
passage of ions and metabolites across the mitochondrial outer membrane.
Cholesterol binds mammalian VDAC, and we investigated the effects
of binding to human VDAC1 with atomistic molecular dynamics simulations
that totaled 1.4 μs. We docked cholesterol to specific sites
on VDAC that were previously identified with NMR, and we tested the
reliability of multiple docking results in each site with simulations.
The most favorable binding modes were used to build a VDAC model with
cholesterol occupying five unique sites, and during multiple 100 ns
simulations, cholesterol stably and reproducibly remained bound to
the protein. For comparison, VDAC was simulated in systems with identical
components but with cholesterol initially unbound. The dynamics of
loops that connect adjacent β-strands were most affected by
bound cholesterol, with the averaged root-mean-square fluctuation
(RMSF) of multiple residues altered by 20–30%. Cholesterol
binding also stabilized charged residues inside the channel and localized
the surrounding electrostatic potentials. Despite this, ion diffusion
through the channel was not significantly affected by bound cholesterol,
as evidenced by multi-ion potential of mean force measurements. Although
we observed modest effects of cholesterol on the open channel, our
model will be particularly useful in experiments that investigate
how cholesterol affects VDAC function under applied electrochemical
forces and also how other ligands and proteins interact with the channel.
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Affiliation(s)
- Brian P Weiser
- Department of Anesthesiology and Critical Care and ‡Department of Pharmacology, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
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15
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Khalili-Araghi F, Ziervogel B, Gumbart JC, Roux B. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. ACTA ACUST UNITED AC 2014; 142:465-75. [PMID: 24081985 PMCID: PMC3787774 DOI: 10.1085/jgp.201311014] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26–27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K+ channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K+ and Na+ concentration gradients and the electrostatic potential difference of living cells.
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Affiliation(s)
- Fatemeh Khalili-Araghi
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, The University of Chicago, Chicago, IL 60637
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16
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Boda D. Monte Carlo Simulation of Electrolyte Solutions in Biology. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63378-1.00005-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Kwon T, Dowd T, Bargiello T. The carboxyl terminal residues 220-283 are not required for voltage gating of a chimeric connexin32 hemichannel. Biophys J 2013; 105:1376-82. [PMID: 24047988 PMCID: PMC3785884 DOI: 10.1016/j.bpj.2013.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/10/2013] [Accepted: 08/12/2013] [Indexed: 11/30/2022] Open
Abstract
Connexin hemichannels display two distinct forms of voltage-dependent gating, corresponding to the operation of Vj- or fast gates and loop- or slow gates. The carboxyl terminus (CT) of connexin 32 has been reported to be required for the operation of the Vj (fast) gates, but this conclusion was inferred from the loss of a fast kinetic component in macroscopic currents of CT-truncated intercellular channels elicited by transjunctional voltage. Such inferences are complicated by presence of both fast and slow gates in each hemichannel and the serial head-to-head arrangement of these gates in the intercellular channel. Examination of voltage gating in undocked hemichannels and Vj gate polarity reversal by a negative charge substitution (N2E) in the amino terminal domain allow unequivocal separation of the two gating processes in a Cx32 chimera (Cx32(∗)43E1). This chimera expresses currents as an undocked hemichannel in Xenopus oocytes and provides a model system to study the molecular determinants and mechanisms of Cx32 voltage gating. Here, we demonstrate that both Vj- and loop gates are operational in a truncation mutation that removes all but the first four CT residues (ACAR(219)) of the Cx32(∗)43E1 hemichannel. We conclude that an operational Cx32 Vj (fast) gate does not require CT residues 220-283, as reported previously by others.
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Affiliation(s)
- Taekyung Kwon
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Terry L. Dowd
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York
| | - Thaddeus A. Bargiello
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
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18
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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19
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Bargiello TA, Tang Q, Oh S, Kwon T. Voltage-dependent conformational changes in connexin channels. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:1807-22. [PMID: 21978595 PMCID: PMC3367129 DOI: 10.1016/j.bbamem.2011.09.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 09/09/2011] [Accepted: 09/17/2011] [Indexed: 10/17/2022]
Abstract
Channels formed by connexins display two distinct types of voltage-dependent gating, termed V(j)- or fast-gating and loop- or slow-gating. Recent studies, using metal bridge formation and chemical cross-linking have identified a region within the channel pore that contributes to the formation of the loop-gate permeability barrier. The conformational changes are remarkably large, reducing the channel pore diameter from 15 to 20Å to less than 4Å. Surprisingly, the largest conformational change occurs in the most stable region of the channel pore, the 3(10) or parahelix formed by amino acids in the 42-51 segment. The data provide a set of positional constraints that can be used to model the structure of the loop-gate closed state. Less is known about the conformation of the V(j)-gate closed state. There appear to be two different mechanisms; one in which conformational changes in channel structure are linked to a voltage sensor contained in the N-terminus of Cx26 and Cx32 and a second in which the C-terminus of Cx43 and Cx40 may act either as a gating particle to block the channel pore or alternatively to stabilize the closed state. The later mechanism utilizes the same domains as implicated in effecting pH gating of Cx43 channels. It is unclear if the two V(j)-gating mechanisms are related or if they represent different gating mechanisms that operate separately in different subsets of connexin channels. A model of the V(j)-closed state of Cx26 hemichannel that is based on the X-ray structure of Cx26 and electron crystallographic structures of a Cx26 mutation suggests that the permeability barrier for V(j)-gating is formed exclusively by the N-terminus, but recent information suggests that this conformation may not represent a voltage-closed state. Closed state models are considered from a thermodynamic perspective based on information from the 3.5Å Cx26 crystal structure and molecular dynamics (MD) simulations. The applications of computational and experimental methods to define the path of allosteric molecular transitions that link the open and closed states are discussed. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics.
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Affiliation(s)
- Thaddeus A Bargiello
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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20
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De Biase P, Solano CJF, Markosyan S, Czapla L, Noskov SY. BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores. J Chem Theory Comput 2012; 8:2540-2551. [PMID: 22798730 PMCID: PMC3396124 DOI: 10.1021/ct3004244] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Indexed: 11/29/2022]
Abstract
A theoretical framework is presented to model ion and DNA translocation across a nanopore confinement under an applied electric field. A combined Grand Canonical Monte Carlo Brownian Dynamics (GCMC/BD) algorithm offers a general approach to study ion permeation through wide molecular pores with a direct account of ion-ion and ion-DNA correlations. This work extends previously developed theory by incorporating the recently developed coarse-grain polymer model of DNA by de Pablo and colleagues [Knotts, T. A.; Rathore, N.; Schwartz, D. C.; de Pablo, J. J. J. Chem. Phys. 2007, 126] with explicit ions for simulations of polymer dynamics. Atomistic MD simulations were used to guide model developments. The power of the developed scheme is illustrated with studies of single-stranded DNA (ss-DNA) oligomer translocation in two model cases: a cylindrical pore with a varying radius and a well-studied experimental system, the staphylococcal α-hemolysin channel. The developed model shows good agreement with experimental data for model studies of two homopolymers: ss-poly(dA)(n) and ss-poly(dC)(n). The developed protocol allows for direct evaluation of different factors (charge distribution and pore shape and size) controlling DNA translocation in a variety of nanopores.
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Affiliation(s)
| | | | | | - Luke Czapla
- Institute for Biocomplexity and Informatics, Department
of Biological Sciences, University of Calgary, Calgary, AB, Canada,
T2N 1N4
| | - Sergei Yu. Noskov
- Institute for Biocomplexity and Informatics, Department
of Biological Sciences, University of Calgary, Calgary, AB, Canada,
T2N 1N4
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21
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Kwon T, Roux B, Jo S, Klauda JB, Harris AL, Bargiello TA. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophys J 2012; 102:1341-51. [PMID: 22455917 DOI: 10.1016/j.bpj.2012.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 01/25/2012] [Accepted: 02/07/2012] [Indexed: 11/29/2022] Open
Abstract
Loop-gating is one of two voltage-dependent mechanisms that regulate the open probability of connexin channels. The loop-gate permeability barrier is formed by a segment of the first extracellular loop (E1) (the parahelix) and appears to be accompanied by straightening of the bend angle between E1 and the first transmembrane domain (TM1). Here, all-atom molecular dynamics simulations are used to identify and characterize interacting van der Waals and electrostatic networks that stabilize the parahelices and TM1/E1 bend angles of the open Cx26 hemichannel. Dynamic fluctuations in an electrostatic network in each subunit are directly linked to the stability of parahelix structure and TM1/E1 bend angle in adjacent subunits. The electrostatic network includes charged residues that are pore-lining and thus positioned to be voltage sensors. We propose that the transition to the closed state is initiated by voltage-driven disruption of the networks that stabilize the open-state parahelix configuration, allowing the parahelix to protrude into the channel pore to form the loop-gate barrier. Straightening of the TM1/E1 bend appears to be a consequence of the reorganization of the interacting networks that accompany the conformational change of the parahelix. The electrostatic network extends across subunit boundaries, suggesting a concerted gating mechanism.
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Affiliation(s)
- Taekyung Kwon
- Dominic P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
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22
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Comer J, Aksimentiev A. Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2012; 116:3376-3393. [PMID: 22606364 PMCID: PMC3350822 DOI: 10.1021/jp210641j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.
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Affiliation(s)
- Jeffrey Comer
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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23
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Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W. Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. J Comput Chem 2012; 33:331-9. [PMID: 22102176 PMCID: PMC3240732 DOI: 10.1002/jcc.21952] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/26/2011] [Accepted: 09/03/2011] [Indexed: 11/06/2022]
Abstract
Brownian dynamics (BD) based on accurate potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for carrying out grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin (α-HL), and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate the system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC, and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-HL, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10-20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5-7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement.
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Affiliation(s)
- Kyu Il Lee
- Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS
| | - Sunhwan Jo
- Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS
| | - Huan Rui
- Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS
| | - Bernhard Egwolf
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Wonpil Im
- Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS
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24
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Krammer EM, Homblé F, Prévost M. Concentration dependent ion selectivity in VDAC: a molecular dynamics simulation study. PLoS One 2011; 6:e27994. [PMID: 22164223 PMCID: PMC3229507 DOI: 10.1371/journal.pone.0027994] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/29/2011] [Indexed: 11/19/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) forms the major pore in the outer mitochondrial membrane. Its high conducting open state features a moderate anion selectivity. There is some evidence indicating that the electrophysiological properties of VDAC vary with the salt concentration. Using a theoretical approach the molecular basis for this concentration dependence was investigated. Molecular dynamics simulations and continuum electrostatic calculations performed on the mouse VDAC1 isoform clearly demonstrate that the distribution of fixed charges in the channel creates an electric field, which determines the anion preference of VDAC at low salt concentration. Increasing the salt concentration in the bulk results in a higher concentration of ions in the VDAC wide pore. This event induces a large electrostatic screening of the charged residues promoting a less anion selective channel. Residues that are responsible for the electrostatic pattern of the channel were identified using the molecular dynamics trajectories. Some of these residues are found to be conserved suggesting that ion permeation between different VDAC species occurs through a common mechanism. This inference is buttressed by electrophysiological experiments performed on bean VDAC32 protein akin to mouse VDAC.
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Affiliation(s)
- Eva-Maria Krammer
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrice Homblé
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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25
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Kwon T, Harris AL, Rossi A, Bargiello TA. Molecular dynamics simulations of the Cx26 hemichannel: evaluation of structural models with Brownian dynamics. J Gen Physiol 2011; 138:475-93. [PMID: 22006989 PMCID: PMC3206306 DOI: 10.1085/jgp.201110679] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/27/2011] [Indexed: 11/21/2022] Open
Abstract
The recently published crystal structure of the Cx26 gap junction channel provides a unique opportunity for elucidation of the structure of the conductive connexin pore and the molecular determinants of its ion permeation properties (conductance, current-voltage [I-V] relations, and charge selectivity). However, the crystal structure was incomplete, most notably lacking the coordinates of the N-terminal methionine residue, which resides within the pore, and also lacking two cytosolic domains. To allow computational studies for comparison with the known channel properties, we completed the structure. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) simulations of the completed and the published Cx26 hemichannel crystal structure indicate that the pore is too narrow to permit significant ion flux. The GCMC/BD simulations predict marked inward current rectification and almost perfect anion selectivity, both inconsistent with known channel properties. The completed structure was refined by all-atom molecular dynamics (MD) simulations (220 ns total) in an explicit solvent and POPC membrane system. These MD simulations produced an equilibrated structure with a larger minimal pore diameter, which decreased the height of the permeation barrier formed by the N terminus. GCMC/BD simulations of the MD-equilibrated structure yielded more appropriate single-channel conductance and less anion/cation selectivity. However, the simulations much more closely matched experimentally determined I-V relations when the charge effects of specific co- and posttranslational modifications of Cx26 previously identified by mass spectrometry were incorporated. We conclude that the average equilibrated structure obtained after MD simulations more closely represents the open Cx26 hemichannel structure than does the crystal structure, and that co- and posttranslational modifications of Cx26 hemichannels are likely to play an important physiological role by defining the conductance and ion selectivity of Cx26 channels. Furthermore, the simulations and data suggest that experimentally observed heterogeneity in Cx26 I-V relations can be accounted for by variation in co- and posttranslational modifications.
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Affiliation(s)
- Taekyung Kwon
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Andrew L. Harris
- Department of Pharmacology and Physiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
| | - Angelo Rossi
- Department of Pharmacology and Physiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
| | - Thaddeus A. Bargiello
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
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26
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Roux B, Bernèche S, Egwolf B, Lev B, Noskov SY, Rowley CN, Yu H. Ion selectivity in channels and transporters. ACTA ACUST UNITED AC 2011; 137:415-26. [PMID: 21518830 PMCID: PMC3082929 DOI: 10.1085/jgp.201010577] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Sciences, University of Chicago, Chicago, IL 60637, USA. roux@uchicago.edu
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27
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Asandei A, Mereuta L, Luchian T. The Kinetics of Ampicillin Complexation by γ-Cyclodextrins. A Single Molecule Approach. J Phys Chem B 2011; 115:10173-81. [DOI: 10.1021/jp204640t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alina Asandei
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, “Alexandru I. Cuza” University, Boulevard Carol I, No. 11, Iasi 700506, Romania
| | - Loredana Mereuta
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, “Alexandru I. Cuza” University, Boulevard Carol I, No. 11, Iasi 700506, Romania
| | - Tudor Luchian
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, “Alexandru I. Cuza” University, Boulevard Carol I, No. 11, Iasi 700506, Romania
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28
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Rui H, Lee KI, Pastor RW, Im W. Molecular dynamics studies of ion permeation in VDAC. Biophys J 2011; 100:602-610. [PMID: 21281574 DOI: 10.1016/j.bpj.2010.12.3711] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 12/13/2010] [Accepted: 12/16/2010] [Indexed: 11/19/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) in the outer membrane of mitochondria serves an essential role in the transport of metabolites and electrolytes between the cell matrix and mitochondria. To examine its structure, dynamics, and the mechanisms underlying its electrophysiological properties, we performed a total of 1.77 μs molecular dynamics simulations of human VDAC isoform 1 in DOPE/DOPC mixed bilayers in 1 M KCl solution with transmembrane potentials of 0, ±25, ±50, ±75, and ±100 mV. The calculated conductance and ion selectivity are in good agreement with the experimental measurements. In addition, ion density distributions inside the channel reveal possible pathways for different ion species. Based on these observations, a mechanism underlying the anion selectivity is proposed; both ion species are transported across the channel, but the rate for K(+) is smaller than that for Cl(-) because of the attractive interactions between K(+) and residues on the channel wall. This difference leads to the anion selectivity of VDAC.
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Affiliation(s)
- Huan Rui
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Kyu Il Lee
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas.
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29
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Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophys J 2011; 100:611-619. [PMID: 21281575 PMCID: PMC3030170 DOI: 10.1016/j.bpj.2010.12.3708] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 12/02/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022] Open
Abstract
It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions.
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Affiliation(s)
- Kyu Il Lee
- Center for Bioinformatics, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Huan Rui
- Center for Bioinformatics, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Wonpil Im
- Center for Bioinformatics, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.
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30
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Eisenberg B. Multiple Scales in the Simulation of Ion Channels and Proteins. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2010; 114:20719-20733. [PMID: 21135913 PMCID: PMC2996618 DOI: 10.1021/jp106760t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Computation of living processes creates great promise for the everyday life of mankind and great challenges for physical scientists. Simulations molecular dynamics have great appeal to biologists as a natural extension of structural biology. Once a biologist sees a structure, she/he wants to see it move. Molecular biology has shown that a small number of atoms, sometimes even one messenger ion, like Ca(2+), can control biological function on the scale of cells, organs, tissues, and organisms. Enormously concentrated ions-at number densities of ~20 M-in protein channels and enzymes are responsible for many of the characteristics of living systems, just as highly concentrated ions near electrodes are responsible for many of the characteristics of electrochemical systems. Here we confront the reality of the scale differences of ions. We show that the scale differences needed to simulate all the atoms of biological cells are 10(7) in linear dimension, 10(21) in three dimensions, 10(9) in resolution, 10(11) in time, and 10(13) in particle number (to deal with concentrations of Ca(2+)). These scales must be dealt with simultaneously if the simulation is to deal with most biological functions. Biological function extends across all of them, all at once in most cases. We suggest a computational approach using explicit multiscale analysis instead of implicit simulation of all scales. The approach is based on an energy variational principle EnVarA introduced by Chun Liu to deal with complex fluids. Variational methods deal automatically with multiple interacting components and scales. When an additional component is added to the system, the resulting Euler Lagrange field equations change form automatically-by algebra alone-without additional unknown parameters. Multifaceted interactions are solutions of the resulting equations. We suggest that ionic solutions should be viewed as complex fluids with simple components. Highly concentrated solutions-dominated by interactions of components-are easily computed by EnVarA. Successful computation of ions concentrated in special places may be a significant step to understanding the defining characteristics of biological and electrochemical systems. Indeed, computing ions near proteins and nucleic acids may prove as important to molecular biology and chemical technology as computing holes and electrons has been to our semiconductor and digital technology.
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Affiliation(s)
- Bob Eisenberg
- Department of Molecular Biophysics and Physiology, Rush University, Chicago IL 60612
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31
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Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores. Proc Natl Acad Sci U S A 2010; 107:8165-70. [PMID: 20400691 DOI: 10.1073/pnas.0914229107] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe single-molecule chemistry, and in the construction of nano- and micro-devices. One important class of pores contains molecular adapters, which provide internal binding sites for small molecules. Mutants of the alpha-hemolysin (alphaHL) pore that bind the adapter beta-cyclodextrin (betaCD) approximately 10(4) times more tightly than the wild type have been obtained. We now use single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and high-resolution x-ray crystallography to provide definitive structural information on these engineered protein nanopores in unparalleled detail.
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