E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Special Issue "Computational Modelling of Biological Membranes"

Quicklinks

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (31 March 2014)

Special Issue Editor

Guest Editor
Dr. Hui Lu

Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60680, USA
Website | E-Mail

Special Issue Information

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF.

Published Papers (10 papers)

View options order results:
result details:
Displaying articles 1-10
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle Effect of Ion Concentration Changes in the Limited Extracellular Spaces on Sarcolemmal Ion Transport and Ca2+ Turnover in a Model of Human Ventricular Cardiomyocyte
Int. J. Mol. Sci. 2013, 14(12), 24271-24292; doi:10.3390/ijms141224271
Received: 27 September 2013 / Revised: 12 November 2013 / Accepted: 19 November 2013 / Published: 13 December 2013
Cited by 2 | PDF Full-text (834 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We have developed a computer model of human cardiac ventricular myocyte (CVM), including t-tubular and cleft spaces with the aim of evaluating the impact of accumulation-depletion of ions in restricted extracellular spaces on transmembrane ion transport and ionic homeostasis in human CVM. The
[...] Read more.
We have developed a computer model of human cardiac ventricular myocyte (CVM), including t-tubular and cleft spaces with the aim of evaluating the impact of accumulation-depletion of ions in restricted extracellular spaces on transmembrane ion transport and ionic homeostasis in human CVM. The model was based on available data from human CVMs. Under steady state, the effect of ion concentration changes in extracellular spaces on [Ca2+]i-transient was explored as a function of critical fractions of ion transporters in t-tubular membrane (not documented for human CVM). Depletion of Ca2+ and accumulation of K+ occurring in extracellular spaces slightly affected the transmembrane Ca2+ flux, but not the action potential duration (APD90). The [Ca2+]i-transient was reduced (by 2%–9%), depending on the stimulation frequency, the rate of ion exchange between t-tubules and clefts and fractions of ion-transfer proteins in the t-tubular membrane. Under non-steady state, the responses of the model to changes of stimulation frequency were analyzed. A sudden increase of frequency (1–2.5 Hz) caused a temporal decrease of [Ca2+] in both extracellular spaces, a reduction of [Ca2+]i-transient (by 15%) and APD90 (by 13 ms). The results reveal different effects of activity-related ion concentration changes in human cardiac t-tubules (steady-state effects) and intercellular clefts (transient effects) in the modulation of membrane ion transport and Ca2+ turnover. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Figures

Open AccessArticle Interaction between Dipolar Lipid Headgroups and Charged Nanoparticles Mediated by Water Dipoles and Ions
Int. J. Mol. Sci. 2013, 14(8), 15312-15329; doi:10.3390/ijms140815312
Received: 10 April 2013 / Revised: 24 May 2013 / Accepted: 25 June 2013 / Published: 24 July 2013
Cited by 13 | PDF Full-text (612 KB) | HTML Full-text | XML Full-text
Abstract
In this work, a theoretical model describing the interaction between a positivelyor negatively charged nanoparticle and neutral zwitterionic lipid bilayers is presented. It isshown that in the close vicinity of the positively charged nanoparticle, the zwitterionic lipidheadgroups are less extended in the direction
[...] Read more.
In this work, a theoretical model describing the interaction between a positivelyor negatively charged nanoparticle and neutral zwitterionic lipid bilayers is presented. It isshown that in the close vicinity of the positively charged nanoparticle, the zwitterionic lipidheadgroups are less extended in the direction perpendicular to the membrane surface, whilein the vicinity of the negatively charged nanoparticle, the headgroups are more extended.This result coincides with the calculated increase in the osmotic pressure between the zwitterionic lipid surface and positively charged nanoparticle and the decrease of osmoticpressure between the zwitterionic lipid surface and the negatively charged nanoparticle.Our theoretical predictions agree well with the experimentally determined fluidity of alipid bilayer membrane in contact with positively or negatively charged nanoparticles. Theprospective significance of the present work is mainly to contribute to better understandingof the interactions of charged nanoparticles with a zwitterionic lipid bilayer, which may beimportant in the efficient design of the lipid/nanoparticle nanostructures (like liposomes withencapsulated nanoparticles), which have diverse biomedical applications, including targetedtherapy (drug delivery) and imaging of cancer cells. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Open AccessArticle Effect of Amphipathic HIV Fusion Inhibitor Peptides on POPC and POPC/Cholesterol Membrane Properties: A Molecular Simulation Study
Int. J. Mol. Sci. 2013, 14(7), 14724-14743; doi:10.3390/ijms140714724
Received: 22 May 2013 / Revised: 22 June 2013 / Accepted: 25 June 2013 / Published: 15 July 2013
Cited by 4 | PDF Full-text (1039 KB) | HTML Full-text | XML Full-text
Abstract
T-20 and T-1249 fusion inhibitor peptides were shown to interact with 1-palmitoyl-2-oleyl-phosphatidylcholine (POPC) (liquid disordered, ld) and POPC/cholesterol (1:1) (POPC/Chol) (liquid ordered, lo) bilayers, and they do so to different extents. Although they both possess a tryptophan-rich domain (TRD), T-20 lacks a pocket
[...] Read more.
T-20 and T-1249 fusion inhibitor peptides were shown to interact with 1-palmitoyl-2-oleyl-phosphatidylcholine (POPC) (liquid disordered, ld) and POPC/cholesterol (1:1) (POPC/Chol) (liquid ordered, lo) bilayers, and they do so to different extents. Although they both possess a tryptophan-rich domain (TRD), T-20 lacks a pocket binding domain (PBD), which is present in T-1249. It has been postulated that the PBD domain enhances FI interaction with HIV gp41 protein and with model membranes. Interaction of these fusion inhibitor peptides with both the cell membrane and the viral envelope membrane is important for function, i.e., inhibition of the fusion process. We address this problem with a molecular dynamics approach focusing on lipid properties, trying to ascertain the consequences and the differences in the interaction of T-20 and T-1249 with ld and lo model membranes. T-20 and T-1249 interactions with model membranes are shown to have measurable and different effects on bilayer structural and dynamical parameters. T-1249’s adsorption to the membrane surface has generally a stronger influence in the measured parameters. The presence of both binding domains in T-1249 appears to be paramount to its stronger interaction, and is shown to have a definite importance in membrane properties upon peptide adsorption. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Open AccessArticle Membrane Binding and Insertion of a pHLIP Peptide Studied by All-Atom Molecular Dynamics Simulations
Int. J. Mol. Sci. 2013, 14(7), 14532-14549; doi:10.3390/ijms140714532
Received: 31 May 2013 / Revised: 24 June 2013 / Accepted: 25 June 2013 / Published: 12 July 2013
Cited by 6 | PDF Full-text (1818 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Recent experiments in function mechanism study reported that a pH low-insertion peptide (pHLIP) can insert into a zwitterionic palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer at acidic pH while binding to the bilayer surface at basic pH. However, the atomic details of the pH-dependent interaction of
[...] Read more.
Recent experiments in function mechanism study reported that a pH low-insertion peptide (pHLIP) can insert into a zwitterionic palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer at acidic pH while binding to the bilayer surface at basic pH. However, the atomic details of the pH-dependent interaction of pHLIP with a POPC bilayer are not well understood. In this study, we investigate the detailed interactions of pHLIP with a POPC bilayer at acidic and basic pH conditions as those used in function mechanism study, using all-atom molecular dynamics (MD) simulations. Simulations have been performed by employing the initial configurations, where pHLIP is placed in aqueous solution, parallel to bilayer surface (system S), partially-inserted (system P), or fully-inserted (system F) in POPC bilayers. On the basis of multiple 200-ns MD simulations, we found (1) pHLIP in system S can spontaneously insert into a POPC bilayer at acidic pH, while binding to the membrane surface at basic pH; (2) pHLIP in system P can insert deep into a POPC bilayer at acidic pH, while it has a tendency to exit, and stays at bilayer surface at basic pH; (3) pHLIP in system F keeps in an α-helical structure at acidic pH while partially unfolding at basic pH. This study provides at atomic-level the pH-induced insertion of pHLIP into POPC bilayer. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Figures

Open AccessArticle SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Int. J. Mol. Sci. 2013, 14(6), 11510-11526; doi:10.3390/ijms140611510
Received: 22 March 2013 / Revised: 2 May 2013 / Accepted: 20 May 2013 / Published: 30 May 2013
Cited by 5 | PDF Full-text (6629 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the
[...] Read more.
Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Open AccessArticle Effects of Antimicrobial Peptide Revealed by Simulations: Translocation, Pore Formation, Membrane Corrugation and Euler Buckling
Int. J. Mol. Sci. 2013, 14(4), 7932-7958; doi:10.3390/ijms14047932
Received: 9 January 2013 / Revised: 5 March 2013 / Accepted: 27 March 2013 / Published: 11 April 2013
Cited by 7 | PDF Full-text (3683 KB) | HTML Full-text | XML Full-text
Abstract
We explore the effects of the peripheral and transmembrane antimicrobial peptides on the lipid bilayer membrane by using the coarse grained Dissipative Particle Dynamics simulations. We study peptide/lipid membrane complexes by considering peptides with various structure, hydrophobicity and peptide/lipid interaction strength. The role
[...] Read more.
We explore the effects of the peripheral and transmembrane antimicrobial peptides on the lipid bilayer membrane by using the coarse grained Dissipative Particle Dynamics simulations. We study peptide/lipid membrane complexes by considering peptides with various structure, hydrophobicity and peptide/lipid interaction strength. The role of lipid/water interaction is also discussed. We discuss a rich variety of membrane morphological changes induced by peptides, such as pore formation, membrane corrugation and Euler buckling. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Figures

Open AccessArticle A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers
Int. J. Mol. Sci. 2013, 14(4), 7702-7715; doi:10.3390/ijms14047702
Received: 1 March 2013 / Revised: 23 March 2013 / Accepted: 29 March 2013 / Published: 9 April 2013
Cited by 4 | PDF Full-text (426 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is
[...] Read more.
Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC), lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC) lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Figures

Review

Jump to: Research

Open AccessReview Atomistic Monte Carlo Simulation of Lipid Membranes
Int. J. Mol. Sci. 2014, 15(2), 1767-1803; doi:10.3390/ijms15021767
Received: 28 August 2013 / Revised: 6 December 2013 / Accepted: 9 January 2014 / Published: 24 January 2014
PDF Full-text (1543 KB) | HTML Full-text | XML Full-text
Abstract
Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the
[...] Read more.
Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Figures

Open AccessReview Engineering Lipid Bilayer Membranes for Protein Studies
Int. J. Mol. Sci. 2013, 14(11), 21561-21597; doi:10.3390/ijms141121561
Received: 6 August 2013 / Revised: 13 October 2013 / Accepted: 21 October 2013 / Published: 31 October 2013
Cited by 19 | PDF Full-text (2017 KB) | HTML Full-text | XML Full-text
Abstract
Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate
[...] Read more.
Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)
Open AccessReview Peptide-Lipid Interactions: Experiments and Applications
Int. J. Mol. Sci. 2013, 14(9), 18758-18789; doi:10.3390/ijms140918758
Received: 18 June 2013 / Revised: 27 August 2013 / Accepted: 28 August 2013 / Published: 12 September 2013
Cited by 15 | PDF Full-text (1095 KB) | HTML Full-text | XML Full-text
Abstract
The interactions between peptides and lipids are of fundamental importance in the functioning of numerous membrane-mediated cellular processes including antimicrobial peptide action, hormone-receptor interactions, drug bioavailability across the blood-brain barrier and viral fusion processes. Moreover, a major goal of modern biotechnology is obtaining
[...] Read more.
The interactions between peptides and lipids are of fundamental importance in the functioning of numerous membrane-mediated cellular processes including antimicrobial peptide action, hormone-receptor interactions, drug bioavailability across the blood-brain barrier and viral fusion processes. Moreover, a major goal of modern biotechnology is obtaining new potent pharmaceutical agents whose biological action is dependent on the binding of peptides to lipid-bilayers. Several issues need to be addressed such as secondary structure, orientation, oligomerization and localization inside the membrane. At the same time, the structural effects which the peptides cause on the lipid bilayer are important for the interactions and need to be elucidated. The structural characterization of membrane active peptides in membranes is a harsh experimental challenge. It is in fact accepted that no single experimental technique can give a complete structural picture of the interaction, but rather a combination of different techniques is necessary. Full article
(This article belongs to the Special Issue Computational Modelling of Biological Membranes)

Journal Contact

MDPI AG
IJMS Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
ijms@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to IJMS
Back to Top