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Using Molecular Dynamics Simulations And Statistical Modeling To Explore Membrane Structure And Membrane Protein Interactions
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Book Synopsis Using Molecular Dynamics Simulations and Statistical Modeling to Explore Membrane Structure and Membrane-protein Interactions by : Shushan He
Download or read book Using Molecular Dynamics Simulations and Statistical Modeling to Explore Membrane Structure and Membrane-protein Interactions written by Shushan He and published by . This book was released on 2018 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structure of cellular membranes gives rise to important biological phenomena, and understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step toward unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. In this dissertation we focus on the spatial organization and compositional heterogeneity of model membrane systems and their interaction with small, biologically relevant peptides. I employed both coarse-grained and atomistic molecular dynamics simulations to study the composition phase diagram of a quaternary mixture of phospholipids and cholesterol, as well as to sample the configurational space of peptide-membrane interactions. I investigate the mechanisms controlling membrane spatial heterogeneity and membrane protein interaction. This work yields important new insight into both the structural properties of lipid bilayer systems with spatial and compositional heterogeneity at vastly different length scales, which has prompted numerous publications in the field seeking for a plausible mechanism. This work will also provide perspectives on configurations of the PAP248-286 peptide upon interacting with membranes, which, despite its importance for human health, has not received as much attention from the research community as other amyloid-forming peptides. In this wide-open field such simulations will have significant scientific impact.
Book Synopsis Biophysical Approaches for the Study of Membrane Structure Part B by :
Download or read book Biophysical Approaches for the Study of Membrane Structure Part B written by and published by Elsevier. This book was released on 2024-07-21 with total page 630 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysical Approaches for the Study of Membrane Structure, Part B, Volume 701 explores lipid membrane asymmetry and lateral heterogeneity. A burst of recent research has shown that bilayers whose leaflets differ in their physical properties—such as composition, phase state, or lateral stress—exhibit many fascinating new characteristics, but also pose a host of challenges related to their creation, characterization, simulation, and theoretical description. Chapters in this new release include Characterization of domain formation in complex membranes: Analyzing the bending modulus from simulations of complex membranes, The density-threshold affinity: Calculating lipid binding affinities from unbiased Coarse-Grain Molecular Dynamics simulations, and much more.Additional sections cover Uncertainty quantification for trans-membrane stresses and moments from simulation, Using molecular dynamics simulations to generate small-angle scattering curves and cryo-EM images of proteoliposomes, Binary Bilayer Simulations for Partitioning Within Membranes, Modeling Asymmetric Cell Membranes at All-atom Resolution, Multiscale remodeling of biomembranes and vesicles, Building complex membranes with Martini 3, Predicting lipid sorting in curved bilayer membranes, Simulating asymmetric membranes using P21 periodic boundary conditions, and many other interesting topics. - Explore the state-of-the-art of lipid membrane asymmetry - Covers experimental, theoretical, and computational techniques to create and characterize asymmetric lipid membranes - Teaches how these kinds of approaches create and characterize laterally inhomogeneous membranes
Book Synopsis Molecular Simulations and Biomembranes by : Mark S P Sansom
Download or read book Molecular Simulations and Biomembranes written by Mark S P Sansom and published by Royal Society of Chemistry. This book was released on 2010-08-01 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.
Book Synopsis Computational Modeling of Membrane Bilayers by : V. Sundararajan
Download or read book Computational Modeling of Membrane Bilayers written by V. Sundararajan and published by Academic Press. This book was released on 2011-08-29 with total page 493 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Topics in Membranes provides a systematic, comprehensive, and rigorous approach to specific topics relevant to the study of cellular membranes. Each volume is a guest edited compendium of membrane biology. *Discusses the current stat of electrostatics in biomolecular simulations and future directions *Includes information on time and length scales in lipid bilayer simulations *Includes a chapter on the nature of lipid rafts
Book Synopsis Cellular Membrane Dynamics and Algorithms for Studying Their Interactions with Pharmaceutical Compounds by : Benjamin D. Madej
Download or read book Cellular Membrane Dynamics and Algorithms for Studying Their Interactions with Pharmaceutical Compounds written by Benjamin D. Madej and published by . This book was released on 2015 with total page 177 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cellular membranes are incredibly complex structures composed of diverse biomolecules including lipids, proteins, and other molecules. Cellular membranes are important because they allow for the transfer of molecules and chemical signals in and out of cells. The structure of membranes and membrane proteins is difficult to determine through experiments. Membrane structure is also highly dynamic and depends on the mixture of molecular components. While the membrane is usually in the liquid-disordered phase, other local membrane assemblies have been observed. It is challenging to predict the permeation of pharmaceutical compounds through the membrane. Molecular dynamics (MD) is a computational method that allows for the study of membrane motions and drug interactions. Based on a chemical model of molecules and Newton's equations of motion, it is possible to predict the dynamics of molecules on a computer. However, in order to simulate new molecules, it is necessary to refine an appropriate force field that models the chemical interactions of the molecules. A new force field was developed for lipids, an essential membrane component in the Amber MD software package. This force field was parameterized with experimental data and quantum mechanical calculations on individual chemical components of the lipid molecule. Afterwords, parameters were validated against available membrane structural data. Parameters have been developed for a set of glycerophospholipids and cholesterol. Molecular dynamics simulations of lipid membranes with the new parameters have accurately predicted membrane structural properties. With an accurate model of lipid membranes, it is now possible to examine complex membrane dynamics. Permeation of small molecules across the membrane is especially interesting in the pharmaceutical industry. Using the inhomogenous solubility-diffusion model it is possible to predict small-molecule permeability across a membrane from potential of mean force calculations. A constrained molecular dynamics algorithm was implemented in Amber for this task. The constraint implementation may be optimized to run on graphics processing units (GPU). This dissertation marks the first expanded lipid force field in Amber for accurate membrane simulations. It also marks the implementation of a accelerated general constraint methods in Amber.
Book Synopsis Statistical Thermodynamics Of Surfaces, Interfaces, And Membranes by : Samuel Safran
Download or read book Statistical Thermodynamics Of Surfaces, Interfaces, And Membranes written by Samuel Safran and published by CRC Press. This book was released on 2018-03-08 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the structural and thermodynamic properties of surfaces, interfaces, and membranes is important for both fundamental and practical reasons. Important applications include coatings, dispersants, encapsulating agents, and biological materials. Soft materials, important in the development of new materials and the basis of many biological systems, cannot be designed using trial and error methods due to the multiplicity of components and parameters. While these systems can sometimes be analyzed in terms of microscopic mixtures, it is often conceptually simpler to regard them as dispersions and to focus on the properties of the internal interfaces found in these systems. The basic physics centers on the properties of quasi-two-dimensional systems embedded in the three-dimensional world, thus exhibiting phenomena that do not exist in bulk materials. This approach is the basis behind the theoretical presentation of Statistical Thermodynamics of Surfaces, Interfaces, and Membranes. The approach adapted allows one to treat the rich diversity of phenomena investigated in the field of soft matter physics (including both colloid/interface science as well as the materials and macromolecular aspects of biological physics) such as interfacial tension, the roughening transition, wetting, interactions between surfaces, membrane elasticity, and self-assembly. Presented as a set of lecture notes, this book is aimed at physicists, physical chemists, biological physicists, chemical engineers, and materials scientists who are interested in the statistical mechanics that underlie the macroscopic, thermodynamic properties of surfaces, interfaces, and membranes. This paperback edition contains all the material published in the original hard-cover edition as well as additional clarifications and explanations.
Download or read book Biomembranes written by Robert B. Gennis and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical thermody namics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the graduate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases, the availability of texts in active research areas should help stimulate the creation of new courses.
Book Synopsis Computational Biophysics of Membrane Proteins by : Carmen Domene
Download or read book Computational Biophysics of Membrane Proteins written by Carmen Domene and published by Royal Society of Chemistry. This book was released on 2016-12-05 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring current themes in modern computational and membrane protein biophysics, this book is ideal for researchers in computational chemistry and computational biophysics.
Book Synopsis Pin the Protein on the Membrane by : Kayla Sapp
Download or read book Pin the Protein on the Membrane written by Kayla Sapp and published by . This book was released on 2016 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structure of the membrane gives rise to important biological phenomena. In this dissertation we focus on the shape of the membrane and its interactions through two different coupling schemes to membrane bound proteins. We develop a model based on the continuum description of the membrane that is used to investigate height-coupled and curvature-coupled membrane-protein systems. For these systems we use coupled Langevin equations to model the dynamics for the Fourier modes of the membrane and protein position in the xy-plane. We investigate similarities and differences in these two coupling schemes in how they alter membrane fluctuations, protein-protein interactions, and lateral protein diffusion. We further expand on previous dynamic membrane-protein models by deriving from the Fokker-Planck formalism a consistent Langevin equations that accurately models the dynamics of systems with protein diffusing along the membrane surface. We investigate how the model differs from previous in the discussion of later protein diffusion.
Book Synopsis Pumps, Channels and Transporters by : Ronald J. Clarke
Download or read book Pumps, Channels and Transporters written by Ronald J. Clarke and published by John Wiley & Sons. This book was released on 2015-10-12 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Describes experimental methods for investigating the function of pumps, channels and transporters Covers new emerging analytical methods used to study ion transport membrane proteins such as single-molecule spectroscopy Details a wide range of electrophysiological techniques and spectroscopic methods used to analyze the function of ion channels, ion pumps and transporters Covers state-of-the art analytical methods to study ion pumps, channels, and transporters, and where analytical chemistry can make further contributions
Book Synopsis Free Energy Calculations by : Christophe Chipot
Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Book Synopsis Molecular Modeling of Proteins by : Andreas Kukol
Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.
Book Synopsis Biological Membranes by : Kenneth M. Merz
Download or read book Biological Membranes written by Kenneth M. Merz and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interface between a living cell and the surrounding world plays a critical role in numerous complex biological processes. Sperm/egg fusion, virus/cell fusion, exocytosis, endocytosis, and ion permeation are a few examples of processes involving membranes. In recent years, powerful tools such as X-ray crystal lography, electron microscopy, nuclear magnetic resonance, and infra-red and Raman spectroscopy have been developed to characterize the structure and dy namics of biomembranes. Despite this progress, many of the factors responsible for the function of biomembranes are still not well understood. The membrane is a very complicated supramolecular liquid-crystalline structure that is largely composed of lipids, forming a bilayer, to which proteins and other biomolecules are anchored. Often, the lipid bilayer environment is pictured as a hydropho bic structureless slab providing a thermodynamic driving force to partition the amino acids of a membrane protein according to their solubility. However, much of the molecular complexity of the phospholipid bilayer environment is ignored in such a simplified view. It is likely that the atomic details of the polar head group region and the transition from the bulk water to the hydrophobic core of the membrane are important. An understanding of the factors responsible for the function of biomembranes thus requires a better characterization at the molec ular level of how proteins interact with lipid molecules, of how lipids affect protein structure and of how lipid molecules might regulate protein function.
Book Synopsis Membrane Organization and Dynamics by : Amitabha Chattopadhyay
Download or read book Membrane Organization and Dynamics written by Amitabha Chattopadhyay and published by Springer. This book was released on 2017-12-06 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume brings together information on membrane organization and dynamics from a variety of spectroscopic, microscopic and simulation approaches, spanning a broad range of time scales. The implication of such dynamic information on membrane function in health and disease is a topic of contemporary interest. The chapters cover various aspects of membrane lipid and protein dynamics, explored using a battery of experimental and theoretical approaches. The synthesis of information and knowledge gained by utilizing multiple approaches will provide the reader with a comprehensive understanding of the underlying membrane dynamics and function, which will help to develop robust dynamic models for the understanding of membrane function in healthy and diseased states. In the last few years, crystal structures of an impressive number of membrane proteins have been reported, thanks to tremendous advances in membrane protein crystallization techniques. Some of these recently solved structures belong to the G protein-coupled receptor (GPCR) family, which are particularly difficult to crystallize due to their intrinsic flexibility. Nonetheless, these static structures do not provide the necessary information to understand the function of membrane proteins in the complex membrane milieu. This volume will address the dynamic nature of membrane proteins within the membrane and will provide the reader with an up-to date overview of the theory and practical approaches that can be used. This volume will be invaluable to researchers working in a wide range of scientific areas, from biochemistry and molecular biology to biophysics and protein science. Students of these fields will also find this volume very useful. This book will also be of great use to those who are interested in the dynamic nature of biological processes.
Book Synopsis Membrane-active Protein Interactions with Phospholipid Bilayers by : Mohammad Hassan Khatami
Download or read book Membrane-active Protein Interactions with Phospholipid Bilayers written by Mohammad Hassan Khatami and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane-active proteins are a class of proteins that interact with lipid membranes in the body. I study two kinds of membrane-active proteins, antimicrobial peptides (AMPs) and lung surfactant (LS) proteins. In the first part of my PhD project I did computer simulation studies with two AMPs, Gaduscidin-1 and -2 (GAD-1 and GAD-2). These peptides are histidine rich and thus expected to exhibit pH-dependent activity. In this work I have performed molecular dynamics (MD) simulations with the peptides in both histidine-charged and histidine-neutral forms, along with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid molecules, employing GROMACS software and an OPLS-AA force field. My results show a high tendency for pairs of histidines to interact with pore regions in both histidine-charged and histidine-neutral simulations. This work is published in Biophysica et Biochimica Acta (BBA)-Biomembranes (2014). In the second part of my PhD research I performed computational simulations on lung surfactant protein B (SP-B) interacting with lipid bilayer. SP-B is a hydrophobic protein with 79 residues, from the saposin superfamily. Because of the extreme hydrophobicity of SP-B, the experimental structure of the protein is unknown. Thus, I combined the Mini-B (a fragment of SP-B) experimental structure and homology modelling based on proteins in saposin family to construct my initial model of SP-B. I run MD (using OPLS-AA and PACE force fields) and replica-exchange MD (using PACE force field) simulations with GROMACS software. I modelled SP-B in open and bent (V-shaped) structures, placed within or near a POPC lipid bilayer. My results demonstrate energetically feasible structures for SP-B, in which salt bridges Membrane-active proteins are a class of proteins that interact with lipid membranes in the body. I study two kinds of membrane-active proteins, antimicrobial peptides (AMPs) and lung surfactant (LS) proteins. In the first part of my PhD project I did computer simulation studies with two AMPs, Gaduscidin-1 and -2 (GAD-1 and GAD-2). These peptides are histidine rich and thus expected to exhibit pH-dependent activity. In this work I have performed molecular dynamics (MD) simulations with the peptides in both histidine-charged and histidine-neutral forms, along with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid molecules, employing GROMACS software and an OPLS-AA force field. My results show a high tendency for pairs of histidines to interact with pore regions in both histidine-charged and histidine-neutral simulations. This work is published in Biophysica et Biochimica Acta (BBA)-Biomembranes (2014). In the second part of my PhD research I performed computational simulations on lung surfactant protein B (SP-B) interacting with lipid bilayer. SP-B is a hydrophobic protein with 79 residues, from the saposin superfamily. Because of the extreme hydrophobicity of SP-B, the experimental structure of the protein is unknown. Thus, I combined the Mini-B (a fragment of SP-B) experimental structure and homology modelling based on proteins in saposin family to construct my initial model of SP-B. I run MD (using OPLS-AA and PACE force fields) and replica-exchange MD (using PACE force field) simulations with GROMACS software. I modelled SP-B in open and bent (V-shaped) structures, placed within or near a POPC lipid bilayer. My results demonstrate energetically feasible structures for SP-B, in which salt bridges Membrane-active proteins are a class of proteins that interact with lipid membranes in the body. I study two kinds of membrane-active proteins, antimicrobial peptides (AMPs) and lung surfactant (LS) proteins. In the first part of my PhD project I did computer simulation studies with two AMPs, Gaduscidin-1 and -2 (GAD-1 and GAD-2). These peptides are histidine rich and thus expected to exhibit pH-dependent activity. In this work I have performed molecular dynamics (MD) simulations with the peptides in both histidine-charged and histidine-neutral forms, along with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid molecules, employing GROMACS software and an OPLS-AA force field. My results show a high tendency for pairs of histidines to interact with pore regions in both histidine-charged and histidine-neutral simulations. This work is published in Biophysica et Biochimica Acta (BBA)-Biomembranes (2014). In the second part of my PhD research I performed computational simulations on lung surfactant protein B (SP-B) interacting with lipid bilayer. SP-B is a hydrophobic protein with 79 residues, from the saposin superfamily. Because of the extreme hydrophobicity of SP-B, the experimental structure of the protein is unknown. Thus, I combined the Mini-B (a fragment of SP-B) experimental structure and homology modelling based on proteins in saposin family to construct my initial model of SP-B. I run MD (using OPLS-AA and PACE force fields) and replica-exchange MD (using PACE force field) simulations with GROMACS software. I modelled SP-B in open and bent (V-shaped) structures, placed within or near a POPC lipid bilayer. My results demonstrate energetically feasible structures for SP-B, in which salt bridges play a significant role. My simulations provide hypotheses for how SP-B promotes the rearrangement of planar lipid bilayers. Part of this work has been accepted for publication in Biophysica et Biochimica Acta (BBA)-Biomembranes (2016). In the third part of my project I employed solid state nuclear magnetic resonance (NMR) using 2H, 31P and 15N experiments, to study SP-B interacting with mechanically oriented lipid bilayer. Here, I used full-length 15N-labelled SP-B, which was recombinantly expressed in our lab, to find the orientation of protein with respect to the bilayer. In this part of my thesis, the final goal was to compare the experimental 15N spectra with the spectra, predicted from the structures we got from computational simulations to help define the protein's structure. Since, I was not able to gain 15N NMR signals in my SP-B in lipid bilayer experiments, I did not fulfill the final goal of this part of my project. However, I was able to predict 15N NMR spectra of my computational SP-B structures. My NMR results indicate that more optimization needs to be done to modify our SP-B preparation protocol to 1) increase the yields of isotope-labelled protein and 2) increase the protein:lipid ratio when refolding into lipids. My simulated 15N spectra indicate that uniform 15N-labelling is unlikely to constrain SP-B's structure and topology very much and it will likely be necessary to use a more specifically labelled sample for these experiments.
Book Synopsis Structure and Dynamics of Membranes by : R. Lipowsky
Download or read book Structure and Dynamics of Membranes written by R. Lipowsky and published by Elsevier. This book was released on 1995-06-15 with total page 537 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first volume of the Handbook deals with the amazing world of biomembranes and lipid bilayers. Part A describes all aspects related to the morphology of these membranes, beginning with the complex architecture of biomembranes, continues with a description of the bizarre morphology of lipid bilayers and concludes with technological applications of these membranes. The first two chapters deal with biomembranes, providing an introduction to the membranes of eucaryotes and a description of the evolution of membranes. The following chapters are concerned with different aspects of lipids including the physical properties of model membranes composed of lipid-protein mixtures, lateralphase separation of lipids and proteins and measurement of lipid-protein bilayer diffusion. Other chapters deal with the flexibility of fluid bilayers, the closure of bilayers into vesicles which attain a large variety of different shapes, and applications of lipid vesicles and liposomes. Part B covers membrane adhesion, membrane fusion and the interaction of biomembranes withpolymer networks such as the cytoskeleton. The first two chapters of this part discuss the generic interactions of membranes from the conceptual point of view. The following two chapters summarize the experimental work on two different bilayer systems. The next chapter deals with the process ofcontact formation, focal bounding and macroscopic contacts between cells. The cytoskeleton within eucaryotic cells consists of a network of relatively stiff filaments of which three different types of filaments have been identified. As explained in the next chapter much has been recently learned aboutthe interaction of these filaments with the cell membrane. The final two chapters deal with membrane fusion.
Book Synopsis Investigating Molecular Effects on Membrane Structure, Dynamics and Function by : Cari Michelle Anderson
Download or read book Investigating Molecular Effects on Membrane Structure, Dynamics and Function written by Cari Michelle Anderson and published by . This book was released on 2019 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological membranes are heterogeneous structures with complex electrostatic profiles arising from lipids, sterols, membrane proteins, and water molecules. We investigated the effect of cholesterol and its derivative 6-ketocholestanol (6-kc) on membrane electrostatics by directly measuring the dipole electric field (F [arrow above F] [subscript d] ) within lipid bilayers containing cholesterol or 6-kc at concentrations of 0−40 mol% through the vibrational Stark effect (VSE). We found that adding low concentrations of cholesterol, up to ∼10 mol %, increases F [arrow above F] [subscript d], while adding more cholesterol up to 40 mol% lowers F [arrow above F] [subscript d]. In contrast, we measured a monotonic increase in F [arrow above F] [subscript d] as 6-kc concentration increased. We proposed that this membrane electric field is affected by multiple factors: the polarity of the sterol molecules, the reorientation of the phospholipid dipole due to sterol, and the impact of the sterol on hydrogen bonding with surface water. We used molecular dynamics simulations to examine the distribution of phospholipids, sterol, and helix in bilayers containing these sterols. At low concentrations, we observed clustering of sterols near the vibrational probe whereas at high concentrations, we observed spatial correlation between the positions of the sterol molecules. This work demonstrated how a one-atom difference in a sterol changes the physicochemical and electric field properties of the bilayer. Additionally, we set out to understand how a small molecule interacts with the lipid bilayer differently based on its charge. Our laboratory had previously reported that tryptophan permeated through a phosphatidylcholine lipid bilayer membrane at a faster rate when it was positively charged (Trp+) than when negatively charged (Trp−), which corresponded to a lower potential of mean force (PMF) barrier determined through simulations. In the work described here, we demonstrated that Trp+ partitions into the lipid bilayer membrane to a greater degree than Trp− by interacting with the ester linkage of a phosphatidylcholine lipid, where it is stabilized by the electron withdrawing glycerol functional group. These results are in agreement with tryptophan's known role as an anchor for transmembrane proteins, though the tendency for binding of a positively charged tryptophan is surprising. We discussed the implications of our results on the mechanisms of unassisted permeation and penetration of small molecules within and across lipid bilayer membranes based on molecular charge, shape, and molecular interactions within the bilayer structure
