Download or read book Molecular Dynamics Simulation Studies of Interaction of Amphiphilic Molecules with Lipid Bilayers written by Jieqiong Lin and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Advances in Planar Lipid Bilayers and Liposomes written by A. Ottova-Leitmannova and published by Gulf Professional Publishing. This book was released on 2005-09 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lipid bilayer is central to life, as all living organisms possess a lipid bilayer structure, thereby underlying the lipid bilayer principle of biomembranes. The lipid bilayer principle and its applications are the main theme of this new book series. This new series on bilayer lipid membranes (BLMs and liposomes) include invited chapters on a broad range of topics, from theoretical investigations, specific studies, experimental methods, to practical applications. Written for newcomers, experienced scientists, and those who are not familiar with these specific research areas, the Series covers all aspects of lipid bilayer investigations, both fundamental and applied. * Covers a broad range of topics ranging from theoretical research, specific studies, experimental methods, to practical applications * Authoritative timely reviews by experts in this field * Indispensable source of information for new scientists
Download or read book Liposomes Lipid Bilayers and Model Membranes written by Georg Pabst and published by CRC Press. This book was released on 2014-03-04 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a result of their unique physical properties, biological membrane mimetics, such as liposomes, are used in a broad range of scientific and technological applications. Liposomes, Lipid Bilayers and Model Membranes: From Basic Research to Application describes state-of-the-art research and future directions in the field of membranes, which has evolved from basic studies of the physicochemical properties of amphiphiles to their application in industry and medicine. Written by leading researchers in their fields, this book describes basic and applied research, and serves as a useful reference for both the novice and the expert. Part one covers a range of basic research topics, from theory and computational simulations to some of the most up-to-date experimental research. Topics discussed include soft matter physics of membranes, nonlamellar phases, extraction of molecules by amphiphiles, lipid models for membrane rafts, membrane dynamics, nanodiscs, microemulsions, active membranes, as well as interactions of bilayers with drugs or DNA to treat disease or for gene transfer, respectively. Part two of the book focuses on technological applications of amphiphiles, such as liposome-based nanoparticles for drug delivery, formulation of liposomes for prolonged in vivo circulation and functionalization for medical purposes, novel drug delivery systems for increased drug loading, and the use of tethered membranes for bio-sensing applications. Chapters also describe the use of liposomes in textile dyeing and how lipidic nanoparticles are used by the food industry.
Download or read book Lipid Bilayer polypeptide Interactions Studied by Molecular Dynamics Simulation written by Olle Edholm and published by . This book was released on 1985 with total page 34 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Numerical Simulations of a Smectic Lamellar Phase of Amphiphilic Molecules written by Claire Loison and published by Cuvillier Verlag. This book was released on 2005 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Theoretical Study of the Interaction of Amphiphilic Block Co polymers with Biological Interfaces and Small Molecules written by Samanta Susruta and published by . This book was released on 2012 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic polymers are versatile materials with an extraordinary range of technological applications playing essential and ubiquitous roles in everyday life. Presently, the applications of polymers are not limited to traditional areas of technology but extend to novel uses in the areas of nanotechnology connected to medicine and pharmacology. Polyethylene oxide (PEO) and polypropylene oxide (PPO) homo-polymers as well as the block co-polymers based on them (Pluronics or Poloxamers) are among the most versatile polymers used in these fields. These polymers have the advantages of being non-toxic, easily available, economic and customizable to meet specific purposes. Despite many experimental and theoretical studies on them, the actual mechanisms of their interactions with bio-systems and drug molecules are still unknown. The research work reported in this PhD thesis is aimed to understand the behavior of these polymers in solution and their interactions with biological interfaces and drug molecules using molecular dynamics simulations. Recently proposed models for the ether based polymers and their monomers were successfully tested in a wide range of non-aqueous solvents to establish their versatility. The thermodynamics and kinetics of the polymers and the monomers were first studied at simple water/n-heptane interface. Eventually the research was extended to study their properties at lipid bilayer interfaces. The percolation behavior of the ether based polymers and their monomers were studied using standard molecular dynamics, steered molecular dynamics and umbrella sampling simulations. It has been shown that the percolation of PPO chains through lipid bilayer is favored compared to their PEO counterparts. PEO chains do not have any preference for the interior of the bilayer and but the PPO chains prefer to stay inside the bilayer. PPO chains with length comparable to the width of the bilayer tend to span across the bilayer. Pluronics also show similar effect with PPO parts spanned along the width of the bilayer and the PEO blocks in the polar headgroup region and water in both sides of the bilayer. The potential of mean force barriers of bilayer percolation were found to be smaller for PPO chains of all lengths than their PEO counterparts. The last part of the project aimed to investigate the mechanism of interaction of Pluronics with hydrophobic drug molecules. Curcumin, a natural drug from the Indian spice turmeric, has recently attracted interest as potential multivalent drug for the treatment of different diseases comprising cancer and Alzheimer's disease. For its hydrophobic nature, it has low solubility in water and therefore efforts are directed to find suitable polymeric carrier. For all these reason, Curcumin was chosen as model of hydrophobic drug for my study. A suitable force field model for this drug was optimized and used to study its interaction with Pluronics. The results of these MD simulation studies evidenced the mechanism of drug-polymer aggregate formation in which Curcumin is embedded into a hydrophobic PPO core surrounded by a hydrophilic PEO shell. The findings of this thesis are useful in the better understanding of the interactions of block co-polymers with bio-membranes at atomic level. Moreover, they provide a better insight on the dynamics and thermodynamics of the drug encapsulation and delivery across cell membranes.
Download or read book Coupling and Clustering in Molecular Dynamics Simulation Studies of Lipid Membrane Biophysics written by Michael David Weiner and published by . This book was released on 2018 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: The plasma membrane defines a eukaryotic cell, separating the cell's interior from its surroundings. Structurally, the plasma membrane is a lipid bilayer, composed of numerous different lipids and proteins. A biophysical approach to understanding this system examines the behavior of the liquid crystal phases of the membrane's lipids. In particular, membrane rafts, regions with distinct physical properties, may be studied in model membranes using coexisting liquid phases containing as few as three lipid components. The findings described in this dissertation employ Molecular Dynamics simulations, computational models of the physics of interacting atoms and molecules, to explore the biophysical chemistry of lipid bilayers. Coarse-grained Molecular Dynamics simulations use simplified molecular models, which makes reproducing spontaneous demixing into coexisting liquid phases computationally feasible. The first study presented uses coarse-grained simulations to examine coupling between the two leaflets of a model membrane. While most publications report alignment of like domains, this study shows that lengthening the acyl chains of the high-melting-temperature phospholipid component or increasing the cholesterol concentration yields an alignment of unlike domains, accompanied by the appearance of a significant presence of cholesterol at the bilayer midplane, between the leaflets. The second study takes a different approach to leaflet coupling, engaging in atomistic simulations of compositionally asymmetric bilayers. Different lipids are present in each leaflet of the plasma membrane, so an asymmetric composition offers a more physiological model. The work reveals that even a single-phase leaflet is coupled to a phase-separated leaflet, as it adopts slightly different physical properties in the regions interacting with different domains. This finding suggests that transmembrane communication through coupling can occur in cells. Finally, the third study considers the role of ions in clusters of phosphatidylinositol 4,5-bisphosphate (PIP2), a lipid that makes up a small fraction of the plasma membrane but plays an outsize role in cell signaling and the retrovirus lifecycle. It confirms experimental evidence that clusters form in the presence of divalent cations but not monovalent ones and examines the interaction of ions and lipids and the impact on the lipids' physical properties.
Download or read book Theoretical Study of the Interaction of Amphiphilic Block Co polymers with Biological Interfaces and Small Molecules written by Samanta Susruta and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic polymers are versatile materials with an extraordinary range of technological applications playing essential and ubiquitous roles in everyday life. Presently, the applications of polymers are not limited to traditional areas of technology but extend to novel uses in the areas of nanotechnology connected to medicine and pharmacology. Polyethylene oxide (PEO) and polypropylene oxide (PPO) homo-polymers as well as the block co-polymers based on them (Pluronics or Poloxamers) are among the most versatile polymers used in these fields. These polymers have the advantages of being non-toxic, easily available, economic and customizable to meet specific purposes. Despite many experimental and theoretical studies on them, the actual mechanisms of their interactions with bio-systems and drug molecules are still unknown. The research work reported in this PhD thesis is aimed to understand the behavior of these polymers in solution and their interactions with biological interfaces and drug molecules using molecular dynamics simulations. Recently proposed models for the ether based polymers and their monomers were successfully tested in a wide range of non-aqueous solvents to establish their versatility. The thermodynamics and kinetics of the polymers and the monomers were first studied at simple water/n-heptane interface. Eventually the research was extended to study their properties at lipid bilayer interfaces. The percolation behavior of the ether based polymers and their monomers were studied using standard molecular dynamics, steered molecular dynamics and umbrella sampling simulations. It has been shown that the percolation of PPO chains through lipid bilayer is favored compared to their PEO counterparts. PEO chains do not have any preference for the interior of the bilayer and but the PPO chains prefer to stay inside the bilayer. PPO chains with length comparable to the width of the bilayer tend to span across the bilayer. Pluronics also show similar effect with PPO parts spanned along the width of the bilayer and the PEO blocks in the polar headgroup region and water in both sides of the bilayer. The potential of mean force barriers of bilayer percolation were found to be smaller for PPO chains of all lengths than their PEO counterparts. The last part of the project aimed to investigate the mechanism of interaction of Pluronics with hydrophobic drug molecules. Curcumin, a natural drug from the Indian spice turmeric, has recently attracted interest as potential multivalent drug for the treatment of different diseases comprising cancer and Alzheimer's disease. For its hydrophobic nature, it has low solubility in water and therefore efforts are directed to find suitable polymeric carrier. For all these reason, Curcumin was chosen as model of hydrophobic drug for my study. A suitable force field model for this drug was optimized and used to study its interaction with Pluronics. The results of these MD simulation studies evidenced the mechanism of drug-polymer aggregate formation in which Curcumin is embedded into a hydrophobic PPO core surrounded by a hydrophilic PEO shell. The findings of this thesis are useful in the better understanding of the interactions of block co-polymers with bio-membranes at atomic level. Moreover, they provide a better insight on the dynamics and thermodynamics of the drug encapsulation and delivery across cell membranes.
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.
Download or read book Understanding Lipid Membranes Interactions with Small Molecules and Cholesterol Using Molecular Dynamics Computer Simulations written by Nihit Pokhrel and published by . This book was released on 2019 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cellular membranes are made up of phospholipids, proteins and cholesterol. The packing of components within the membrane gives rise to important biological phenomena. Understanding these interactions is the most critical step towards predicting membrane behavior. In this dissertation, I focus on lipid bilayer interactions with various molecules. At biologically relevant scale, we investigate how phospholipids interact with small molecules like amino acid residues and cholesterol. At field scale, we study the structure and dynamics of lipid molecules as they bind with clay minerals. I utilize molecular dynamics simulation, both equilibrium and biased, at both coarse-grained and atomistic level to study how these interactions impact membrane thermodynamic properties. I first study membrane permeation by evaluating the efficiency of different computational methods to sample the configurational space of various amino acid and lipid membranes. I show that replica exchange umbrella sampling out-performs others because of the algorithm's ability to sample transition state. Using this method, I calculate cholesterol chemical potential in seven binary lipid membranes. These results demonstrate the sensitivity of the cholesterol chemical potential to the lipid tail unsaturation only if the difference in tail saturation is big, and show that cholesterol has the greatest affinity to saturated PC lipids. These studies provide practical guidance for studying membrane permeation and yield important insight into the thermodynamic properties of lipid bilayer systems. This work will also contribute towards the understanding of cholesterol's effect of membranes, which is a vast and still ongoing field of research. Finally, this research also sheds lights on soil water repellency at the molecular scale. I investigate structural properties of organic matter that are found in soil and find that zwitterionic lipid aggregates bind to the surface of the clay. In this relatively new field, such molecular simulations will have significant scientific impact.
Download or read book Molecular Dynamics written by Lichang Wang and published by BoD – Books on Demand. This book was released on 2012-04-11 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines
Download or read book Water in Biological and Chemical Processes written by Biman Bagchi and published by Cambridge University Press. This book was released on 2013-11-14 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: A unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.
Download or read book Molecular Dynamics Studies of Peptide Nanoparticle and Lipid Interactions Using Multiscale Simulations written by Hwan Kyu Lee and published by . This book was released on 2006 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
Download or read book Computational Biochemistry and Biophysics written by Oren M. Becker and published by CRC Press. This book was released on 2001-02-09 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret b
Download or read book Molecular Dynamics Studies of Lipid Monolayer and Bilayer Systems written by Bin Liu and published by . This book was released on 2016 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lipids are a crucial ingredient of biomembranes in cells, and they play a pivotal role in many chemical and biological processes. Lipid based structures, such as lipid monolayers and lipid bilayers, both natural and artificial, are gaining their importance and popularity in drug delivery. In this thesis, our main interest is on using molecular modeling and atomistic molecular dynamics simulations to study lipid monolayers and bilayers, and their physical properties and interactions with an antibiotic molecule called daptomycin. This thesis is composed of the research results from two projects. The first project focuses on an atomistic molecular dynamcis study of lipid Langmuir monolayers composed of both pure zwitterionic dipalmitoylphosphatidylcholine (DPPC) and a mixture of DPPC and cationic cetyltrimethylammonium bromide (CTAB). The cationic CTAB lipids have been found to have significant condensing effect on the DPPC / CTAB monolayers, i.e., at the same surface tension or surface pressure, monolayers with higher CTAB molar fraction have smaller area per lipid. With this condensing effect, the DPPC / CTAB monolayers are also able to achieve negative surface tension without introducing buckling into the monolayer structure. The condensing effect is caused by the interplay between the cationic CTAB headgroups and the zwitterionic phosphatidylcholine (PC) headgroups which has electrostatic origin. Moreover, detailed analysis of the structural properties of the monolayers, such as the density profile analysis, hydrogen bonding analysis, chain order parameter calculations and radial distribution function calculations were also performed for better understanding of cationic DPPC/CTAB monolayers. A chapter is dedicated to the discussion of the mean and Gaussian curvatures of the pure DPPC and DPPC/CTAB mixture monolayers. In the second project, MD simulations were employed to study the atomistic details of the antimicrobial activities of daptomycin, a cyclic anionic lipopeptide which treats infections caused by Gram-positive bacteria, with emphasis on its interactions with a model bacteria membrane. Despite having itself a net negative charge, it is selective against negatively charged bacterial membranes. It has been established that daptomycin's antibiotic activity is based on targeting the bacterial membranes and that this antibacterial activity depends on calcium ions. Importantly, however, both the precise role of ions and the physical mechanisms responsible for daptomy-cin's action remain poorly understood. We investigate these issues using three types of molecular dynamics simulations: free energy calculations for a single daptomycin, unbiased simulations for daptomycin tetramers and micellation of daptomycin both in the absence and presence of calcium ions.
Download or read book Molecular Dynamic Simulations of the Interaction of Natural Compounds with Lipid Bilayer Membranes written by Gabin Fabre and published by . This book was released on 2012 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt: Based on the structures of natural molecules, many new derivatives are continuously synthetized to enhance therapeutic. To understand the mechanism of action of these compounds, one of the key steps is the capacity to incorporate/cross lipid bilayer membranes. Molecular dynamics (MD) has recently appeared as a powerful tool to rationalize these interactions at the molecular level. Here we report on two different types of derivatives. The first class concerns antioxidants. One of the most important oxidative processes in the organism is lipid peroxidation in cell membrane. To efficiently stop lipid peroxidation, potential antioxidants have to (i) scavenge free radicals and (ii) incorporate inside the membrane. Lipocarbazole exhibits an efficient antioxidant activity against lipid peroxidation in vitro, which can be correlated to its actual position and orientation inside the membrane. The second class concerns antibacterials. Plantazolicin A exhibits antibacterial activity against Gram+ strains. In order to understand this activity (i) the 3D re-arrangement and (ii) its interaction with bacterial membrane must be fully understood. Using a model of lipid bilayer membrane, the capacity of this compound to form pores is evaluated here.
