Influence Of Local Ph Environment And Znii On The Structure Of The Antimicrobial Peptide Clavanin A And Its Dynamics With Different Membrane Models In Md Simulations

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Influence of Local PH Environment and Zn(II) on the Structure of the Antimicrobial Peptide Clavanin A and Its Dynamics with Different Membrane Models in MD Simulations

Author : Searle Aichelle Duay
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (141 download)

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Book Synopsis Influence of Local PH Environment and Zn(II) on the Structure of the Antimicrobial Peptide Clavanin A and Its Dynamics with Different Membrane Models in MD Simulations by : Searle Aichelle Duay

Download or read book Influence of Local PH Environment and Zn(II) on the Structure of the Antimicrobial Peptide Clavanin A and Its Dynamics with Different Membrane Models in MD Simulations written by Searle Aichelle Duay and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the latest report from the Centers for Disease Control and Prevention (CDC) on antimicrobial resistance, this problem remains to be an urgent global threat, infecting about three million people and killing about 36,000 people in the United States annually. Antimicrobial peptides (AMPs) offer a number of advantages over small molecule antibiotics, such as their structural flexibility in response to different local environments, allowing for having environment-responsive modes of action. In this dissertation, we will focus on Clavanin A (ClavA), an AMP that was identified and can be extracted from the tunicate Styela clava. Experimentally, it was shown that ClavA acts via different mechanisms at different pHs, pointing to a more membrane-active mechanism at pH 7 than at pH 5. Its antimicrobial activity is also enhanced by 16-fold in the presence of Zn2+ ions. In Chapter 2, we used unbiased molecular dynamics (MD) simulations to explore the structure of ClavA and its interaction with different membrane models of Escherichia coli in different environments. It was shown that the gain in positive charge increases electrostatic attraction between ClavA and the negatively charged model membrane. We proposed the domino-effect model showing how Zn2+ enhances the initial attraction of ClavA to the model membrane. In Chapter 3, we explored different enhanced sampling techniques to generate pathways of ClavA translocation across a more complex model of an E. coli outer membrane. The advantages and disadvantages of using these techniques in novel AMP-membrane systems were described. The free energy profiles constructed from Hamiltonian replica exchange simulations showed that monomeric translocation of ClavA across the model membrane is unlikely. In Chapter 4, we used principal component analyses with bacterial cytological profiling to identify the mechanisms enforced by ClavA under different environmental conditions. In Chapter 5, the applicability of metadynamics in a different protein-metal ion system was showcased. This dissertation is a significant contribution to complement the existing body of empirical knowledge on Clavanin A. Through this work, we have exposed the strengths and limitations of using molecular dynamics simulations in metal ion-binding AMPs, which is an exciting set of AMPs that can be further studied.

Elucidating the Mechanism of Action of Unnatural Amino Acid Containing Antimicrobial Peptides in Membrane Environments

Author : Tiffany D. Clark
Publisher :
ISBN 13 :
Total Pages : 321 pages
Book Rating : 4.:/5 (824 download)

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Book Synopsis Elucidating the Mechanism of Action of Unnatural Amino Acid Containing Antimicrobial Peptides in Membrane Environments by : Tiffany D. Clark

Download or read book Elucidating the Mechanism of Action of Unnatural Amino Acid Containing Antimicrobial Peptides in Membrane Environments written by Tiffany D. Clark and published by . This book was released on 2012 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: Organism resistance continues to develop to the currently available antimicrobial compounds necessitating the development of innovative new therapeutic compounds with different specificities and mechanisms of action that provide acceptable therapeutic indices. Unnatural amino acid containing antimicrobial peptides could provide a novel avenue for the development of therapies with improved efficacy and pharmacokinetics over natural amino acid containing peptides which are prone to protease degradation. Molecular dynamics (MD) simulations of antimicrobial peptides containing unnatural amino acids have been performed using explicit water and multiple model membrane types in all-atom simulations. The structural properties of peptides were investigated using both the canonical and isothermal-isobaric ensembles to further understand the mechanism through which the collections of AMPs exert their in vitro activity. Simulations with micelle membrane models were conducted at 300 K to correlate with experimental circular dichroism (CD) data showing the secondary structure the peptides adopt in the presence of an electrostatic membrane model. Analysis of the stabilized MD trajectory reflects peptide structural consistency with experimental data. Simulations of the peptides with bilayer model membranes were conducted at the physiologically relevant 310 K to correlate with experimental cellular activity data which demonstrated the antimicrobial activity of the peptides without providing insight into the mechanism through which the activity was achieved. Long time scale simulations have noted distinct differences between bilayers in the presence of AMPs as compared to those without the peptide. Mixed bilayers with an anionic charge modeled bacterial membranes while a confluent zwitterionic bilayer modeled the mammalian membrane. This research has demonstrated that force field parameters for unnatural amino acids can be derived from QM calculations. FF parameters derived from structures identified from a DFT approach have also been used to expand the AMBER ff03 force field. The FF parameters were able to able to model the interaction of the peptides which contain unnatural amino acids. The data is consistent with NMR data and further supported with CD spectroscopy.

A Non-equilibrium Work Study of Antimicrobial Peptide-membrane Interactions

Author : Mostafa Nategholeslam
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis A Non-equilibrium Work Study of Antimicrobial Peptide-membrane Interactions by : Mostafa Nategholeslam

Download or read book A Non-equilibrium Work Study of Antimicrobial Peptide-membrane Interactions written by Mostafa Nategholeslam and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

OECD Health Policy Studies Stemming the Superbug Tide

Author : OECD.
Publisher : Org. for Economic Cooperation & Development
ISBN 13 : 9789264307582
Total Pages : 224 pages
Book Rating : 4.3/5 (75 download)

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Book Synopsis OECD Health Policy Studies Stemming the Superbug Tide by : OECD.

Download or read book OECD Health Policy Studies Stemming the Superbug Tide written by OECD. and published by Org. for Economic Cooperation & Development. This book was released on 2019-01-21 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Antimicrobial resistance (AMR) is a large and growing problem with the potential for enormous health and economic consequences, globally. As such, AMR has become a central issue at the top of the public health agenda of OECD countries and beyond. In this

Tyrant's Throne

Author : Sebastien de Castell
Publisher : Jo Fletcher Books
ISBN 13 : 1681441934
Total Pages : 465 pages
Book Rating : 4.6/5 (814 download)

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Book Synopsis Tyrant's Throne by : Sebastien de Castell

Download or read book Tyrant's Throne written by Sebastien de Castell and published by Jo Fletcher Books. This book was released on 2017-06-06 with total page 465 pages. Available in PDF, EPUB and Kindle. Book excerpt: After years of struggle and sacrifice, Falcio val Mond, First Cantor of the Greatcoats, is on the brink of fulfilling his dead king's dream: Aline, the king's daughter, is about to take the throne and restore the rule of law once and for all. But for the Greatcoats, nothing is ever that simple. In the neighboring country of Avares, an enigmatic new warlord is uniting the barbarian armies that have long plagued Tristia's borders--and even worse, he is rumored to have a new ally: Trin, who's twice tried to kill Aline to claim the throne of Tristia for herself. With the armies of Avares at her back, led by a bloodthirsty warrior, she'll be unstoppable. Falcio, Kest, and Brasti race north to stop her, but in those cold and treacherous climes they discover something altogether different, and far more dangerous: a new player is planning to take the throne of Tristia, and with a sense of dread the three friends realize that the Greatcoats, for all their skill, may not be able to stop him. As the nobles of Tristia and even the Greatcoats themselves fight over who should rule, the Warlord of Avares threatens to invade. With so many powerful contenders vying for power, it will fall to Falcio to render the one verdict he cannot bring himself to utter, much less enforce. Should he help crown the young woman he vowed to put on the throne, or uphold the laws he swore to serve?

Host-Microbe Interactions

Author :
Publisher : Academic Press
ISBN 13 : 0128096179
Total Pages : 346 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Host-Microbe Interactions by :

Download or read book Host-Microbe Interactions written by and published by Academic Press. This book was released on 2016-08-03 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Host-Microbe Interactions, the latest volume in the Progress in Molecular Biology series, provides a forum for the discussion of new discoveries, approaches, and ideas in molecular biology. It contains contributions from leaders in their respective fields, along with abundant references. This volume is dedicated to the subject of host-microbe interactions. Provides the latest research on host-microbe interactions, including new discoveries, approaches, and ideas Contains contributions from leading authorities on topics relating to molecular biology Informs and updates on all the latest developments in the field

Gold Nanoparticles For Physics, Chemistry And Biology (Second Edition)

Author : Catherine Louis
Publisher : World Scientific
ISBN 13 : 1786341263
Total Pages : 681 pages
Book Rating : 4.7/5 (863 download)

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Book Synopsis Gold Nanoparticles For Physics, Chemistry And Biology (Second Edition) by : Catherine Louis

Download or read book Gold Nanoparticles For Physics, Chemistry And Biology (Second Edition) written by Catherine Louis and published by World Scientific. This book was released on 2017-06-02 with total page 681 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gold Nanoparticles for Physics, Chemistry and Biology offers an overview of recent research into gold nanoparticles, covering their discovery, usage and contemporary practical applications.This Second Edition begins with a history of over 2000 years of the use of gold nanoparticles, with a review of the specific properties which make gold unique. Updated chapters include gold nanoparticle preparation methods, their plasmon resonance and thermo-optical properties, their catalytic properties and their future technological applications. New chapters have been included, and reveal the growing impact of plasmonics in research, with an introduction to quantum plasmonics, plasmon assisted catalysis and electro-photon conversion. The growing field of nanoparticles for health is also addressed with a study of gold nanoparticles as radiosensibiliser for radiotherapy, and of gold nanoparticle functionalisation. This new edition also considers the relevance of bimetallic nanoparticles for specific applications.World-class scientists provide the most up-to-date findings for an introduction to gold nanoparticles within the related areas of chemistry, biology, material science, optics and physics. It is perfectly suited to advanced level students and researchers looking to enhance their knowledge in the study of gold nanoparticles.

Microbial Physiology

Author : Albert G. Moat
Publisher : John Wiley & Sons
ISBN 13 : 0471461199
Total Pages : 715 pages
Book Rating : 4.4/5 (714 download)

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Book Synopsis Microbial Physiology by : Albert G. Moat

Download or read book Microbial Physiology written by Albert G. Moat and published by John Wiley & Sons. This book was released on 2003-03-31 with total page 715 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Fourth Edition of Microbial Physiology retains the logical, easy-to-follow organization of the previous editions. An introduction to cell structure and synthesis of cell components is provided, followed by detailed discussions of genetics, metabolism, growth, and regulation for anyone wishing to understand the mechanisms underlying cell survival and growth. This comprehensive reference approaches the subject from a modern molecular genetic perspective, incorporating new insights gained from various genome projects.

Peptide and Protein Engineering

Author : Olga Iranzo
Publisher : Humana
ISBN 13 : 9781071607220
Total Pages : 289 pages
Book Rating : 4.6/5 (72 download)

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Book Synopsis Peptide and Protein Engineering by : Olga Iranzo

Download or read book Peptide and Protein Engineering written by Olga Iranzo and published by Humana. This book was released on 2021-07-23 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough book aims to present the methods that have enabled the success of peptides and proteins in a wide variety of applications. It opens with a section on chemical tools applied to the production or engineering of peptides and proteins, and concludes with a collection of chapters on biological approaches used to engineer structure and function in peptides and proteins. As a book in the Springer Protocols Handbooks series, chapters include the kind of detailed descriptions and tips necessary for successful results in practice. Authoritative and practical, Peptide and Protein Engineering: From Concepts to Biotechnological Applications will be of great use to scientists in academia and industry seeking a better understanding of the emerging principles and methodologies in peptide and protein engineering.

Interrelations between Essential Metal Ions and Human Diseases

Author : Astrid Sigel
Publisher : Springer Science & Business Media
ISBN 13 : 9400775008
Total Pages : 603 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis Interrelations between Essential Metal Ions and Human Diseases by : Astrid Sigel

Download or read book Interrelations between Essential Metal Ions and Human Diseases written by Astrid Sigel and published by Springer Science & Business Media. This book was released on 2014-01-27 with total page 603 pages. Available in PDF, EPUB and Kindle. Book excerpt: MILS-13 provides an up-to-date review on the relationships between essential metals and human diseases, covering 13 metals and 3 metalloids: The bulk metals sodium, potassium, magnesium, and calcium, plus the trace elements manganese, iron, cobalt, copper, zinc, molybdenum, and selenium, all of which are essential for life. Also covered are chromium, vanadium, nickel, silicon, and arsenic, which have been proposed as being essential for humans in the 2nd half of the last century. However, if at all, they are needed only in ultra-trace amounts, and because of their prevalence in the environment, it has been difficult to prove whether or not they are required. In any case, all these elements are toxic in higher concentrations and therefore, transport and cellular concentrations of at least the essential ones, are tightly controlled; hence, their homeostasis and role for life, including deficiency or overload, and their links to illnesses, including cancer and neurological disorders, are thoroughly discussed. Indeed, it is an old wisdom that metals are indispensable for life. Therefore, Volume 13 provides in an authoritative and timely manner in 16 stimulating chapters, written by 29 internationally recognized experts from 7 nations, and supported by more than 2750 references, and over 20 tables and 80 illustrations, many in color, a most up-to-date view on the vibrant research area of the Interrelations between Essential Metal Ions and Human Diseases.

Amino Acids, Peptides and Proteins

Author : J S Davies
Publisher : Royal Society of Chemistry
ISBN 13 : 184755525X
Total Pages : 455 pages
Book Rating : 4.8/5 (475 download)

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Book Synopsis Amino Acids, Peptides and Proteins by : J S Davies

Download or read book Amino Acids, Peptides and Proteins written by J S Davies and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 455 pages. Available in PDF, EPUB and Kindle. Book excerpt: Amino Acids, Peptides and Proteins comprises a comprehensive review of significant developments at this biology/chemistry interface. Each volume of this Specialist Periodical Report opens with an overview of amino acids and their applications. Work on peptides is reviewed over several chapters, ranging from current trends in their synthesis and conformational and structural analysis, to peptidomimetics and the discovery of peptide-related molecules in nature. The application of advanced techniques in structural elucidation is incorporated into all chapters, whilst periodic chapters on metal complexes of amino acids, peptides and beta-lactams extend the scope of coverage. Efficient searching of specialist topics is facilitated by the sub-division of chapters into discrete subject areas, allowing annual trends to be monitored. Researchers in the pharmaceutical and allied industries, and at the biology/chemistry interface in academia will find this an indispensable reference source. Specialist Periodical Reports provide systematic and detailed review coverage in major areas of chemical research. Compiled by teams of leading experts in their specialist fields, this series is designed to help the chemistry community keep current with the latest developments in their field. Each volume in the series is published either annually or biennially and is a superb reference point for researchers. www.rsc.org/spr

Hybrid Nanomaterials

Author : Rafael Vargas-Bernal
Publisher : BoD – Books on Demand
ISBN 13 : 1838803378
Total Pages : 150 pages
Book Rating : 4.8/5 (388 download)

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Book Synopsis Hybrid Nanomaterials by : Rafael Vargas-Bernal

Download or read book Hybrid Nanomaterials written by Rafael Vargas-Bernal and published by BoD – Books on Demand. This book was released on 2020-06-10 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: Two of the hottest research topics today are hybrid nanomaterials and flexible electronics. As such, this book covers both topics with chapters written by experts from across the globe. Chapters address hybrid nanomaterials, electronic transport in black phosphorus, three-dimensional nanocarbon hybrids, hybrid ion exchangers, pressure-sensitive adhesives for flexible electronics, simulation and modeling of transistors, smart manufacturing technologies, and inorganic semiconductors.

Chemical Reactivity Theory

Author : Pratim Kumar Chattaraj
Publisher : CRC Press
ISBN 13 : 1420065440
Total Pages : 612 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Chemical Reactivity Theory by : Pratim Kumar Chattaraj

Download or read book Chemical Reactivity Theory written by Pratim Kumar Chattaraj and published by CRC Press. This book was released on 2009-02-23 with total page 612 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the 1970s, Density Functional Theory (DFT) was borrowed from physics and adapted to chemistry by a handful of visionaries. Now chemical DFT is a diverse and rapidly growing field, its progress fueled by numerous developing practical descriptors that make DFT as useful as it is vast. With 34 chapters written by 65 eminent scientists from 13 diffe

Heusler Alloys

Author : Claudia Felser
Publisher : Springer
ISBN 13 : 3319214497
Total Pages : 492 pages
Book Rating : 4.3/5 (192 download)

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Book Synopsis Heusler Alloys by : Claudia Felser

Download or read book Heusler Alloys written by Claudia Felser and published by Springer. This book was released on 2015-11-12 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives an overview of the physics of Heusler compounds ranging from fundamental properties of these alloys to their applications. Especially Heusler compounds as half-metallic ferromagnetic and topological insulators are important in condensed matter science due to their potential in magnetism and as materials for energy conversion. The book is written by world-leaders in this field. It offers an ideal reference to researchers at any level.

Computational Approaches in Cheminformatics and Bioinformatics

Author : Rajarshi Guha
Publisher : John Wiley & Sons
ISBN 13 : 0470384417
Total Pages : 299 pages
Book Rating : 4.4/5 (73 download)

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Book Synopsis Computational Approaches in Cheminformatics and Bioinformatics by : Rajarshi Guha

Download or read book Computational Approaches in Cheminformatics and Bioinformatics written by Rajarshi Guha and published by John Wiley & Sons. This book was released on 2012-01-04 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: A breakthrough guide employing knowledge that unites cheminformatics and bioinformatics as innovation for the future Bridging the gap between cheminformatics and bioinformatics for the first time, Computational Approaches in Cheminformatics and Bioinformatics provides insight on how to blend these two sciences for progressive research benefits. It describes the development and evolution of these fields, how chemical information may be used for biological relations and vice versa, the implications of these new connections, and foreseeable developments in the future. Using algorithms and domains as workflow tools, this revolutionary text drives bioinformaticians to consider chemical structure, and similarly, encourages cheminformaticians to consider large biological systems such as protein targets and networks. Computational Approaches in Cheminformatics and Bioinformatics covers: Data sources available for modelling and prediction purposes Developments of conventional Quantitative Structure-Activity Relationships (QSAR) Computational tools for manipulating chemical and biological data Novel ways of probing the interactions between small molecules and proteins Also including insight from public (NIH), academic, and industrial sources (Novartis, Pfizer), this book offers expert knowledge to aid scientists through industry and academic study. The invaluable applications for drug discovery, cellular and molecular biology, enzymology, and metabolism make Computational Approaches in Cheminformatics and Bioinformatics the essential guidebook for evolving drug discovery research and alleviating the issue of chemical control and manipulation of various systems.

Density Functional Theory Calculations

Author : Sergio Ricardo De Lazaro
Publisher : BoD – Books on Demand
ISBN 13 : 183881082X
Total Pages : 120 pages
Book Rating : 4.8/5 (388 download)

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Book Synopsis Density Functional Theory Calculations by : Sergio Ricardo De Lazaro

Download or read book Density Functional Theory Calculations written by Sergio Ricardo De Lazaro and published by BoD – Books on Demand. This book was released on 2021-02-03 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a contribution to the fast and broad Density Functional Theory (DFT) applications of the last few years. Since 2000, the DFT has grown exponentially in several computational areas because of its versatility and reliability to calculate energy from electronic density. The fast DFT’s calculations show how scientists develop more codes focused to simulate molecular and material properties reaching better conclusions than with previous theories. More powerful computers and lower computational costs have certainly assisted the increased growth of interest in this theory. Each chapter presents a specific subject contributing to a vision of the great potential of the quantum/DFT simulations in high pressure, chemical reactivity, ionic liquid, chemoinformatic, molecular docking, and non-equilibrium state.

Applications of Density Functional Theory to Biological and Bioinorganic Chemistry

Author : Mihai V. Putz
Publisher : Springer
ISBN 13 : 3642327508
Total Pages : 245 pages
Book Rating : 4.6/5 (423 download)

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Book Synopsis Applications of Density Functional Theory to Biological and Bioinorganic Chemistry by : Mihai V. Putz

Download or read book Applications of Density Functional Theory to Biological and Bioinorganic Chemistry written by Mihai V. Putz and published by Springer. This book was released on 2013-02-01 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: The series Structure and Bonding publishes critical reviews on topics of research concerned with chemical structure and bonding. The scope of the series spans the entire Periodic Table and addresses structure and bonding issues associated with all of the elements. It also focuses attention on new and developing areas of modern structural and theoretical chemistry such as nanostructures, molecular electronics, designed molecular solids, surfaces, metal clusters and supramolecular structures. Physical and spectroscopic techniques used to determine, examine and model structures fall within the purview of Structure and Bonding to the extent that the focus is on the scientific results obtained and not on specialist information concerning the techniques themselves. Issues associated with the development of bonding models and generalizations that illuminate the reactivity pathways and rates of chemical processes are also relevant. The individual volumes in the series are thematic. The goal of each volume is to give the reader, whether at a university or in industry, a comprehensive overview of an area where new insights are emerging that are of interest to a larger scientific audience. Thus each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years should be presented using selected examples to illustrate the principles discussed. A description of the physical basis of the experimental techniques that have been used to provide the primary data may also be appropriate, if it has not been covered in detail elsewhere. The coverage need not be exhaustive in data, but should rather be conceptual, concentrating on the new principles being developed that will allow the reader, who is not a specialist in the area covered, to understand the data presented. Discussion of possible future research directions in the area is welcomed. Review articles for the individual volumes are invited by the volume editors. Readership: research scientists at universities or in industry, graduate students Special offer For all customers who have a standing order to the print version of Structure and Bonding, we offer free access to the electronic volumes of the Series published in the current year via SpringerLink.