Multiscale Molecular Dynamics Studies of Peptide Aggregation and Protein-ligand Association PDF Download
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Author: Andrea Magno
Publisher:
ISBN:
Category :
Languages : en
Pages : 153
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Book Description
Author: Andrea Magno
Publisher:
ISBN:
Category :
Languages : en
Pages : 153
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Book Description
Author: Hwan Kyu Lee
Publisher:
ISBN:
Category :
Languages : en
Pages : 358
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Book Description
Author: Fabio Trovato
Publisher: Frontiers Media SA
ISBN: 2889740250
Category : Science
Languages : en
Pages : 322
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Author: Sandra Steiner
Publisher:
ISBN:
Category :
Languages : en
Pages : 139
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Author: Gurpreet Singh
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Author: Subhadra Thapa
Publisher:
ISBN:
Category : Molecular dynamics
Languages : en
Pages : 0
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Book Description
Peptide self-assembly plays an important role in biomedical and material discovery, offering a promising insight for development of nanostructures, serving as bio-materials for drug delivery. The tendency of peptide aggregating to certain nanostructures help in forming the basis for tissue engineering scaffolds and enabling the development of innovative diagnostic and therapeutic biologics. The designing of peptide through experiment is expensive and time consuming. The virtual screening of natural tendency of peptide aggregation is cost effective to evaluate numerous designs and prioritize synthesis and characterization efforts. We have characterized the propensity of peptide aggregation utilizing the all-atom (AA), and coarse-grained (CG) simulations. We have studied the widely explored di-phenylalanine (FF) and di-Glycine (GG) as a toy model to benchmark the AA and CG simulation. Furthermore, we have investigated the intrinsic properties such as the system size, terminal modification and salinity and their effects in peptide aggregation. We have used the aggregation propensity (AP) metrics to differentiate between the aggregated and non-aggregated structure. We have also proposed the new AP metrics called APcontact which is also able to differentiate between the aggregated and non-aggregated structure.The second project includes the top-down approach to screen the peptideâs tendency to aggregate to the hydrogel like structure. We started with predicting the AP scores for each amino acid using the optimization method, L-BFGS-B, to refine our initially assigned AP values. The initial AP values was assigned based on the physiochemical properties of the amino acids, such as hydrophobicity, aromaticity, polarity, tendency of forming beta-sheets, alpha-helix etc. This allows us to screen the various peptides of varying length and their tendency to aggregate. We further simulate those top list using CG simulation followed by all-atom simulation and the top list of the peptides from the all-atom simulation were further selected for synthesis. The final stage of this research involves the co-assembly of peptides with optimized AP scores to explore the formation of diverse nanostructures These discoveries establish a foundation for prospective virtual screening of nanostructures assembled by peptides and the computer-aided design of biologics.
Author: Massimiliano Bonomi
Publisher: Humana
ISBN: 9781493996100
Category : Science
Languages : en
Pages : 581
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Book Description
This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.
Author: Defang Ouyang
Publisher: John Wiley & Sons
ISBN: 1118573994
Category : Science
Languages : en
Pages : 350
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Book Description
Molecular modeling techniques have been widely used in drug discovery fields for rational drug design and compound screening. Now these techniques are used to model or mimic the behavior of molecules, and help us study formulation at the molecular level. Computational pharmaceutics enables us to understand the mechanism of drug delivery, and to develop new drug delivery systems. The book discusses the modeling of different drug delivery systems, including cyclodextrins, solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein/peptide formulations, non-viral gene delivery systems, drug-protein binding, silica nanoparticles, carbon nanotube-based drug delivery systems, diamond nanoparticles and layered double hydroxides (LDHs) drug delivery systems. Although there are a number of existing books about rational drug design with molecular modeling techniques, these techniques still look mysterious and daunting for pharmaceutical scientists. This book fills the gap between pharmaceutics and molecular modeling, and presents a systematic and overall introduction to computational pharmaceutics. It covers all introductory, advanced and specialist levels. It provides a totally different perspective to pharmaceutical scientists, and will greatly facilitate the development of pharmaceutics. It also helps computational chemists to look for the important questions in the drug delivery field. This book is included in the Advances in Pharmaceutical Technology book series.
Author: Sidney A. Simon
Publisher: Academic Press
ISBN: 0080925855
Category : Science
Languages : en
Pages : 606
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Book Description
This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction
Author: Monika Fuxreiter
Publisher: Springer Science & Business Media
ISBN: 1461406595
Category : Medical
Languages : en
Pages : 210
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Book Description
Detailed characterization of fuzzy interactions will be of central importance for understanding the diverse biological functions of intrinsically disordered proteins in complex eukaryotic signaling networks. In this volume, Peter Tompa and Monika Fuxreiter have assembled a series of papers that address the issue of fuzziness in molecular interactions. These papers provide a broad overview of the phenomenon of fuzziness and provide compelling examples of the central role played by fuzzy interactions in regulation of cellular signaling processes and in viral infectivity. These contributions summarize the current state of knowledge in this new field and will undoubtedly stimulate future research that will further advance our understanding of fuzziness and its role in biomolecular interactions.
