[PDF] Towards The Rational Design Of Peptide Based Enzyme Like Assemblies eBook

Author : Swapil Paliwal
Publisher :
Page : 77 pages
File Size : 23,46 MB
Release : 2017
Category :
ISBN :

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Rational design and analysis of protein databanks via data-driven algorithms have significantly accelerated drug discovery, in particular, and a wide range of biological research topics, in general, during last decades. A similar approach is gaining momentum in materials research but has garnered limited attention in areas such as the design of soft interfaces formed by solid-binding peptides at solid materials interfaces. The GEMSEC Laboratory (Genetically-Engineered Materials Science and Engineering Center) has been working towards expanding this strategy in materials research via the development of peptide-based bioelectronic interfaces incorporating solid-binding peptides and single layer materials and, thereby, bridge biology to solid-state devices such as graphene field-effect transistors. We are presented with a challenge in peptide-based materials design as, in general, a vast store of relevant data is not available in materials science that is similar to protein databanks that are available in fields such as molecular biology. Thus, there is need for a knowledge-base, but that requires decades of research to draw on. In the present research, this was accounted by utilizing an innovative integration of combinatorial selection of solid-binding peptides, their rational design and bioinformatics based approach to model specific peptide-material interactions. From a data-base of 10s if not hundreds of peptides selected by this approach, the basis of the present method is to generate libraries of materials specific super-peptides that can attach, assemble and perform specific functions on atomically-flat material surfaces. As solid-state systems, single atomic layer materials, such as graphene and those that provide flat surfaces, such as quartz, have been chosen. Using these libraries, peptides that are capable of binding to their counterpart solid material of interest can be identified by performing combinatorial selection based on phage display approach. Typically, 50+ individual peptides are selected from of an original pool of ~1015 variants, which are then classified based on their binding strength using, e.g., fluorescent microscopy. Needleman-Wunsch based similarity analysis and machine learning algorithms are then used to create a scoring matrix capable of identifying robust and weak binders for the particular material amongst millions of random permutations of amino acid sequences in the peptides. The most powerful of these binders are fed into a decision-tree based rational design consisting of selection rules on hydropathicity, iconicity, aromaticity, and polarity of peptides identified to be capable of self-assembly from the previously conduted experiments. This process filters peptides and identifies those that are capable of strongly binding to as well as readily assembling on the atomically flat solid crystals. These model-based designed peptide sequences are then chemically synthesized and subsequently evaluated experimentally in terms of their binding and assembly characteristics using, e.g., atomic force microscopy to validate the success of the predictive model. As the experimental data become available in the assembly of the peptides under specific experimental parameters that are related to the particular chemistry of the sequences, the approach progressively creates a better outcome. Consequently, the model upon each experimental validation is further improvised and provides further knowledge and supply related sequences to the library to advance peptide-guided functional solid-state materials for practical nanotechnology and nanomedicine applications.

Author : Karthikan Rajagopal
Publisher :
Page : 235 pages
File Size : 34,50 MB
Release : 2007
Category :
ISBN : 9781109861860

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The significance of peptide design in the context of self-assembly and its relationship to the nanostructure was studied by designing a series of peptides derived from MAX1. Evolving from these studies is an understanding of the relationship between molecular level peptide structure and the nanoscale supra-molecular morphology. Based on this, it has been shown that alternate morphologies distinct from those observed with the gel forming peptides, such as non-twisting laminates or tube-like structures can be constructed. Lastly, it is shown that within amphiphilic beta-hairpin peptides, the turn sequence can be used as a design element to control the stiffness of the hydrogel which is an important property from an application point of view. These studies demonstrate that rationally designed peptides are robust building blocks to construct functional materials via molecular self-assembly.

Author : John Howl
Publisher : Springer Science & Business Media
Page : 263 pages
File Size : 17,44 MB
Release : 2008-02-02
Category : Science
ISBN : 1592598773

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Hands-on experts describe in step-by-step detail the key methodologies of contemporary peptide synthesis and illustrate their numerous applications. The techniques presented include protocols for chemical ligation, the synthesis of cyclic and phosphotyrosine-containing peptides, lipoamino acid- and sugar-conjugated peptides, and peptide purification and analyses. Additional chapters detail methodologies and instrumentation for high-throughput peptide synthesis, many different applications of peptides as novel research tools and biological probes, and the design and application of fluorescent substrate-based peptides that can be used to determine the selectivity and activity of peptidases. A practical guide to the identification of proteins using mass spectrometric analyses of peptide mixtures is also included.

Author : Timothy Deming
Publisher : Springer Science & Business Media
Page : 184 pages
File Size : 14,86 MB
Release : 2012-01-10
Category : Technology & Engineering
ISBN : 3642271391

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Synthesis of Polypeptides by Ring-Opening Polymerization of α-Amino Acid N-Carboxyanhydrides, by Jianjun Cheng and Timothy J. Deming.- Peptide Synthesis and Self-Assembly, by S. Maude, L. R. Tai, R. P. W. Davies, B. Liu, S. A. Harris, P. J. Kocienski and A. Aggeli.- Elastomeric Polypeptides, by Mark B. van Eldijk, Christopher L. McGann, Kristi L. Kiick andJan C. M. van Hest.- Self-Assembled Polypeptide and Polypeptide Hybrid Vesicles: From Synthesis to Application, by Uh-Joo Choe, Victor Z. Sun, James-Kevin Y. Tan and Daniel T. Kamei.- Peptide-Based and Polypeptide-Based Hydrogels for Drug Delivery and Tissue Engineering, by Aysegul Altunbas and Darrin J. Pochan.-

Author : Eric Mark Krauland
Publisher :
Page : 141 pages
File Size : 20,62 MB
Release : 2007
Category :
ISBN :

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(cont.) Biopanning a random peptide YSD library and subsequent characterization of the identified binding partners revealed the importance of multiple basic amino acids in the binding event. Study of rationally designed basic peptides revealed a preference for those amino acids to be spaced in such a manner that maximized simultaneous interaction with the surface. Fusing peptides to maltose binding protein (MBP) allowed for quantitative affinity measurement with the best peptides having low nanomolar equilibrium dissociation constants. Finally, peptides were demonstrated as facile affinity tags for protein immobilization in micro-patterning and biosensor assays.

Author : Sotirios Koutsopoulos
Publisher : Woodhead Publishing
Page : 655 pages
File Size : 11,63 MB
Release : 2017-11-16
Category : Technology & Engineering
ISBN : 0081007426

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Peptide Applications in Biomedicine, Biotechnology and Bioengineering summarizes the current knowledge on peptide applications in biomedicine, biotechnology and bioengineering. After a general introduction to peptides, the book addresses the many applications of peptides in biomedicine and medical technology. Next, the text focuses on peptide applications in biotechnology and bioengineering and reviews of peptide applications in nanotechnology. This book is a valuable resource for biomaterial scientists, polymer scientists, bioengineers, mechanical engineers, synthetic chemists, medical doctors and biologists. Presents a self-contained work for the field of biomedical peptides Summarizes the current knowledge on peptides in biomedicine, biotechnology and bioengineering Covers current and potential applications of biomedical peptides

Author : Xuehai Yan
Publisher : John Wiley & Sons
Page : 933 pages
File Size : 48,12 MB
Release : 2024-02-09
Category : Science
ISBN : 3527841253

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Peptide Self-Assembly and Engineering State-of-the-art research in peptide self-assembly, with coverage of fundamental aspects of how peptides self-assemble and an extensive number of applications Peptide Self-Assembly and Engineering: Fundamentals, Structures, and Applications (2V set) covers the latest progresses in the field of peptide self-assembly and engineering, including the fundamental principles of peptide self-assembly, new theory of nucleation and growth, thermodynamics and kinetics, materials design rules, and precisely controlled structures and unique functions. The broad contents from this book enable readers to obtain a systematical and comprehensive knowledge in the field of peptide self-assembly and engineering. Contributed by the leading scientists and edited by a highly qualified academic and an authority in the field, Peptide Self-Assembly and Engineering includes information on: Emerging areas in peptide assembly, such as immune agents, bioelectronics, energy conversion, flexible sensors, biomimetic catalysis, and more Existing applications in biomedical engineering, nanotechnology, and photoelectronics, including tissue engineering, drug delivery, and biosensing devices History of peptide self-assembly for design of functional materials and peptides’ unique mechanical, optical, electronic, and biological properties Various solvent conditions, such as pH, ionic strength, and polarity, that can affect the structure and stability of peptide assemblies A very comprehensive reference covering the latest progresses in the field of peptide self-assembly and engineering, Peptide Self-Assembly and Engineering is an essential resource for all scientists performing research intersecting with the subject, including biochemists, biotechnologists, pharmaceutical chemists, protein chemists, materials scientists, and medicinal chemists.

Author : Jennifer J. McManus
Publisher : Humana
Page : 266 pages
File Size : 12,40 MB
Release : 2020-08-08
Category : Science
ISBN : 9781493996803

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This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. 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. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.