Protein Scaffolds
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Protein Scaffolds
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Author : Andrew K. Udit
language : en
Publisher: Humana
Release Date : 2019-06-19
Protein Scaffolds written by Andrew K. Udit and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-06-19 with Science categories.
This volume provides a wide range of methods and protocols detailing various protein structures as platforms for building architectures with targeted application. Chapters guide the readers through exploiting a number of protein scaffolds including virus nanoparticles, elastin and collagen peptides and proteins, and other protein templates for either building materials or presentation of ligands. Site-specific bioconjugation methods, some unique protein architectures, and techniques that exploit peptide amphiphile micelles and assembly of chaperones are also featured. 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. Authoritative and cutting-edge, Protein Scaffolds: Design, Synthesis, and Applications aims to ensure successful results in the study of this vital field.
Design Characterization And Applications Of Symmetric Protein Scaffolds A
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Author : David Leibly
language : en
Publisher:
Release Date : 2016
Design Characterization And Applications Of Symmetric Protein Scaffolds A written by David Leibly and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Proteins are essential macromolecules for all living organisms. They provide cellular structure and perform most of the metabolic functions essential for all life. The importance of proteins makes them the most studied and exploited macromolecules. We can exploit the structure of a protein to design a specific therapeutic to treat a disease or we can use proteins as biocatalysts for the efficient creation of molecules. In many instances, these applications of proteins are difficult to achieve. The work in this dissertation focuses on the development and evaluations of novel techniques to aid in the study and use of proteins. The first part of this dissertation focus on the creation of a series of symmetric oligomers to be used as crystallization scaffolds. Such scaffolds are intended to induce their symmetry onto asymmetric protein crystallization target proteins. The ability to determine the crystal structure can be essential for the creation of new targeted drugs or the better understanding of a biological process. Unfortunately many proteins fail to crystallize for reasons that are not well understood. It is thought that such induction of symmetry and variety of geometrically distinct scaffolds will aid in the crystallization of difficult-to-crystallize proteins. Preliminary results of these novel scaffolds and existing scaffolds are described. In the second part, applications of symmetric scaffolds for the creation of enzymatic materials are presented. These purely proteinaceous assemblies are designed to replicate previous described enzyme encapsulating materials. These materials typically improve enzyme reaction rates and product extraction. The final part of the dissertation focuses on the shell protein PduA from the 1,2-propanediol-utilization bacterial microcompartment (MCPs). These MCPs encapsulate metabolic pathways and contain volatile or toxic pathway intermediates. Research into turning these MCPs into bioreactors containing non-native enzymes is ongoing in many labs. Full realization of this technology relies on the encapsulation of new metabolic enzymes and transport of novel substrate and products through the shells. These processes are poorly understood, here structural studies of shell protein permutations. These permutations alter the topology of the shell protein allowing the scaffolding of proteins to the exterior surface of the MCPs. Finally, the efforts to elicited the interaction of specific targeting sequences to shell protein by x-ray crystallography are discussed.
Engineered Protein Scaffolds As Tools For Studying Intracellular Proteins
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Author : Sabriyeh Alibai
language : en
Publisher:
Release Date : 2018
Engineered Protein Scaffolds As Tools For Studying Intracellular Proteins written by Sabriyeh Alibai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with categories.
Molecules that bind to targets with high specificity and affinity are used as therapeutic and diagnostic agents in medicine and research. Protein and non-protein ligands are used for introduction of mutations within the binding region to increase the binding affinity. Phage-display technology is used to screen multiple scaffolds against target proteins to select for high affinity binders. Scaffolds are displayed on phage particles and can be tested for binding to targets with standard binding assays. Various target proteins are encoded by essential genes to disrupt cellular proliferation and were identified as fitness genes in CRISPR screens. Altogether, utilizing the two technologies facilitates making and screening of binders to intracellular targets and accelerates the production of highly efficient synthetic binders. To develop and optimize the technique, the Sidhu lab generated 27 protein scaffold libraries that were tested against 25 target proteins and selected several variants for further analysis in mammalian cells.
Protein Scaffolds For Cell Culture
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Author : Ana Isabel Machado Roque
language : en
Publisher:
Release Date : 2013
Protein Scaffolds For Cell Culture written by Ana Isabel Machado Roque and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with categories.
Metalloprotein Engineering Using Heme Protein Scaffolds To Investigate The Oxidation Of Endogenous Aromatic Amino Acids And Exogenous Substrates
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Author : Thomas Daniel Pfister
language : en
Publisher:
Release Date : 2006
Metalloprotein Engineering Using Heme Protein Scaffolds To Investigate The Oxidation Of Endogenous Aromatic Amino Acids And Exogenous Substrates written by Thomas Daniel Pfister and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with categories.
Protein engineering by rational design has been used to study heme proteins and artificial Mn-salen containing metalloenzymes using heme protein scaffolds. Heme proteins perform a wide variety of functions including the catalysis of numerous different reactions. Some of the structural features involved in conferring these functional properties have been examined in this thesis. Heme protein models have been made of peroxidases and P450 to gain insight into the native function of these enzymes. The role of role of redox active amino acids in heme proteins was studied by mutating Trp an Tyr residues in cytochrome c peroxidase (CcP). Sequential mutation of these residues resulting in increased lifetime of the compound I intermediate. An Engineered Trp in the active site of myoglobin (Mb) was used to mimic bound substrate. The Trp was stoichiometrically hydroxylated to 6-hydroxytryptophan. Factors required to engineer metal binding sites were studied by the redesign of an engineered manganese binding site in CcP. Kinetic parameters and crystal structures of the protein demonstrate the importance of the metal and ligands in engineering metal binding sites. Finally the role of cofactors in catalysis was probed by dually anchoring a Mn-salen complex in the active site of a heme protein scaffold (Mb). Dual anchoring was shown to increase ee and rate in this artificial metalloenzyme. It is concluded that the control of reactive intermediates, presence of appropriate substrate binding sites and the choice of an appropriate scaffold and cofactor are essential in engineering protein models and biocatalysts.
Engineering Scaffolds For Modular Proteins Assembly
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Author : Qi Chen
language : en
Publisher:
Release Date : 2017
Engineering Scaffolds For Modular Proteins Assembly written by Qi Chen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Proteins associate with each other to form complex collaborative network in order to perform certain functions, such as multi-step reactions in metabolic process, receiving and transferring signals in signaling pathways, and host cell infection. Scaffolds have evolved in nature to organize proteins to enhance collaborative efficiency. Inspired by features and advantages of natural scaffolds, synthetic scaffolds are developed for customized applications by organizing proteins into functional modules. ☐ In the first objective of this thesis, DNA was used as a scaffold to organize 5 proteins involved in cellulosic fuel cell. DNA scaffolds feature simple hybridization rules and precise programming of structures. These features allow precise control of order and distance of the 5 proteins, enabling investigation on substrate channeling effect of adjacent enzymes and synergistic effect of enzymes in close proximity. Although DNA can be programmed into structures in 1 to 3-dimenions, the heavy programming load and cost prevented the use of DNA as 3-dimensional scaffolds, leading to the exploration of native 3-dimensional scaffolds. ☐ In the second objective, functionalization of protein nanoparticles was investigated to develop 3-dimensional scaffolds, which plays an important role in signal amplification of biosensors, drug delivery and biocatalysis. Native protein nanoparticles can self-assemble into stable and biocompatible structures. Previous functionalization methods can lead to incorrect folding of 3-dimensional structures or loss of control over specific modifications that limit and complicate the application of protein nanoparticles. To develop a simple and modular functionalization method, an enzyme-mediated ligation strategy was investigated; sortase-mediated ligation enabled specific conjugation of functional proteins onto E2 protein nanoparticles from Bacillus stearothermophilus, a model 3-dimesnional scaffold. ☐ Finally, to further simplify the use of native 3-dimensional scaffolds, one-pot synthesis of protein scaffolds that are ready to use after production were developed. It is inspired by the biogenesis of outer membrane vesicles (OMVs), which naturally form into proteoliposomes during growth cycle of bacteria. They feature the simultaneous formation of nanostructures and displaying of functional proteins. Membrane proteins were investigated as anchors for displaying heterologous proteins, which allowed simultaneous display of proteins of different functionalities, such as detection and reporter moieties. One-pot synthesized sensors were generated based on OMVs and successful antigen detection by ELISA and cell imaging were demonstrated. ☐ In summary, three different types of synthetic scaffolds were engineered for customized applications and novel functionalization strategies have been developed for 3-dimensional scaffolds. The findings discussed in this thesis can expand the applications of synthetic scaffolds.
Evolvability Of Designed Protein Scaffolds For Binding Affinity And Catalytic Activity
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Author : Maren Butz
language : en
Publisher:
Release Date : 2011
Evolvability Of Designed Protein Scaffolds For Binding Affinity And Catalytic Activity written by Maren Butz and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Hyperthermophilic Protein Scaffolds For Engineering Biomolecular Recognition
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Author : Nimish Gera
language : en
Publisher:
Release Date : 2012
Hyperthermophilic Protein Scaffolds For Engineering Biomolecular Recognition written by Nimish Gera and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
Electrospun Plant Protein Scaffolds With Fibers Oriented Randomly And Evenly In Three Dimensions For Soft Tissue Engineering Applications
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Author : Shaobo Cai
language : en
Publisher:
Release Date : 2013
Electrospun Plant Protein Scaffolds With Fibers Oriented Randomly And Evenly In Three Dimensions For Soft Tissue Engineering Applications written by Shaobo Cai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with categories.
Engineering Bivalency And Bispecificity In Protein Therapeutics And Protein Scaffold Development
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Author : Cassie J. Liu
language : en
Publisher:
Release Date : 2016
Engineering Bivalency And Bispecificity In Protein Therapeutics And Protein Scaffold Development written by Cassie J. Liu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Multivalent and multifunctional proteins are abundant in nature. The avidity effect, a core principle of multivalent molecules, allows these proteins to tune biological functions and responses across a large dynamic range with varying specificity. Many protein therapeutics also take advantage of this evolvable tunability, the canonical example being the antibody. This thesis consists of two separate sections. Section One: I focus on the avidity effect of multivalent proteins and its therapeutic uses. As an illustrative case, our lab had previously created a protein variant that monomerically binds the c-MET tyrosine kinase. By dimerizing this variant, we find that we greatly increase its efficacy through increased apparent affinity to cell surface c-MET. Section Two: I focus on multispecific proteins and their uses in medical applications. Most current therapeutic protein scaffolds are single protein domains with monomeric binding and function. Combining these scaffolds to create multispecific functionality presents manufacturing challenges. Here the vascular endothelial growth factor (VEGF) protein is used as a stable, naturally bivalent scaffold for engineering bispecific proteins.