Theory Design And Characterization Of Protein Symmetry Combination Materials
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Theory Design And Characterization Of Protein Symmetry Combination Materials
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Author : Joshua Laniado
language : en
Publisher:
Release Date : 2020
Theory Design And Characterization Of Protein Symmetry Combination Materials written by Joshua Laniado and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with categories.
ABSTRACT OF THE DISSERTATIONTheory, Design and Characterization of Protein Symmetry Combination Materials by Joshua Laniado Doctor of Philosophy in the Molecular Biology Interdepartmental Doctoral Program: Biochemistry, Biophysics & Structural Biology University of California, Los Angeles, 2020 Professor Todd O. Yeates, Chair Nature has evolved a plethora of sophisticated protein complexes to carry out fundamental biological processes. While most of these exquisite macromolecular machines exhibit complex architectures, many are composed of only a few different types of subunits. Understanding how protein molecules combine to form these remarkable self-assembling structures only makes sense in the light of symmetry. By limiting the number of distinct interactions required between individual subunits, symmetry offers a simpler route for the evolution of supramolecular assemblies such as viral capsids and bacterial microcompartments. Principles of symmetry and self-assembly have invigorated recent efforts in molecular engineering giving rise to a growing suite of novel protein materials such as finite cages and extended crystalline arrays. These designed assemblies are rapidly finding applications in areas as diverse as vaccine design, atomic imaging, enzyme scaffolding and molecular delivery. Despite significant advances in computational approaches and design strategies, constructing these materials remains extremely challenging. Here, we address key experimental and theoretical limitations to improve the prospects for the routine design of novel symmetric protein materials. In Chapter 1, we review current methodologies for designing self-assembling protein nanomaterials. A first approach presented the idea that when two separate symmetric oligomers associate in some geometrically defined way, a structure with higher symmetry can be obtained through self-assembly. There, an alpha-helical linker is used to connect two oligomeric components and to control their relative geometry. A second approach does not involve genetic fusion but relies instead on the computational design of a novel protein-protein interface. After reviewing the successful constructions resulting from both methods, challenges and limitations are discussed. In the fusion approach, the inherent flexibility of the alpha helical linker can lead to the formation of unintended assemblies. Alternatively, the interface design strategy exhibits limited success in predicting viable protein interfaces. The prevalence of such limitations dramatically hinders the creation of novel materials, motivating the development of alternate strategies. In the next chapter, we introduce a new approach for the design of symmetric self-assembling nanomaterials. Building upon the fusion approach, the original alpha-helical linker is replaced with a heterodimeric coiled coil as an attempt to reduce flexibility. Further, the use of a known heterodimeric interface to combine component oligomers alleviates the challenges associated with de novo interface design. Ten symmetric protein cages were designed using this method among which two were structurally characterized. One design assembled as intended while the other crystallized in an alternate form. Geometric distinctions between the two help explain the different degrees of success, leading to crucial lessons and establishing clearer principles for the creation of novel nanoscale protein architectures. While some experimental aspects have been addressed, only a small fraction of the possible design space has been explored. That space, which is anticipated to offer a multitude of symmetry-based combinations, has not been described in theory. In Chapter 3, we articulate all of the possible kinds of protein-based materials that can be created by combining two symmetric oligomers. Specifically, 13 types of cages, 35 types of 2-D layers and 76 types of 3-D crystals are identified as possible targets for design. We lay out a complete rule set for constructing all such symmetry combination materials (SCMs) and introduce a unified system for parameterizing and searching the construction space for each case. This theoretical and computational study provides a blueprint for a blossoming area of macromolecular design. Owing to the complexity and our limited understanding of the rules that govern protein behavior, designing protein-protein interfaces remains challenging. Current approaches rely on empirical or knowledge-based energy functions and optimization algorithms that often fail to produce stable interfaces. On the other hand, there is growing evidence that the database of known protein structures is now sufficiently large to cover the structural landscape of protein interfaces. In Chapter 4, we argue that carefully-selected structural motifs can be used as templates for interface design. We introduce Nanohedra, a fragment-based docking tool that harnesses the power of our theoretical framework to enable the design of all possible SCMs. Prospective designs of symmetric materials are proposed along with a retrospective analysis of recent design studies. In this analysis, our tool recapitulates all successful designs while poorly ranking failed ones. With a user-friendly interface and a unified protocol for symmetric protein design, Nanohedra enables the creation of a universe of novel nanomaterials and opens new avenues for nanobiotechnology.
Protein Design
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Author : Valentin Köhler
language : en
Publisher: Humana Press
Release Date : 2014-09-11
Protein Design written by Valentin Köhler and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-09-11 with Science categories.
Protein Design: Method and Applications, Second Edition expands upon the previous edition with current, detailed ideas on how to approach a potential protein design project. With new chapters on metals as structure-forming elements and functional sites, the design and characterization of fluorinated proteins, top-down symmetric deconstruction and the design of protein libraries and novel or repurposed enzymes. Written in the highly successful Methods in Molecular Biologyseries 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 intuitive, Protein Design: Method and Applications, Second Edition provides a number of practical protocols and instructive reviews to aid in the creation of new experiments.
Characterization Design And Application Of Natural And Engineered Symmetric Protein Complexes
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Author : Yuxi Liu
language : en
Publisher:
Release Date : 2018
Characterization Design And Application Of Natural And Engineered Symmetric Protein Complexes written by Yuxi Liu 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.
We frequently find proteins exist in oligomeric forms in nature. The abundance of dimers, trimers and tetramers with cyclic or dihedral symmetries in the Protein Data Bank is a good testimony. Even more, it is not rare to find proteins form highly ordered, symmetric, large complexes. These oligomeric forms are usually essential for their functions. Ferritin forms an octahedral cage with 24 subunits to store iron; some virus capsid proteins assemble into icosahedral cages; vaults, which are large dihedral particles widely conserved in eukaryotes, have biological functions yet to be discovered. These fascinating structures inspire three types of questions: How do individual subunits interact form such symmetric complexes? How can we reproduce such complexes with protein engineering? How do we put engineered symmetric protein complexes to application? My thesis work consists of projects addressing all three questions. My first project, described in Chapter 1, concerns bacterial microcompartments (MCP), which are large proteinaceous organelles enclosed by an icosahedral or pseudo-icosahedral shell. MCPs usually enclose special metabolic pathways that are inefficient or toxic in the cytosol. To do so, MCPs must form a sealed barrier with its shell proteins. It was hypothesized that at least one type of the proteins forming the shell of MCPs has to be pentameric instead of hexameric. Indeed, we proved that the BMV proteins, a family of protein highly conserved in MCP operons, formed pentamers in solution. Together with other crystallographic evidence, we conclude BMV proteins form pentamers to cap and seal the MCP shell. In addition to MCPs, I worked on another natural oligomeric protein, bactofilin. Bactofilins are fiber-forming proteins that are widely conserved among bacteria. These proteins have roles in diverse biological functions including but not limited to cell motility, cell wall synthesis and modification. Chapter 2 describe my preliminary biochemical and structural work on bactofilins. Next, I moved on to symmetry-based engineering protein complexes. In Chapter 3, I included a recent review paper on the theory and successes in symmetry-based protein engineering that I participated in preparing. Designed complexes need to be validated at high resolution with X-ray crystallography, but for a long time, the low yield and solubility of the designs complicated their validation. In Chapter 4, we show that mutating solvent-exposed side chains to charged amino acids improved the solubility of a previously low yield tetrahedral design and enabled validation by crystallography. Next, I advanced to a bigger challenge in designing symmetric nanoparticles--icosahedral particles. Icosahedral particles are made up of 60 asymmetric units, as compared to 12 in tetrahedral particles, making them much more difficult to design with accuracy. I was able to validate three different icosahedral design with crystallography, making them the largest designed protein assemblies ever crystallized to date. This work is described in Chapter 5. Additionally, I have made other independent design efforts, one to combine DNA and protein as building materials to design tetrahedral complexes, another to design protein sheets with layer group symmetry. These efforts are documented in Chapter 6.I In the last chapter, I utilized the validated tetrahedral designs as a scaffold in cryo-electron microscope (cryo-EM) for small targets. Despite recent advancements in cryo-EM techniques, small targets remain difficult. By arranging small targets around tetrahedral particles, we can overcome the size limit and provide multiple views to alleviate the commonly seen orientation preference. My project used a type of versatile adaptor protein, designed ankyrin repeat proteins (DARPins), to connect the tetrahedral particles to the imaging targets. We show that the resulting construct is amenable to structural analysis by single particle cryo-EM, allowing us to identify and solve the structure of the attached DARPin at near-atomic detail. The result demonstrates that proteins considerably smaller than the theoretical limit of 50 kDa for cryo-EM can be visualized clearly when arrayed in a rigid fashion on a symmetric designed protein scaffold. Because the amino acid sequence of a DARPin can be chosen to confer tight binding to various other proteins, the system provides a future route for imaging diverse macromolecules, potentially broadening the application of cryo-EM to proteins of typical size in the cell. In conclusion, my thesis work contributes to the understanding of natural oligomeric complexes, expands our capacity in designing symmetric assemblies, and puts forward an example of a useful application of the designed assemblies.
Protein Self Assembly
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Author : Jennifer J. McManus
language : en
Publisher: Humana
Release Date : 2020-08-08
Protein Self Assembly written by Jennifer J. McManus and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-08-08 with Science categories.
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.
Journal
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Author : American Chemical Society
language : en
Publisher:
Release Date : 2004
Journal written by American Chemical Society and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with Chemistry categories.
Bioinspired Structures And Design
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Author : Wole Soboyejo
language : en
Publisher: Cambridge University Press
Release Date : 2020-09-17
Bioinspired Structures And Design written by Wole Soboyejo and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-09-17 with Science categories.
Human cortical bone as a structural material : Hierarchical design and biological degradation / Robert Ritchie and Elizabeth A. Zimmermann -- Bio-inspiration from nacre / Nima Rahbar and Sina Askarinejad -- Bio-inspiration from bamboo / Ting Tan and Wole Soboyejo.
Physics Briefs
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Author :
language : en
Publisher:
Release Date : 1992
Physics Briefs written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992 with Physics categories.
When Machines Play Chopin
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Author : Katherine Hirt
language : en
Publisher: Walter de Gruyter
Release Date : 2010-05-26
When Machines Play Chopin written by Katherine Hirt and has been published by Walter de Gruyter this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-05-26 with Literary Criticism categories.
When Machines Play Chopin brings together music aesthetics, performance practices, and the history of automated musical instruments in nineteenth-century German literature. Philosophers defined music as a direct expression of human emotion while soloists competed with one another to display machine-like technical perfection at their instruments. When Machines Play Chopin looks at this paradox between thinking about and practicing music to show what three literary works say about automation and the sublime in art.
Cumulated Index Medicus
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Author :
language : en
Publisher:
Release Date : 1999
Cumulated Index Medicus written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1999 with Medicine categories.
Protein Cages
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Author : Brendan P. Orner
language : en
Publisher: Humana
Release Date : 2016-08-23
Protein Cages written by Brendan P. Orner and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-08-23 with Science categories.
This volume emphasizes new techniques to help understand protein cages and to apply them to a variety of technologies, highlighting the expertise of researchers based on three continents. Protein cages are currently inspiring diverse scientific disciplines and are therefore at the crossroads of extremely widely-scoped research, which is reflected in the detailed chapters of Protein Cages: Methods and Protocols. From nanomaterials studies and iron particles to computational strategies and Atomic Force Microscopy, the chapters herein collectively provide an introduction to the rich world of protein cage research and specific techniques to understand and exploit this fascinating class of proteins. Written in the highly successful Methods in Molecular Biology series format, chapters begin with an introduction to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and cutting-edge, Protein Cages: Methods and Protocols will help to inspire and further propel the current multi-disciplinary enthusiasm in studying and discovering new applications for protein cages.