Multistate Computational Protein Design
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Multistate Computational Protein Design
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Author : James A. Davey
language : en
Publisher:
Release Date : 2016
Multistate Computational Protein Design written by James A. Davey 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.
Engineering Of Multi Substrate Enzyme Specificity And Conformational Equilibrium Using Multistate Computational Protein Design
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Author : Antony D. St-Jacques
language : en
Publisher:
Release Date : 2018
Engineering Of Multi Substrate Enzyme Specificity And Conformational Equilibrium Using Multistate Computational Protein Design written by Antony D. St-Jacques 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.
The creation of enzymes displaying desired substrate specificity is an important objective of enzyme engineering. To help achieve this goal, computational protein design (CPD) can be used to identify sequences that can fulfill interactions required to productively bind a desired substrate. Standard CPD protocols find optimal sequences in the context of a single state, for example an enzyme structure with a single substrate bound at its active site. However, many enzymes catalyze reactions requiring them to bind multiple substrates during successive steps of the catalytic cycle. The design of multi-substrate enzyme specificity requires the ability to evaluate sequences in the context of multiple substrate-bound states because mutations designed to enhance activity for one substrate may be detrimental to the binding of a second substrate. Additionally, many enzymes undergo conformational changes throughout their catalytic cycle and the equilibrium between these conformations can have an impact on their substrate specificity. In this thesis, I present the development and implementation of two multistate computational protein design methodologies for the redesign of multi-substrate enzyme specificity and the modulation of enzyme conformational equilibrium. Overall, our approaches open the door to the design of multi-substrate enzymes displaying tailored specificity for any biocatalytic application.
Computational Protein Design
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Author : Ilan Samish
language : en
Publisher: Methods in Molecular Biology
Release Date : 2018-12-17
Computational Protein Design written by Ilan Samish and has been published by Methods in Molecular Biology this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-17 with Science categories.
Protein Engineering And Design
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Author : Sheldon J. Park
language : en
Publisher: CRC Press
Release Date : 2009-09-25
Protein Engineering And Design written by Sheldon J. Park and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-09-25 with Medical categories.
Experimental protein engineering and computational protein design are broad but complementary strategies for developing proteins with altered or novel structural properties and biological functions. By describing cutting-edge advances in both of these fields, Protein Engineering and Design aims to cultivate a synergistic approach to protein science
Molecular Modeling And Artificial Intelligence For Computational Protein Design
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Author : Jelena Vucinic
language : en
Publisher:
Release Date : 2021
Molecular Modeling And Artificial Intelligence For Computational Protein Design written by Jelena Vucinic and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
Proteins are fundamental components of life. Over the billions of years of evolution, proteins have evolved to perform certain functions better and faster or to achieve new functions in order to pursue the biological needs under diverse and changing conditions. The field of protein engineering is becoming a research domain of great importance. The interest of proteins with new or improved properties is increasing in health, nano/biotechnology and green chemistry.Computational Protein Design (CPD) plays a critical role in advancing the field of protein engineering and accelerating the delivery of novel proteins displaying high specificity, high efficiency and better stability. The CPD problem can be formalized as an optimization problem. Using an all-atom energy function and a reliable search method, CPD tries to identify amino acid sequences that fold into a target structure and ultimately perform a desired function. The traditional Single State Protein Design (SSD) contrasts with the increasing evidence that proteins do not remain in a unique conformational state but rather sample conformational ensembles. In this thesis we propose a MultiState Design (MSD) method which aims at alleviating SSD limitations by simultaneously considering several conformational states.In the second part of this thesis, MSD was applied on two projects that led to an experimental characterization and validation. These two projects concern two application domains: health and white biotechnologies. The first one targets GH11 Xylanases. To understand the molecular basis underlying its thermal stability and activity, Molecular Dynamics simulations were used and revealed useful characteristics to design this enzyme. This produced GH11 xylanases with improved thermal stability and catalytic activity.The second project concerns the design of a synthetic humanized nanobody scaffold. The resulting nanobody is highly expressed and shows suitable affinity with different CDR loops.
Introducing Specificity Into Protein Design
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Author : James Joseph Havranek
language : en
Publisher:
Release Date : 2002
Introducing Specificity Into Protein Design written by James Joseph Havranek and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2002 with categories.
Protein Design And Structure
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Author : Rossen Donev
language : en
Publisher: Academic Press
Release Date : 2022-05-06
Protein Design And Structure written by Rossen Donev and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-05-06 with Science categories.
Protein Design and Structure, Volume 130 in the Advances in Protein Chemistry and Structural Biology series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of authors. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Advances in Protein Chemistry and Structural Biology series Includes the latest information on protein design and structure
Development And Validation Of A Structure Based Computational Method For The Prediction Of Protein Specificity Profiles
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Author : Olivier Gagnon
language : en
Publisher:
Release Date : 2019
Development And Validation Of A Structure Based Computational Method For The Prediction Of Protein Specificity Profiles written by Olivier Gagnon and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with categories.
Post-translational modification (PTM) of proteins by enzymes such as methyltransferases, kinases and deacetylases play a crucial role in the regulation of many metabolic pathways. Determining the substrate scope of these enzymes is essential when studying their biological role. However, the combinatorial nature of possible protein substrate sequences makes experimental screening assays intractable. To predict new substrates for proteins, various computational approaches have been developed. Our method relies on crystallographic data and a novel multistate computational protein design algorithm. We previously used our method to successfully predict four new substrates for SMYD2 (Lanouette S & Davey J.A., 2015), doubling the number of known targets for this PTM enzyme that has been difficult to characterize using other methods. This was possible by first extracting a specificity profile of Smyd2 using our algorithm and subsequently screening a peptide library for matching sequences. However, our method did not yield successful results when attempting to reproduce specificity profiles of other proteins (64% accuracy on average). Different protein environments have demonstrated limitations in the methodology and lead us to further develop the algorithm on a more thorough dataset. Using our new optimized method, specificity profile predictions increase by roughly 20% (84% accuracy on average), independent of the structural template used. The algorithm was then used to blindly predict a specificity profile for the methyltransferase Smyd3, an enzyme for which limited data is currently available. A library of 2550 peptides was screened with the predicted profile, yielding 123 matching sequences. We randomly chose 64 for experimental validation (SPOT peptide array) of methylation by Smyd3 and found 45 methylated and 19 non-methylated peptides (70% success rate). Finally, we released to the community a web version of the algorithm, which can be accessed as http://viper.science.uottawa.ca.
Large Scale Computational Protein Design
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Author : Stefan Mathias Larson
language : en
Publisher:
Release Date : 2004
Large Scale Computational Protein Design written by Stefan Mathias Larson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
Protein Design
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Author : Raphael Guerois
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-02-04
Protein Design written by Raphael Guerois and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-02-04 with Science categories.
Protein Design: Methods and Applications presents the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with a maximum chance of success. The authors present integrated computational approaches that require various degrees of computational complexity, and the major accomplishments that have been achieved in the design and structural characterization of helical peptides and proteins.