Protein interactions design.

Protein-protein interactions are key to many biological processes. Engineering these interactions aids in the creation of vaccines, protein inhibitors, new synthetic reactants, etc. Therefore, leading to the development of different computational design strategies. However, these design strategies h...

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Main Author: Tay, Connie Gui Ching.
Other Authors: School of Biological Sciences
Format: Final Year Project
Language:English
Published: 2012
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Online Access:http://hdl.handle.net/10356/49337
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-493372023-02-28T18:01:26Z Protein interactions design. Tay, Connie Gui Ching. School of Biological Sciences A*STAR Bioinformatics Institute M.S. Madhusudhan Minh Ngoc Nguyen DRNTU::Science::Biological sciences Protein-protein interactions are key to many biological processes. Engineering these interactions aids in the creation of vaccines, protein inhibitors, new synthetic reactants, etc. Therefore, leading to the development of different computational design strategies. However, these design strategies have thus far failed to accurately capture the energy functions that contribute to the stability of protein interfaces. The aim of this project is to devise a general computational design strategy, which incorporates native residues that are involved in hydrogen bonds. In designing these interactions, we hope to accurately reproduce the residue-residue interactions, including inter-protein hydrogen bonding. The first step of the design protocol is to define key surface residues that are involved in an interaction. The definition of these residues was another challenge faced in protein interface design. In our design protocol, we used a general cutoff distance of 4.75Å obtained by taking into consideration hydrogen bond residues and solvent accessibility. The design protocol was benchmarked and then tested by designing an MDM2 inhibitor. The suggested candidates were observed to retain at least half of the native hydrogen bonds. Therefore, we believe that, with further in-depth analysis, this computational design strategy would be a useful tool in designing protein interfaces. Bachelor of Science in Biological Sciences 2012-05-17T08:01:14Z 2012-05-17T08:01:14Z 2012 2012 Final Year Project (FYP) http://hdl.handle.net/10356/49337 en Nanyang Technological University 37 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Science::Biological sciences
spellingShingle DRNTU::Science::Biological sciences
Tay, Connie Gui Ching.
Protein interactions design.
description Protein-protein interactions are key to many biological processes. Engineering these interactions aids in the creation of vaccines, protein inhibitors, new synthetic reactants, etc. Therefore, leading to the development of different computational design strategies. However, these design strategies have thus far failed to accurately capture the energy functions that contribute to the stability of protein interfaces. The aim of this project is to devise a general computational design strategy, which incorporates native residues that are involved in hydrogen bonds. In designing these interactions, we hope to accurately reproduce the residue-residue interactions, including inter-protein hydrogen bonding. The first step of the design protocol is to define key surface residues that are involved in an interaction. The definition of these residues was another challenge faced in protein interface design. In our design protocol, we used a general cutoff distance of 4.75Å obtained by taking into consideration hydrogen bond residues and solvent accessibility. The design protocol was benchmarked and then tested by designing an MDM2 inhibitor. The suggested candidates were observed to retain at least half of the native hydrogen bonds. Therefore, we believe that, with further in-depth analysis, this computational design strategy would be a useful tool in designing protein interfaces.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Tay, Connie Gui Ching.
format Final Year Project
author Tay, Connie Gui Ching.
author_sort Tay, Connie Gui Ching.
title Protein interactions design.
title_short Protein interactions design.
title_full Protein interactions design.
title_fullStr Protein interactions design.
title_full_unstemmed Protein interactions design.
title_sort protein interactions design.
publishDate 2012
url http://hdl.handle.net/10356/49337
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