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A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies

Ankush Aggarwal Orcid Logo, Jiun-Shyan Chen, William S. Klug

Computer Modeling in Engineering & Sciences, Volume: 98, Issue: 1, Pages: 69 - 99

Swansea University Author: Ankush Aggarwal Orcid Logo

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DOI (Published version): 10.3970/cmes.2014.098.069

Abstract

Mechanical properties of proteins play an important role in their biological function. For example, microtubules carry large loads to transport organelles inside the cell, and virus shells undergo changes in shape and mechanical properties during maturation which affect their infectivity. Various th...

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Published in: Computer Modeling in Engineering & Sciences
Published: 2014
Online Access: http://www.techscience.com/doi/10.3970/cmes.2014.098.069.html
URI: https://cronfa.swan.ac.uk/Record/cronfa21666
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first_indexed 2015-05-23T02:05:05Z
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spelling 2016-05-11T08:56:27.1963720 v2 21666 2015-05-22 A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies 33985d0c2586398180c197dc170d7d19 0000-0002-1755-8807 Ankush Aggarwal Ankush Aggarwal true false 2015-05-22 EEN Mechanical properties of proteins play an important role in their biological function. For example, microtubules carry large loads to transport organelles inside the cell, and virus shells undergo changes in shape and mechanical properties during maturation which affect their infectivity. Various theoretical models including continuum elasticity have been applied to study these structural properties, and a significant success has been achieved. But, the previous frameworks lack a connection between the atomic and continuum descriptions. Here this is accomplished through the development of a meshfree framework based on reproducing kernel shape functions for the large deformation mechanics of protein structures. The framework is validated by comparing thermal fluctuations of small proteins against well established elastic network model. To demonstrate the usability of this framework, solutions to several other problems are presented. The response of virus shells to indentation under atomic force microscope tip is simulated and compared to the finite element results. Finally, the large scale conformational changes of viruses are analyzed by computing the deformations/strains associated with the conformational motions. Excellent agreement with the previously published results is observed while increasing the efficiency of numerical analysis. Furthermore, the results provide insights into the continuum behavior of proteins and the optimum amount of geometric details necessary for calculating their mechanical properties. Journal Article Computer Modeling in Engineering & Sciences 98 1 69 99 Proteins, Meshfree method, RKPM, SNNI, AFM indentation, Conformational change. 30 4 2014 2014-04-30 10.3970/cmes.2014.098.069 http://www.techscience.com/doi/10.3970/cmes.2014.098.069.html COLLEGE NANME Engineering COLLEGE CODE EEN Swansea University 2016-05-11T08:56:27.1963720 2015-05-22T16:42:53.3205839 Faculty of Science and Engineering School of Engineering and Applied Sciences - Uncategorised Ankush Aggarwal 0000-0002-1755-8807 1 Jiun-Shyan Chen 2 William S. Klug 3
title A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies
spellingShingle A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies
Ankush Aggarwal
title_short A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies
title_full A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies
title_fullStr A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies
title_full_unstemmed A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies
title_sort A Meshfree Method For Mechanics and Conformational Change of Proteins and Their Assemblies
author_id_str_mv 33985d0c2586398180c197dc170d7d19
author_id_fullname_str_mv 33985d0c2586398180c197dc170d7d19_***_Ankush Aggarwal
author Ankush Aggarwal
author2 Ankush Aggarwal
Jiun-Shyan Chen
William S. Klug
format Journal article
container_title Computer Modeling in Engineering & Sciences
container_volume 98
container_issue 1
container_start_page 69
publishDate 2014
institution Swansea University
doi_str_mv 10.3970/cmes.2014.098.069
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Engineering and Applied Sciences - Uncategorised{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Engineering and Applied Sciences - Uncategorised
url http://www.techscience.com/doi/10.3970/cmes.2014.098.069.html
document_store_str 0
active_str 0
description Mechanical properties of proteins play an important role in their biological function. For example, microtubules carry large loads to transport organelles inside the cell, and virus shells undergo changes in shape and mechanical properties during maturation which affect their infectivity. Various theoretical models including continuum elasticity have been applied to study these structural properties, and a significant success has been achieved. But, the previous frameworks lack a connection between the atomic and continuum descriptions. Here this is accomplished through the development of a meshfree framework based on reproducing kernel shape functions for the large deformation mechanics of protein structures. The framework is validated by comparing thermal fluctuations of small proteins against well established elastic network model. To demonstrate the usability of this framework, solutions to several other problems are presented. The response of virus shells to indentation under atomic force microscope tip is simulated and compared to the finite element results. Finally, the large scale conformational changes of viruses are analyzed by computing the deformations/strains associated with the conformational motions. Excellent agreement with the previously published results is observed while increasing the efficiency of numerical analysis. Furthermore, the results provide insights into the continuum behavior of proteins and the optimum amount of geometric details necessary for calculating their mechanical properties.
published_date 2014-04-30T03:25:44Z
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score 11.031507

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