Proceedings of the 3rd International Conference on Computation for Science and Technology

Molecular Dynamics Simulation on Designed Antibodies of HIV-1 Capsid Protein (p24)

Authors
Hana Atiqah Abdul Karim, Chatchai Tayapiwatana, Piyarat Nimmanpipug, Sharifuddin M. Zain, Noorsaadah Abdul Rahman, Vannajan Sanghiran Lee
Corresponding Author
Hana Atiqah Abdul Karim
Available Online January 2015.
DOI
10.2991/iccst-15.2015.15How to use a DOI?
Keywords
Antibody, complementary determining region, hiv, molecular dynamics simulation, mm-gbsa, single chain variable fragment, single point mutation, molecular docking
Abstract

Computational approaches have been used by the molecular biologists all around the world as a vital tool in developing and improving the functional and binding properties of proteins, particularly antibody-antigen (Ab-Ag) complexes. Based on a previous work, it has been identified that several residues located in the complementary determining region (CDR) of antibody fragment of FAB23.5 may serve as a potential point mutation modification in order to improve the binding interaction and the inhibitory activity between the single chain variable fragment (scFv) antibody and the epitope variant of HIV-1 p24 capsid protein. In this study, several binding residues from the variable chain domain of scFv anti-p24 were modified. The designed antibody along with the bound antigen was then subjected for molecular dynamics (MD) simulation by using PMEMD.CUDA under Amber 12 with NVIDIA® Kepler® GPUs system. GPU system has been fully utilized in this work as a mean to speed up the calculation time. From the simulated model, the newly possessed binding interaction of the modified Ab-Ag complex were acquired by using the Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA) and Molecular Mechanics/Generalized Born surface area (MM-GBSA), respectively.

Copyright
© 2015, the Authors. Published by Atlantis Press.
Open Access
This is an open access article distributed under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).

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Volume Title
Proceedings of the 3rd International Conference on Computation for Science and Technology
Series
Advances in Computer Science Research
Publication Date
January 2015
ISBN
978-94-62520-46-2
ISSN
2352-538X
DOI
10.2991/iccst-15.2015.15How to use a DOI?
Copyright
© 2015, the Authors. Published by Atlantis Press.
Open Access
This is an open access article distributed under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).

Cite this article

TY  - CONF
AU  - Hana Atiqah Abdul Karim
AU  - Chatchai Tayapiwatana
AU  - Piyarat Nimmanpipug
AU  - Sharifuddin M. Zain
AU  - Noorsaadah Abdul Rahman
AU  - Vannajan Sanghiran Lee
PY  - 2015/01
DA  - 2015/01
TI  - Molecular Dynamics Simulation on Designed Antibodies of HIV-1 Capsid Protein (p24)
BT  - Proceedings of the 3rd International Conference on Computation for Science and Technology
PB  - Atlantis Press
SP  - 85
EP  - 88
SN  - 2352-538X
UR  - https://doi.org/10.2991/iccst-15.2015.15
DO  - 10.2991/iccst-15.2015.15
ID  - AtiqahAbdulKarim2015/01
ER  -