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

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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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  -