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Dynamics of βB2-Crystallin Motion Based on Principal Component Analysis and Normal Mode Analysis

Received: 8 April 2015     Accepted: 20 April 2015     Published: 30 April 2015
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Abstract

The primary function of lens is to focus images perfectly on the retina. Lens crystallins however are flexible nanomachines that frequently accomplish their biological function by collective atomic motions in and/or out the lens. Although genetic and biochemical data on the βB2-crystallin protein are available from several sources, the correlation between conformational changes and dynamic behavior at the atomic level remains to be understood. The βB2-crystallin dimer has studied through a combination of molecular dynamics simulations, principal component analysis (PCA) and normal mode analyses. The changes in interface buried surface shows the mutual orientation of individual domains in βB2-crystallin dimer. The dominant PCA modes for concerted motions of the protein atoms were monitored in a lower-dimensions subspace. Three types of movements found in βB2-crystallin dimer, which are a twist propeller motion, a scissors type hinge motion, and a shear motion between the domains. Both the RMSF and the normal-mode dynamics showed that N-terminal β-sheet is the most correlated segments.

Published in Computational Biology and Bioinformatics (Volume 3, Issue 2)
DOI 10.11648/j.cbb.20150302.12
Page(s) 31-39
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2015. Published by Science Publishing Group

Keywords

Conformational Change, Essential Dynamics, Normal Mode Analysis, Elastic Network Model, Molecular Dynamics, Β-Crystallin

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  • APA Style

    Alaa El-Din A. Gawad. (2015). Dynamics of βB2-Crystallin Motion Based on Principal Component Analysis and Normal Mode Analysis. Computational Biology and Bioinformatics, 3(2), 31-39. https://doi.org/10.11648/j.cbb.20150302.12

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    ACS Style

    Alaa El-Din A. Gawad. Dynamics of βB2-Crystallin Motion Based on Principal Component Analysis and Normal Mode Analysis. Comput. Biol. Bioinform. 2015, 3(2), 31-39. doi: 10.11648/j.cbb.20150302.12

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    AMA Style

    Alaa El-Din A. Gawad. Dynamics of βB2-Crystallin Motion Based on Principal Component Analysis and Normal Mode Analysis. Comput Biol Bioinform. 2015;3(2):31-39. doi: 10.11648/j.cbb.20150302.12

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  • @article{10.11648/j.cbb.20150302.12,
      author = {Alaa El-Din A. Gawad},
      title = {Dynamics of βB2-Crystallin Motion Based on Principal Component Analysis and Normal Mode Analysis},
      journal = {Computational Biology and Bioinformatics},
      volume = {3},
      number = {2},
      pages = {31-39},
      doi = {10.11648/j.cbb.20150302.12},
      url = {https://doi.org/10.11648/j.cbb.20150302.12},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20150302.12},
      abstract = {The primary function of lens is to focus images perfectly on the retina. Lens crystallins however are flexible nanomachines that frequently accomplish their biological function by collective atomic motions in and/or out the lens. Although genetic and biochemical data on the βB2-crystallin protein are available from several sources, the correlation between conformational changes and dynamic behavior at the atomic level remains to be understood. The βB2-crystallin dimer has studied through a combination of molecular dynamics simulations, principal component analysis (PCA) and normal mode analyses. The changes in interface buried surface shows the mutual orientation of individual domains in βB2-crystallin dimer. The dominant PCA modes for concerted motions of the protein atoms were monitored in a lower-dimensions subspace. Three types of movements found in βB2-crystallin dimer, which are a twist propeller motion, a scissors type hinge motion, and a shear motion between the domains. Both the RMSF and the normal-mode dynamics showed that N-terminal β-sheet is the most correlated segments.},
     year = {2015}
    }
    

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  • TY  - JOUR
    T1  - Dynamics of βB2-Crystallin Motion Based on Principal Component Analysis and Normal Mode Analysis
    AU  - Alaa El-Din A. Gawad
    Y1  - 2015/04/30
    PY  - 2015
    N1  - https://doi.org/10.11648/j.cbb.20150302.12
    DO  - 10.11648/j.cbb.20150302.12
    T2  - Computational Biology and Bioinformatics
    JF  - Computational Biology and Bioinformatics
    JO  - Computational Biology and Bioinformatics
    SP  - 31
    EP  - 39
    PB  - Science Publishing Group
    SN  - 2330-8281
    UR  - https://doi.org/10.11648/j.cbb.20150302.12
    AB  - The primary function of lens is to focus images perfectly on the retina. Lens crystallins however are flexible nanomachines that frequently accomplish their biological function by collective atomic motions in and/or out the lens. Although genetic and biochemical data on the βB2-crystallin protein are available from several sources, the correlation between conformational changes and dynamic behavior at the atomic level remains to be understood. The βB2-crystallin dimer has studied through a combination of molecular dynamics simulations, principal component analysis (PCA) and normal mode analyses. The changes in interface buried surface shows the mutual orientation of individual domains in βB2-crystallin dimer. The dominant PCA modes for concerted motions of the protein atoms were monitored in a lower-dimensions subspace. Three types of movements found in βB2-crystallin dimer, which are a twist propeller motion, a scissors type hinge motion, and a shear motion between the domains. Both the RMSF and the normal-mode dynamics showed that N-terminal β-sheet is the most correlated segments.
    VL  - 3
    IS  - 2
    ER  - 

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Author Information
  • Biophysics and Laser Science Unit, Research Institute of Ophthalmology, Giza, Egypt

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