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

Alaa El-Din A. Gawad

doi:doi:10.11648/j.cbb.20150302.12

| Peer-Reviewed

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

Alaa El-Din A. Gawad

Published in Computational Biology and Bioinformatics (Volume 3, Issue 2)

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

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

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

References

[1]	McCammon JA (1984). Protein dynamics. Rep Prog Phys 47: 1-46.
[2]	Ma J (2005). Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13: 373–380.
[3]	Bahar I, Lezon TR, Bakan A, and Shrivastava IH (2010). Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev. 110: 1463-97.
[4]	Kitao A and Go N (1999). Investigating protein dynamics in collective coordinate space. Curr Opin Struc Biol 9: 164-l 69.
[5]	Delarue M and Dumas P (2004). On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. PNAS 101: 6957–6962.
[6]	Bassnett S, Shi Y and Vrensen GFJM (2011). Biological glass: structural determinants of eye lens transparency. Phil. Trans. R. Soc. B 366, 1250–1264.
[7]	Pierscionek B and Augusteyn RC (1988). Protein distribution patterns in concentric layers from single bovine lenses: changes with development and ageing. Curr Eye Res 7: 11-23.
[8]	van Rens GLM, Driessen HPC, Nalini V, Slingsby C, de Jong WW, Bloemendal H (1991). Isolation and characterization of the cDNAs of the last two acidic β-crystallins, βA2 and βA4: Heterologous interaction in the predicted βA4-βB2 heterodimer. Gene 102:179-188.
[9]	Bindels JG, Koppers A, and Hoenders HJ (1981). Structural aspects of bovine β-crystallins: Physical characterization including dissociation-association behavior. Exp Eye Res 33: 333-343.
[10]	Driessen, H. P. C., He Liu BF, Liang JJ (2007). Protein-protein interactions among human lens acidic and basic beta-crystallins. FEBS Lett. 581: 3936-42.
[11]	Liu B-F and Liang J J-N (2006). Domain interaction sites of human lens βB2-crystallin. J Biol Chem 281: 26-24- 2630.
[12]	Bax B, Lapatto R, Nalini V, Driessen H, Lindley PF, Mahadevan D, Blundell TL, and Slingsby C (1990). X-ray analysis of βB2-Crystallin and evolution of oligomeric lens proteins. Nature 347: 776−780.
[13]	Nalini V, Bax B, Driessen H, Moss DS, Lindley PF, and Slingsby C (1994). Close packing of an oligomeric eye lens beta-crystallin induces loss of symmetry and ordering of sequence extensions. J Mol Biol 236: 1250−1258.
[14]	Berbers, GA. M., Boerman, 0. C., Bloemendal H, and de Jong, WW (1982). Primary gene products of bovine β-crystallin and reassociation behavior of its aggregates. Eur J Biochem 128: 495-502.
[15]	Kroone RC, Elliott GS, Ferszt A, Slingsby C, Lubsen NH and Schoenmakers JGG (1994). The role of the sequence extensions in β–crystallin assembly. Protein Eng 7: 1395–1399.
[16]	Trinkl S, Glockshuber R and Jaenicke R (1994). Dimerisation of βB2-crystallin: The role of the linker peptide and the N– and C-terminal extensions. Protein Sci. 3: 1392–1400.
[17]	Zhang J, Li J, Huang C, Xue L, Peng Y, Fu Q, Gao L, Zhang J, Li W(2008). Targeted knockout of the mouse βB2-crystallin gene (Crybb2) induces age-related cataract. Invest Ophthalmol Vis Sci. 49: 5476-83.
[18]	Skjaerven L, Hollup SM, and Reuter N (2009). Normal mode analysis for proteins. J Mol Str: THEOCHEM 898 (2009) 42–48.
[19]	Noguti, T and Gō, N (1989). Structural basis of hierarchical multiple substrates of a protein. IV: rearrangements in atom packing and local determinations. Proteins 5: 125-131.
[20]	Hayward, S, Kitao, A, and Gō, N (1995). Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins 23: 177-186.
[21]	Ma J (2004). New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Prot Pept Sci 5: 119–123
[22]	Bahar I, Rader AJ (2005). Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15: 586–592.
[23]	Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I (2001). Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80: 505–515.
[24]	Tirion MM (1996). Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett. 77: 1905-1908.
[25]	Eyal E, Chennubhotla C, Yang L-W, and Bahar I (2007). Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Bioinformatics 23: i175-i184.
[26]	Isin B, Doruker P, and Bahar I (2002).Functional Motions of Influenza Virus Hemagglutinin: A Structure-Based Analytical Approach. Biophys J 82: 569–581.
[27]	Hung A, Tai K, and Sansom MSP (2005). Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: structure and collective motions, Biophys J 88: 3321–3333.
[28]	Deriu MA, Soncini M, Orsi M, Patel M, Essex JW, Montevecchi FM, Redaelli A (2010). Anisotropic elastic network modeling of entire microtubules. Biophys J 99: 2190–2199.
[29]	Bakan A, and Bahar I (2011). Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments. Pacific Symposium on Biocomputing: 181-192.
[30]	Stoyanova R, Brown TR (2001). NMR spectral quantitation by principal component analysis. NMR Biomed 14: 271-7.
[31]	Ramadan Z, Jacobs D, Grigorov M, Kochhar S (2006). Metabolic profiling using principal component analysis, discriminant partial least squares, and genetic algorithms. Talanta 68: 1683–1691.
[32]	Gendoo DMA and Harrison PM (2012). The landscape of the prion protein’s structural response to mutation revealed by principal component analysis of multiple NMR ensembles. PLoS Comput Biol 8: e1002646
[33]	Salomon-Ferrer R, Case DA and Walker RC (2013). An overview of the Amber biomolecular simulation package. WIREs Comput Mol Sci 3: 198-210.
[34]	Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., and Pedersen, L.G. (1995). A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577–8593.
[35]	Ryckaert, J.P., Ciccotti, G., and Berendsen, H.J.C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327–341.
[36]	Berendsen, H. J. C., Postma, J. P. M., van Gunsteren,W. F., DiNola, A., Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. J Chem Phys 81, 3684–3690.
[37]	Amadei A, Linssen AB, Berendsen HJ (1993). Essential dynamics of proteins. Proteins 17: 412–425.
[38]	Teodoro ML, Phillips GN Jr, and Kavraki LE (2003). Understanding protein flexibility through dimensionality reduction. J. Comput. Biol 10: 617–634.
[39]	Eyal E, Yang LW, and Bahar I (2006). Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics 22: 2619-27
[40]	Lee RA, Razaz M, Hayward S (2003). The DynDom database of protein domain motions. Bioinformatics 19: 1290-1291.
[41]	Krissinel E and Henrick K (2007). Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
[42]	Raman B, Ramakrishna T, and Rao CM (1995). Temperature dependent chaperone-like activity of alpha-crystallin. FEBS Lett 365: 133-6.
[43]	Das BK, Liang JJ, Chakrabarti B (1997). Heat-induced conformational change and increased chaperone activity of lens alpha-crystallin. Curr Eye Res 16: 303-309.
[44]	del Valle LJ, Escribano C, Pe´rez JJ, Garriga P (2002). Calcium-induced decrease of the thermal stability and chaperone activity of a-crystallin. Bioch Biophys Acta 1601: 100– 109.
[45]	Beebe DC, Holekamp NM, Shui Y-B (2010). Oxidative damage and the prevention of age-related cataracts. Ophthalmic Res 44:155–165.
[46]	Lampi KJ, Wilmarth PA, Murray MR, and David LL (2014). Lens β-crystallins: The role of deamidation and related modifications in aging and cataract. Prog Biophys Mol Biol 115: 21-31.
[47]	Moreau KL and King JA (2012). Cataract-causing defect of a mutant γ-crystallin proceeds through an aggregation pathway which bypasses recognition by the α-Crystallin Chaperone. PLoS ONE 7(5): e37256.
[48]	Tama F. (2003). Normal mode analysis with simplified models to investigate the global dynamics of biological systems. Prot Pept Lett 10: 119-32.
[49]	Su JG, Xu XJ, Li CH, Chen WZ, and Wang CX (2011). An analysis of the influence of protein intrinsic dynamical properties on its thermal unfolding behavior. J Biomol Struct Dyn. 29:105-21.
[50]	Skliros A, Zimmermann MT, Chakraborty D, Saraswathi S, Katebi AR, Leelananda SP, Kloczkowski A and Jernigan RL (2012). The importance of slow motions for protein functional loops. Phys Biol 9: 014001.
[51]	Lapatto R, Nalini V, Bax B, Driessen H, Lindley PF, Blundell TL, and Slingsby C (1991). High resolution structure of an oligomeric eye lens β-crystallin. Loops, arches, linkers and interfaces in βB2 dimer compared to monomeric γ-crystallin. J Mol Biol 222: 1067-1083.
[52]	Norledge BV, Trinkl S, Jaenicke R and Slingsby ( 1997). The x-ray structure of a mutant eye lens βB2-crystallin with truncated sequence extensions. Protein Sci 6: 1612-1620.
[53]	MacDonald JT, Purkiss AG, Smith MA, Evans P, Goodfellow JM, and Slingsby C (2005). Unfolding crystallins: the destabilizing role of a beta-hairpin cysteine in betaB2-crystallin by simulation and experiment. Protein Sci 14: 1282-92.
[54]	Evans P, Slingsby C, and Wallace BA (2008). Association of partially folded lens betaB2-crystallins with the alpha-crystallin molecular chaperone. Biochem J 409: 691-699
[55]	Lampi KJ, Fox CB, David LL (2012). Changes in solvent accessibility of wild-type and deamidated βB2-crystallin following complex formation with αA-crystallin. Exp Eye Res 104: 48-58.
[56]	Lange OF and Grubmüller H (2006). Can principal component yield a dimension reduced description of protein dynamics on long time scale? J Phy Chem B 110: 22842-22852.
[57]	Skjaerven L, Martinez A, and Reuter N. (2011). Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins 79: 232-243.
[58]	Luo J and Bruice TC (2007). Low-frequency normal modes in horse liver alcohol dehydrogenase and motions of residues involved in the enzymatic reaction. Biophys Chem 126: 80–85.
[59]	Adamovic I, Mijailovich SM, and Karplus M (2008). The elastic properties of the structurally characterized myosin II S2 subdomain: A molecular dynamics and normal mode analysis. Biophys J 94: 3779–3789
[60]	Vemparala S, Mehrotra S, Balaram H (2011). Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: A molecular dynamics and normal mode analysis study. Biochim Biophys Acta 1814: 630–637.
[61]	Lu M and Ma J (2005) The role of shape in determining molecular motions. Biophysical Journal 89: 2395–2401.
[62]	Fenwick RB, Orellana L, Esteban-Martίn S, Orozco M, Salvatella X (2014). Correlated motions are a fundamental property of β-sheets. Nat. Commun. 5: 4070-
[63]	Liu B-F, Liang J J-N (2005). Interaction and biophysical properties of human lens Q155* βB2-crystallin mutant. Mol Vis 11: 321-327.
[64]	Takata T, Smith JP, Arbogast B, David LL, and Lampi KJ (2010). Solvent accessibility of betaB2-crystallin and local structural changes due to deamidation at the dimer interface. Exp Eye Res 91: 336-346.
[65]	Zhang K, Zhao W-J, Leng XY, Wang SY, Yao K, Yan YB (2014). The importance of the last strand at the C-terminus in beta B2-crystallin stability and assembly. Biochim Biophys Acta. 1842: 44-55.

Cite This Article

Plain Text BibTeX RIS

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

Copy | Download

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

Copy | Download

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

Copy | Download

@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}
}

Copy | Download

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  -

Copy | Download

Author Information

Alaa El-Din A. Gawad

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

Download PDF

Sections

Plain Text BibTeX RIS

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

Copy | Download

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

Copy | Download

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

Copy | Download

@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}
}

Copy | Download

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  -

Copy | Download