CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins

BACK TO CONTENTS | PDF | PREVIOUS | NEXT

Title	CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins
Authors	Rajasekaran Ekambaram¹*, Akila Kannaiyan², Vijayasarathy Marimuthu³, Vinobhav⁴, Senthil Ranganathan⁴ & Anandagopu Perumal⁴
Affiliation	¹Department of Bioinformatics, School of Biotechnology and Health Sciences, Karunya University, Karunya Nagar, Coimbatore – 641114, Tamil Nadu, India; ²Department of Bioinformatics, Bishop Heber College, Trichy-620017, Tamil Nadu, India; ³Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India; ⁴Department of Bioinformatics, Marudhu Pandiyar College, Vallam, Thanjavur – 620024, Tamil Nadu, India
Email	ersekaran@gmail.com; *Corresponding author
Article Type	Hypothesis
Date	Received October 28, 2013; Revised January 27, 2014; Accepted January 30, 2014; Published March 19, 2014
Abstract	Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein’s atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.
Keywords	crystal structure, carbon distribution, protein structure, hydrophobic scale, carbon fraction, CARd3D.
Citation	*Ekambaram et al.* Bioinformation 10(3): 138-143 (2014)
Edited by	P Kangueane
ISSN	0973-2063
Publisher	Biomedical Informatics
License	This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.