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

Ekambaram R, Kannaiyan A, Marimuthu V, Swaminathan VC, Renganathan S, Perumal AG - Bioinformation (2014)

Bottom Line: Particularly, the carbon fractions around individual atoms are compared.The results reveal that globular protein's atoms follow this principle.The carbon fraction distributions in fiber and toxin protein are compared.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, School of Biotechnology and Health Sciences, Karunya University, Karunya Nagar, Coimbatore -641114, Tamil Nadu, India.

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.

No MeSH data available.


Carbon distribution profile of globular protein (superoxide dismutase) compared with fiber protein (Coronin). Thefiber protein does not follow the normal distribution curve.
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Related In: Results  -  Collection


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Figure 3: Carbon distribution profile of globular protein (superoxide dismutase) compared with fiber protein (Coronin). Thefiber protein does not follow the normal distribution curve.

Mentions: The carbon distribution in muscle (fiber-2AQ5) protein wasanalysed for existence of such pattern. The pattern wascompared with globular protein (SOD-1SPD) as given inFigure 3. The fiber protein is in no way following the carbondistribution pattern. It is not important for its functional role.The distribution curve is flat on top. There is no narrowdistribution curve but broad curve. The fibrous protein doesnot maintain carbon distribution profile for its survival likeglobular protein-(for example SOD). But both proteinsmaintain a definite carbon fraction distribution along thesequence. The CFD is different for fiber proteins than theglobular proteins. That is why the fiber proteins are staticwhile globular proteins are dynamic. The solution structure ofdimeric form of SOD (1L3N) determined from NMR iscompared (result not shown here) with X-ray structure (1SPD).The solution structure allows better CFD than the solidstructure. Of course the medium influences the structure. Solidstructure is slightly distorted over the solution structure.


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

Ekambaram R, Kannaiyan A, Marimuthu V, Swaminathan VC, Renganathan S, Perumal AG - Bioinformation (2014)

Carbon distribution profile of globular protein (superoxide dismutase) compared with fiber protein (Coronin). Thefiber protein does not follow the normal distribution curve.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3974240&req=5

Figure 3: Carbon distribution profile of globular protein (superoxide dismutase) compared with fiber protein (Coronin). Thefiber protein does not follow the normal distribution curve.
Mentions: The carbon distribution in muscle (fiber-2AQ5) protein wasanalysed for existence of such pattern. The pattern wascompared with globular protein (SOD-1SPD) as given inFigure 3. The fiber protein is in no way following the carbondistribution pattern. It is not important for its functional role.The distribution curve is flat on top. There is no narrowdistribution curve but broad curve. The fibrous protein doesnot maintain carbon distribution profile for its survival likeglobular protein-(for example SOD). But both proteinsmaintain a definite carbon fraction distribution along thesequence. The CFD is different for fiber proteins than theglobular proteins. That is why the fiber proteins are staticwhile globular proteins are dynamic. The solution structure ofdimeric form of SOD (1L3N) determined from NMR iscompared (result not shown here) with X-ray structure (1SPD).The solution structure allows better CFD than the solidstructure. Of course the medium influences the structure. Solidstructure is slightly distorted over the solution structure.

Bottom Line: Particularly, the carbon fractions around individual atoms are compared.The results reveal that globular protein's atoms follow this principle.The carbon fraction distributions in fiber and toxin protein are compared.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, School of Biotechnology and Health Sciences, Karunya University, Karunya Nagar, Coimbatore -641114, Tamil Nadu, India.

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.

No MeSH data available.