Structural Complexity of Proteins

Find proteins by median feature count for various molecular functions

Use the

"Protein"

entity type to obtain a list of three sample proteins:

In[1]:=

exampleProteins=

alpha 1 type I collagen preproprotein

PROTEIN

eukaryotic translation initiation factor 5

PROTEIN

filamin A, alpha isoform 1

PROTEIN

;

Show the proteins and ribbon diagrams in a grid:

In[2]:=

EntityValueexampleProteins,

entity

ribbon diagram

//

display as grid

Out[2]=

alpha 1 type I collagen preproprotein
eukaryotic translation initiation factor 5
filamin A, alpha isoform 1

Get the secondary structures, such as helices and sheets, and molecular function of protein entities:

In[3]:=

data=EntityValue"Protein",

entity

molecular functions

secondary structure rules

;{commonProteins,commonProteinsWithMolecularFunction,commonProteinsWithSecondaryStructure}=DeleteMissing[data,1,2][[All,#]]&/@{1,{1,2},{1,3}};

Define a function to count the number of secondary structures for each protein and apply it to the data:

In[4]:=

featureStructureCount[secStructures:{__Rule}]:=Length[Flatten[secStructures〚All,2〛,2]];featureTotalsByProtein=Function[{protein,structures},proteinfeatureStructureCount[structures]]@@@commonProteinsWithSecondaryStructure;

Take a look at a random sample:

In[5]:=

RandomSample[featureTotalsByProtein,5]

Out[5]=



acidic (leucine-rich) nuclear phosphoprotein 32 family, member A

78,

cyclin-dependent kinase inhibitor 1B

86,

polymeric immunoglobulin receptor

64,

lymphocyte-specific protein tyrosine kinase precursor

13,

gastric lipase precursor

62

Obtain the feature counts for each molecular function. As the number of features can vary widely per protein, use the median of the structure count:

In[6]:=

featureCount[{protein_,functions_}]:={#,featureTotalsByProtein[protein]}&/@functionsfeatureMediansByFunction=Sort[Round[Median[#〚All,2〛]]&/@GroupBy[Flatten[featureCount/@commonProteinsWithMolecularFunction,1],First]];

Here is a sample of the result:

In[7]:=

RandomSample[featureMediansByFunction,5]

Out[7]=

AmineOxidaseActivity50,TelomericDNABinding54,Interleukin3ReceptorActivity8,ATPBindingAndPhosphorylationDependentChlorideChannelActivity81,HomocysteineSMethyltransferaseActivity40

Find the proteins that have the median feature count for each molecular function:

In[8]:=

countIndex=PositionIndex[featureMediansByFunction];featureCountIndex=PositionIndex[featureTotalsByProtein];medianProteinsByFunction=DeleteMissing[(#1featureCountIndex[#2])&@@@Normal[featureMediansByFunction],1,3];

Show a sample of the result:

In[9]:=

RandomSample[medianProteinsByFunction,5]//(RandomSample[#,UpTo[2]]&/@#)&

Out[9]=

SuperoxideDismutaseActivity

estrogen-related receptor alpha

short heterodimer partner

,ProteinDomainSpecificBinding

glutathione transferase

D-dopachrome tautomerase

,MAPKinaseKinaseActivity

cAMP-dependent protein kinase inhibitor alpha isoform 6

FK506-binding protein 2 precursor

,CytoskeletalProteinBinding

HtrA serine peptidase 2 isoform 1 preproprotein

CD74 antigen isoform a

,PyruvateCarboxylaseActivity

pyruvate carboxylase precursor



To show the variety of structural complexity, find a ribbon diagram for an example median protein for each function, where available:

In[10]:=

firstNonmissingRibbon[ents_List]:=EntityValueSelectFirstents,HeadEntityValue#,

ribbon diagram

=!=Missing&,

ribbon diagram

;

In[11]:=

Image[firstNonmissingRibbon[#],ImageSizeTiny]&/@Values[medianProteinsByFunction〚1;;400;;40〛]

Out[11]=

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Contributed by: Wolfram Staff

Structural Complexity of Proteins

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