Protein Secondary Structure And Prediction Biology Essay

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A polymer's secondary structure (2° structure) is defined as the local conformation of its backbone. For proteins, this has come to mean the specification of regular polypeptide backbone folding patterns: helices, pleated sheets, and turns. A few types of secondary structure are particularly stable and occur widely in proteins. The most prominent are the α helix and β conformations. In proteins, the secondary structure is defined by the patterns of hydrogen bonds between backbone amide and carboxyl groups. The secondary structure may be also defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot.

Amino acids vary in their ability to form the various secondary structure elements. Proline and glycine are sometimes known as "helix breakers" because they disrupt the regularity of the α helical backbone conformation; however, both have unusual conformational abilities and are commonly found in turns.

Amino acids that prefer to adopt helical conformations in proteins include methionine, alanine, leucine, glutamate andlysine ("MALEK" in amino-acid 1-letter codes); by contrast, the large aromatic residues (tryptophan, tyrosineand phenylalanine) and \mathrm{C^{\beta}}-branched amino acids (isoleucine, valine, and threonine) prefer to adopt β-strand conformations.

Secondary structure prediction

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 Chou & Fasman Secondary Structure Prediction Server: This server predicts secondary structure of protein from the amino acid sequence. The Chou-Fasman is an empirical algorithm for the prediction of protein secondary structure originally developed by Robert S. Chao and Gerald D. Fasman in 1978. The method is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography. From these frequencies a set of probability parameters were derived for the appearance of each amino acid in each secondary structure type, and these parameters are used to predict the probability that a given sequence of amino acids would form a helix, a beta strand, or a turn in a protein.

Exercise: predict the secondary structure of the given protein sequence

>2POR:A|PDBID|CHAIN|SEQUENCE

EVKLSGDARMGVMYNGDDWNFSSRSRVLFTMSGTTDSGLEFGASFKAHESVGAETGEDGTVFLSGAFGKIEMGDALGASEALFGDLYEVGYTDLDDRGGNDIPYLTGDERLTAEDNPVLLYTYSAGAFSVAASMSDGKVGETSEDDAQEMAVAAAYTFGNYTVGLGYEKIDSPDTALMADMEQLELAAIAKFGATNVKAYYADGELDRDFARAVFDLTPVAAAATAVDHKAYGLSVDSTFGATTVGGYVQVLDIDTIDDVTYYGLGASYDLGGGASIVGGIADNDLPNSDMVADLGVKFKF

Protocol:

Go to http://www.biogem.org/tool/chou-fasman/

Paste the sequence in FASTA format

Click on submit

Analyse the results

Result: Name of the sequence is 2POR:A|PDBID|CHAIN|SEQUENCE. 

Sequence consists of 301 amino acids.

Target Sequence:

EVKLSGDARM GVMYNGDDWN FSSRSRVLFT MSGTTDSGLE FGASFKAHES VGAETGEDGT VFLSGAFGKI

EMGDALGASE ALFGDLYEVG YTDLDDRGGN DIPYLTGDER LTAEDNPVLL YTYSAGAFSV AASMSDGKVG

ETSEDDAQEM AVAAAYTFGN YTVGLGYEKI DSPDTALMAD MEQLELAAIA KFGATNVKAY YADGELDRDF

ARAVFDLTPV AAAATAVDHK AYGLSVDSTF GATTVGGYVQ VLDIDTIDDV TYYGLGASYD LGGGASIVGG

IADNDLPNSD MVADLGVKFK F

http://www.biogem.org/images/graph.png

Secondary Structure:

* * * * *

Query 1 EVKLSGDARMGVMYNGDDWNFSSRSRVLFTMSGTTDSGLEFGASFKAHESVGAETGEDGT 60

Helix 1 <> <------> <----> <---------------> 60

Sheet 1 EEEE EEEEEEEE E 60

Turns 1 T TT T T T T T TT 60

* * * * *

Query 61 VFLSGAFGKIEMGDALGASEALFGDLYEVGYTDLDDRGGNDIPYLTGDERLTAEDNPVLL 120

Helix 61 <------------------------> <> 120

Sheet 61 EEEEEEEEE EEEEEEEEEEEE EEEE EEE 120

Turns 61 T T T T T TTT TT 120

* * * * *

Query 121 YTYSAGAFSVAASMSDGKVGETSEDDAQEMAVAAAYTFGNYTVGLGYEKIDSPDTALMAD 180

Helix 121 <-------> <--------------> <> <--------- 180

Sheet 121 EE EEEEEEEEEEEEEEEEEEEE EEEEEE 180

Turns 121 TT TT TT 180

* * * * *

Query 181 MEQLELAAIAKFGATNVKAYYADGELDRDFARAVFDLTPVAAAATAVDHKAYGLSVDSTF 240

Helix 181 -------------------------------------------------> 240

Sheet 181 EEEEEEEEEEEEEEEEEEEE EEEEEEEEEEE EEEEEEEEE 240

Turns 181 TT T T 240

* * * * *

Query 241 GATTVGGYVQVLDIDTIDDVTYYGLGASYDLGGGASIVGGIADNDLPNSDMVADLGVKFK 300

Helix 241 <--------> <-------> <---------> 300

Sheet 241 EEEEEEEEEEEEEEEEEEEEEEEE EEEE EEEEEEEE 300

Turns 241 T T T TT 300

Query 301 F 301

Helix 301 301

Sheet 301 301

Turns 301 301

Total Residues: H: 178 E: 145 T: 35

Percent: H: 59.1 E: 48.2 T: 11.6

Predicting the secondary structure using GOR

GOR: The GOR method is based on information theory and was developed by J.Garnier, D. Osguthorpe and B. Robson. The program gives two outputs, one eye-friendly giving the sequence and the predicted secondary structure in rows, H=helix, E=extended or beta strand and C=coil; the second gives the probability values for each secondary structure at each amino acid position.

Exercise: Predict the secondary structure of the given sequence

GSAMDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH

Protocol:

Goto http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html

Copy and paste the sequence

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Click on submit

Analyse the results

Result: The secondary structure prediction by GOR are

10 20 30 40 50 60 70

| | | | | | |

GSAMDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNC

ccccccchhhhhhhhhhhhhhhhhcccccchhhhhhhhhccccccccccccccccccccccchhhhcccc

RKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGS

cceeeccccccccccchhhhhhhhhhhccccccceeeeccccceeeeeeeceeeeeeeccccceeecccc

YFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH

ccceeeeecccccceeecccceeeeeeccccccchhhhhhhhhhhhhhhhhhhhhhhhcccccceec

Sequence length : 207

GOR4 :

Alpha helix (Hh) : 65 is 31.40%

310 helix (Gg) : 0 is 0.00%

Pi helix (Ii) : 0 is 0.00%

Beta bridge (Bb) : 0 is 0.00%

Extended strand (Ee) : 40 is 19.32%

Beta turn (Tt) : 0 is 0.00%

Bend region (Ss) : 0 is 0.00%

Random coil (Cc) : 102 is 49.28%

Ambigous states (?) : 0 is 0.00%

Other states : 0 is 0.00%

http://npsa-pbil.ibcp.fr/tmp/b5f269665096.gor4.mpsa_state.gif

http://npsa-pbil.ibcp.fr/tmp/b5f269665096.gor4.mpsa1.gif

Retrieving protein structure data from PDB

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. It includes the x ray crystallographic data and NMR data for the macromolecules submitted by various biologists and biochemists.

Protocol:

Goto http://www.rcsb.org/pdb/home/home.do

Select macromolecule by clicking on it

Type the name of the protein and search

Select the hyperlink and click

Click on download and download in PDB text format and save

Use the file for analysis

Result: PDB file of Transthyretin (TTR) a serum and cerebrospinal fluid carrier of the thyroid hormone thyroxine (T4) and retinol binding protein bound to retinol was downloaded and saved for further analysis.

Analysis of protein structure using Ramachandran plot 2.0

Introduction to Ramachandran plot 2.0: A World Wide Web graphics package has been developed to display the main chain torsion angles phi,psi (Ramachandran angles) in a protein of known structure. This package allows users to find the Ramachandran angles for a particular amino acid type, present in the protein structure. Also, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. In addition to displaying the Ramachandran angles for various options, a detailed analysis output contains the information about the occurrence of the individual amino acid residues at various regions of the plot. This software is incorporated with all the protein structures available in the Protein Data Bank.

Protocol:

Goto http://dicsoft1.physics.iisc.ernet.in/rp/

Click on "ENTER"

Select the option upload file and upload the PDB file

Select the next option ( entire polypeptide or phi psi limits)

Select the residues for analysis

Click on submit

Select the particular chain or all the chain

Select the region for analysis

Click on submit

Results : click on particular yellow spots and analyse the results

Result: The analysis of the Ramachandran plot of the protein Transthyrectin is as follows

In Transthyrectin 185(82.22%) residues fall in the fully allowed region 34 (15.11%) fall in the additionally allowed region 2 (0.89%) fall in the generously allowed regions whereas 4 (1.78%) fall in the outside region.

It has 45 (24.32%) residues in the alpha helical region,138 (74.59%) in the beta sheet egion whereas 2 (1.08%) residues in 3-10 helical region hence it is predominently a beta pleated structure and the points in the disallowed region are Gly..

CONCLUSION

Secondary structure are the areas of folding or coiling within a protein; examples include alpha helices and pleated sheets, which are stabilized by hydrogen bonding.Various bioinfomatics tools like Chou &amp; Fasman Secondary Structure Prediction Server,GOR can be used to determine the secondary structure of proteins whereas secondary structure of known proteins can retrieved from various databases like the Protein Data Bank (PDB). The Ramachandran plot of the given protein is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide,Plotting the torsional angles in this way graphically shows which combination of angles are possible. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.