Bioinformatics 2

Presented By

Pallabi

Odisha NET Academy ONA

Odisha NET Academy -09337727724

Salt stress is the most severe environmental abiotic stress.

Organisms which withstand against this situation are called halophilic

organisms .and others are called non halophilic.

They sense and adapt to hypersaline condition such that their protein

machinary also require high salt for their native form.

The secret of salinity tolerance capability of halotolerant proteins

is due to the presence of more no. of negatively charged acidic

residues at their surface which are having the capacity of binding

to the salt ions very effectively through electrostatic interaction.


To choose one model organism growing in hypersaline condition .

To choose one halophilic protein from that organism.

To find out whether that particular protein survivivg during salinity condition in other halotolerant species or not through in-silico

comparative proteomics analysis .


H.salinarum was chosen as the model organism from a list of no. of halotolerant species on the basis of its salt stress tolerating capability.

This microbe is an extreme halophile survives in world’s most salted environment, the dead sea. It can tolerate upto 4.5 M NaCl or higher.

Colour of the dead sea looks purple or reddish colour due to high density of these halo archaeons.


Ferredoxin was detected as a halophilic protein from H.salinarum through various article search.

Ferredoxin is an ubiqutous electron transferring protein involving in various metabolic reactions diversely found among almost all organisms also surviving as a halophilic protein in an extreme haloarcheon Halobacterium salinarum .


NCBIBLASTCLUSTAL X2MEGA 5.0MODELLER 9.10PYTHON 2.7I-TASSER SERVERRAMPAGE SERVERMODLOOP SERVERYASARA MINIMIZATION SERVERDISCOVERY STUDIO 3.0




Sr.no Accession no.

Species Class Domain Length of aa

1. CAA48224.1 H.salinarum Haloarchaeon 29262 129

2. ACV46987.1 H. mukohataei Haloarchaeon 29262 129

3. EAR18064.1 Synechococcus sp.

Marinecyanobacteria

29262 93

4. NP_893469.1 p.marinus Marine bacterium

29262 99

5. ACV11951.1 H. utahensis Haloarchaeon 31324,207724 129


6. ABW30398.1 A. marina Marine cyanobateria

29262 99

7. AACO8206.1 P.purpurea Marine algae 29262 99

8. AAB61593.1 Common ice plant Halophyte 29262 148

9. AAV24967.1 O.sativa Japonica Group

Crop 29262 148

10. AEE28669.1 A.thaliana Halophyte 29262 148



IDENTICAL : 16 residues

99(Leu),102(Ala),106(Gly),112(Ser).113(Cys),115(Ala),116(Gly),118(Cys),121(Cys),122(Ala),128(Gly),131(Asp),150(Leu),156(Cys),159(Asp)

STRONG : 10 residues 98(Ile/Val),103(Asp/Glu),108(Asp/Glu),114(Arg/His),119(Ser/Trp/Ala),

124(Met/Val/Ile),130(Val/Ile),138(Leu/Val)

WEAK : 11 reidues 96(Asp/Gly),101(Asp/Glu/Ser),102(Ala/Val),120(Trp/Asp/Ser),123(Gly/

Ala/Ser),133(Ser/Asp),139(Ser/Asp),147(Gly/Asp/Glu),154(Ser/Ala/Gly)164(Trp/Val/Ala),168(Glu/Gln,Lys/Asp)



Example : Halomicrobium mukohataei (ACV46987.1)


SOFTWARES USED : MODELLER 9.10 , PYTHON 2.7, ClustalX2

Input files for modeller : PDB file of known structure(.pdb) Alignment file of target and template(.ali)Python script file for generating model(.py)












Sr.no. Accession no. Favoured region Allowed region Outlier region

1. ACV46987.1 125(98.4%) 2(1.6%) 0(0.0%)

2. ACV11951.1 127(100%) 0(0.0%) 0(0.0%)

3. NP_893469.1 92(94.8%) 5(5.2%) 0(0.0%)

4. EAR18064.1 90(98.9%) 0(0.0%) 1(1.1%)

5. ABW30398.1 93(95.9%) 4(4.1%) 0(0.0%)

6. AAC08206.1 96(99.0%) 1(1.0%) (0.00%)

7. AAB61593.1 132(90.4%) 10(6.8%) 4(2.7%)

8. AAV24967.1 129(88.4%) 12(8.2%) 5(3.4%)

9. AEE28669.1 121(82.9%) 13(8.9%) 12(8.2%)



Sr. no

Species ProteinName

Initial potential energy(kj/mole

Final potential

energy(kj/mole)

Initial

Z-

score

Final

Z-

score

1. H.salinarum Ferredoxin -39066.0 -70742.8 -6.54 -1.94

2. H.utahensis Ferredoxin -39988.6 -77027.3 -1.54 -0.10

3. H.mukohatei Ferredoxin -42746.9 -78604.0 -1.60 0.02

4. Prochlorococcus

marinus

Ferredoxin -24676.9 -52205.6 -1.79 -0.21

5. Acaryochloris marina Ferredoxin 4827.0 -48052.1 -2.82 -0.58

6. Synechococcus sp. Ferredoxin -9593.4 -42829.3 -3.26 -1.07

7. Porphyra purpurea Ferredoxin -16813.2 -51899.3 -2.65 -0.62

8. Common ice plant Ferredoxin -11409.0 -62018.3 -5.10 -1.96

9. Oryza sativa Japonica

Group

Ferredoxin 3434.4 -59400.0 -5.12 -2.02

10. Arabidopsis thaliana Ferredoxin 313.1 -62823.5 -6.45 -3.05Odisha NET Academy -09337727724



SPECIES IDENTICAL STRONG WEAK

Common ice plant

ALA100 Asp109 Met103 Val108 Glu78 Gly101 Gly124 Glu145

P.purpurea Ala51 Asp60 Val54 Val59 Asp29 Gly52 Gly75 Gln96

O.sativa

Japonica Group

Ala100 Asp109 Met103 Val108 Glu78 Gly101 Gly124 Glu145

A. marina Ala50 Asp59 Ile53 Val58 Ser28 Gly51 Gly74 Asp95

H.utahensis Ala73 Asp82 Val76 Ile81 Glu51 Ala74 Gly98 Lys119

H.mukohatei Ala73 Asp82 Val76 Ile81 Glu51 Ala74 Asn98 Lys119

A.thaliana Ala100 Asp109 Val103 Ile108 Asp78 Gly101 Gly124 Glu145

H.salinarum Ala72 Asp81 Val75 Ile80 Glu50 Ser73 Asp97 Lys118

Synechococcus

sp.

Ala46 Asp55 Val49 Val54 Asp24 Gly47 Gly70 Asp91

P. marinus Ala51 Asp60 Ile54 Val59 Asp29 Gly52 Gly75 Glu96




Protein structure enhances protein function

As we got the proof for structural conservedness for ferredoxin protein among these species ,it is expected that somehow this protein survives during salinity condition not only in H.salinarum, but also in other microbes and plant species which we have detected as halotolerant species. Odisha NET Academy -09337727724

R.H. Reed, in: R.A. Herbert, G.A. Codd (Eds.) Microbes in extreme environments, Special publications for the Society for General Microbiology, Academic Press, London, 17, 1986, pp. 51.

L.D. Mermelstein, J.G. Zeikus in: Edited by K. Horikoshi, W.D. Grant (Eds.) Extremophiles. Microbial life in extreme environments, Wiley-Liss, New York, 1998.

Frolow, F., Harel, M., Sussman, J.L., Mevarech, M., Shoham, M. Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe–2S ferredoxin. Nat. Struct. Biol. 1996;3:452–458.

Halobacterium salinarum. Membrane Biochemistry Dieter Oesterhelt. Max PlanckinstituteofBiochemistry.10/22/2011. http://mnphys.biochem.mpg.de/en/eg/oesterhelt/web_page_list/Org_Hasal/index.html/

Ishibashi, M., Tokunaga, H., Hiratsuka, K., Yonezawa, Y., Turumaru, H., Arakawa, T., Tokunaga, M. NaCl-activated nucleoside diphosphate kinase from extremely halophilic archaeon,Halobacterium salinarum, maintain native conformation without salt. FEBS Lett.2001;493:134–138.

Electrostatic contribution to the stability of halophilic proteinBandyopadhyay AK, Krishnamoorthy G, Sonawat HM (2001) Structural stabilization of [2Fe–2S] ferredoxin from Halobacterium salinarum. Biochemistry 40:1284–1292

Schweimer K, Marg B-L, Oesterhelt D, Rosch P, Sticht H (2000) Sequence-specific 1H, 13C and 15N resonance assignments and secondary structure of [2Fe–2S] ferredoxin from Halobacterium salinarum. J Biomol NMR 16:347–348

. Werber MM, Mevarech M (1978) Purification and characterization of a highly acidic 2Fe–2S ferredoxin from Halobacterium of the Dead Sea. Arch Biochem Biophys 187:447–456

Marg B-L, Schweimer K, Sticht H, Oesterhelt D (2005) A two-a-helix extra domain mediates the halophilic character of a plant type ferredoxin from halophilic archaea. Biochemistry 44:29–39


http://www.ncbi.nlm.nih.gov/BLASThttp://www.clustal.orghttp://www.salilab.org/modeller/http://www.modbase.compbio.ucsf.edu/modloop/http://www.mordred.bioc.cam.ac.uk/~rapper/rampage.phphttp://www.yasara.org/http://accelrys.com/products/discovery-studio/visualization-download.php/



Science

Bioinformatics 2