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Bioinformatics & Proteomics Open Access Journal Research Article 7 min read

In Silico Analysis of Dimethylsulfoxide Reductases from Phototrophic Rhodobacter Species

Sireesha R, Karunakar Rao K, Swetha G and Ramchander M*
* Corresponding author
ISSN: 2642-6129  10.23880/bpoj-16000111  Received: September 11, 2017  Published: November 03, 2017
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Keywords
&lt p&gt DMSO Reductases Rhodobacter sps Silico Analysis Instability Index&lt /p&gt
Abstract

<p>In the present study in silico modeling of Dimethylsulfoxide reductases were done and the results are presented. The composition of cysteine and lysine were lowest when compared to the aminoacids alanine and glycine. The instability index of all the enzymes varied but was less than 40 showing that all of them are stable. The negative aminoacids were more compared to the positively charged aminoacids. SOSUI server analysis has shown that all the enzymes were soluble in nature.</p>

Introduction

Dimethylsulfoxide (DMSO) is a dipolar aprotic solvent, colorless liquid readily miscible in a wide range of organic solvents as well as water. DMSO is used as a solvent in NMR as a cryoprotectant for storage of embryonic stem cells and hematopoietic stem cell in the electronics industry. Dimethyl Sulfoxide may have anti-inflammatory, antioxidant and analgesic activities. Dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes are found in bacteria and archaea. These enzymes are involved in reduction of certain toxic oxoanions. The molybdenum of the oxidized dimethyl sulfoxide (DMSO) reductase enzyme contains one terminal oxygen ligand (Mo=O), four thiolate ligands and one oxygen. The enzyme reduced by dimethylsulfide contains a desoxo active site with four Mo-S and two different Mo-O ligands. Recombinant wild-type Rhodobacter sphaeroides DMSO reductase expressed in Escherichia coli. [1]. High degree of similarity in tertiary structure DMSO reductase family. Reduced dimethylsulfoxide reductase (DMSOR) enzymes have an active-site which (a) lacks a terminal oxo ligand and has two pyranopterin-ene-1,2-dithiolate ligands [2]. Tungsten is also found in enzymes of the DMSO reductase and xanthine dehydrogenase family in thermophilic bacteria and archaea that grow under anaerobic reducing conditions [3] There exist very small differences in the active site of Mo indicating diversity of the enzyme catalyzed reaction mechanism [4]. Disruption of dmsA gene encoding Dimethyl sulfoxide/trimethylamine N- oxide reductase results in the inability to use DMSO or TMAO as the terminal electron acceptor [5]. Rhodobacter sphaeroides enzyme suggested hexacoordinated active site geometry, whereas for the R. capsulatus enzyme extended X absorption fine structure Bioinformatics & Proteomics Open Access Journal

indicated seven ligands [6]. The DMSOR from R. sphaeroides reveals plasticity at the active site where Mo is exists in a hexa coordinated and a pentacoordinated ligation sphere [7] the observed differences in the Mo co- ordination environment is due to structural flexibility at the active site [8]. The Rhodobacter enzyme catalyses the reduction of DMSO using the pentaheme c-type cytochrome DorC as the physiological source of reducing equivalents. Various spectroscopic studies on molybdenum center of DMSO reductases have been reported and were found to have unique absorption features [9, 10, 11]. X-ray crystallography studies on the group of these enzymes were also reported [12, 13]. Li, et al. have determined the crystal structure of DMSO reductase at 1.3 Å resolutions and found the heterogenous nature of the oxidized enzyme with two conformations [6]. Dimethylsulfoxide (DMSO) is enzymatically reduced to dimethylsulfide (DMS) by bacteria, which helps in measurement of respiratory activity of bacteria. Hence in the present study, an insilico analysis was done to investigate the physico chemical characteristics and nature of the dimethyl sulfoxide enzymes from different Rhodobacter species.

Material and Methods

Retrieval of nitrogenase sequences was done from UniProtKB/Swiss-Prot [14]. These sequences were used for further analysis. ExPASy's ProtParam tool was used for the computation of various physical and chemical parameters [15]. SOPMA tool (Self-Optimized Prediction Method with Alignment) server was used to characterize the secondary structural features [16]. The transmembrane regions classified as membrane bound and soluble proteins were predicted by SOSUI server [17].

Results and Discussion

In continuation of earlier studies on phototrophic bacteria [18, 19, 20, 21, 22, 23], a study has been done on the DMSO reductases which are known to play a crucial role in DMSO reduction by the bacteria. DMSO reductase is a membrane-bound terminal respiratory oxidase consisting of separate molybdenum- and ironsulfur-containing subunits in Escherichia coli while in phototrophic bacteria it is a soluble periplasmic protein with only a molybdenum center. This was found to over express when grown on Malate medium. The active site consists of pyranopterin cofactor via an enedithiolate linkage [24]. Reductases of different Rhodobacter species obtained from database are presented in (Table 1). Table 2 shows that the amino acid composition of six different DMSO reductases from Rhodobacter species. The composition of cysteine and lysine were lowest when compared to the aminoacids alanine and glycine. The number of negative charged residues was found to be more when compared to positively charged residues (Table 3). Molecular weight of DMSO5 was the highest while molecular weight of DMSO1 was the lowest. pI value of DMSO1 was the highest while the lowest pI was seen in DMSO4 .The instability index of all the enzymes varied but was less than 40 showing that all of them are stable. Aliphatic index which shows the relative volume of protein occupied by aliphatic side chains was found to be within a range of 75 to 77. From Table 4, Secondary structural analysis of the enzymes showed the dominance of α- helices and random coils almost equally for all the DMSO reductases. Beta turns were less in number for all the enzymes. SOSUI server analysis (Table 5) has shown that all the DMSO reductases so far characterized from Rhodobacter genus are soluble proteins.

DMSO reductaseNCBI/Gen Bank Reference SequenceRhodobacter Species /strain
DMSO1WP_012640770.1Rhodobacter sphaeroides
DMSO2AAB07230.1Rhodobacter sphaeroides
DMSO3AAB94874.1Rhodobacter sphaeroides
DMSO4ACM03079.1Rhodobacter sphaeroides KD131
DMSO5AAD13674.1Rhodobacter capsulatus
DMSO6CAA64689.1Rhodobacter capsulatus

Table 1: Different DMSO Reductases From Rhodobacter Species

  • Bioinformatics & Proteomics Open Access Journal
  • No of
  • Amino
  • Negatively
  • Positively
  • S.No
  • Dimethylsulfoxide
  • Extinction coefficients
  • MWt
  • PI charged residues charged residues reductase acids
  • DMSO1
  • Rhodobacter sphaeroides
  • 763
  • 83681.5 5.74
  • 94
  • 71
  • 132850/132350
  • 33.24
  • 76.82
  • -0.29
  • DMSO2
  • Rhodobacter sphaeroides
  • 822
  • 89207.51 5.08
  • 103
  • 71
  • 142835/142210
  • 30.03
  • 77.45
  • -0.214
  • DMSO3
  • Rhodobacter sphaeroides
  • 822
  • 89385.76 5.08
  • 103
  • 71
  • 141345/140720
  • 29.98
  • 76.23
  • -0.243
  • DMSO4
  • Rhodobacter
  • SphaeroidesKD131
  • 819
  • 89078.3 5.03
  • 105
  • 71
  • 142835/142210
  • 32.15
  • 76.63
  • -0.247
  • DMSO5
  • Rhodobacter capsulatus
  • 823
  • 89561.39 5.39
  • 101
  • 76
  • 143950/143700
  • 27.91
  • 76.35
  • -0.225

Table 2: Physico Chemical Characteristics Of Dimethylsulfoxide Reductase From Rhodobacter Species.

S.NoAlaArgAsnAspCysGlnGluGlyHisIleLeuLysMet
DMSO111.97.62.65.5136.89.84.73.48.71.73
DMSO211.24.93.36.11.22.86.410.52.43.983.82.8
DMSO310.24.63.46.11.23.26.410.72.43.97.842.9
DMSO410.34.63.36.21.23.16.610.72.44.27.742.8
DMSO510.14.42.760.52.36.310.72.74.17.24.93.2
DMSO610.142.66.20.52.46.310.72.84.26.953.1

Table 3: Amino Acid Composition of Dimethylsulfoxide Reductase From Rhodobacter Species.

Pi HelixOther state
310BeetaExtendedBetaBendRandomAmbiguous
S.NoAlfa Helix
HelixBridgeStrandturnregionCoilState
DMSO136.1700015.9910.75037.0900
DMSO236.0100016.6711.68035.6400
DMSO333.820001812.53035.6400
DMSO433.5800018.5612.33035.5300
DMSO533.900018.9612.15034.9900
DMSO63300019.1412.09035.7700

Table 4: Secondary Structure Analysis of Dimethylsulfoxide Reductase from Rhodobacter Species.

EnzymeNature of the enzyme
DMSO1This Amino acid sequence is of a SOLUBLE protein
DMSO2This Amino acid sequence is of a SOLUBLE protein
DMSO3This Amino acid sequence is of a SOLUBLE protein
DMSO4This Amino acid sequence is of a SOLUBLE protein
DMSO5This Amino acid sequence is of a SOLUBLE protein
DMSO6This Amino acid sequence is of a SOLUBLE protein

Table 7: Sosui Analysis of Analysis of Dimethylsulfoxide Reductases from Rhodobacter Species.

i Helix

Table 5: Sosui Analysis of Analysis of Dimethylsulfoxide Reductases from Rhodobacter Species.

Other state

Table 6: Sosui Analysis of Analysis of Dimethylsulfoxide Reductases from Rhodobacter Species.

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References

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@article{sireesha2017,
  title   = {In Silico Analysis of Dimethylsulfoxide Reductases from Phototrophic Rhodobacter Species},
  author  = {Sireesha R, Karunakar Rao K, Swetha G and Ramchander M},
  journal = {Bioinformatics & Proteomics Open Access Journal},
  year    = {2017},
  volume  = {1},
  number  = {2},
  doi     = {10.23880/bpoj-16000111}
}
Sireesha R, Karunakar Rao K, Swetha G and Ramchander M (2017). In Silico Analysis of Dimethylsulfoxide Reductases from Phototrophic Rhodobacter Species. Bioinformatics & Proteomics Open Access Journal, 1(2). https://doi.org/10.23880/bpoj-16000111
TY  - JOUR
TI  - In Silico Analysis of Dimethylsulfoxide Reductases from Phototrophic Rhodobacter Species
AU  - Sireesha R, Karunakar Rao K, Swetha G and Ramchander M
JO  - Bioinformatics & Proteomics Open Access Journal
PY  - 2017
VL  - 1
IS  - 2
DO  - 10.23880/bpoj-16000111
ER  -