| Research Article |
Open Access |
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| Secondary Structure of Butyrylcholinesterase |
| Srinivas K1, Sridhar GR2* and Appa Rao Allam3 |
| 1V R Siddhartha Engineering College, Vijayawada, India |
| 2Endocrine and Diabetes Centre, Visakhapatnam, India |
| 3C R Rao Advanced Institute for Mathematics, Statistics & Computer Science (AIMSCS), University of Hyderabad Campus, India |
| *Corresponding author: |
Sridhar GR
Endocrine and Diabetes Centre
15-12-15
Krishnanagar, Visakhapatnam 530 002, India
E-mail: sridharvizag@gmail.com |
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| Received May 14, 2012; Accepted June 20, 2012; Published June 25, 2012 |
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| Citation: Srinivas K, Sridhar GR, Allam AR (2012) Secondary Structure of
Butyrylcholinesterase. J Diabetes Metab 3:199. doi:10.4172/2155-6156.1000199 |
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| Copyright: © 2012 Srinivas K, et al. This is an open-access article distributed under
the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and
source are credited. |
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| Abstract |
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| Objective: Butyrylcholinesterase, a protein from the esterase family of enzymes, has been shown to modulate
the expression of insulin resistance syndrome. In order to identify related proteins with more well established
functions, the current in silico work was done to delineate the secondary structure of the enzyme and compare it
with other proteins of similar structure. The purpose was to predict possible role(s) of BchE in comparison to related
proteins based on their secondary structures. |
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| Methods: With the input as amino acid sequences of BchE, we obtained the secondary structure using the
SOPM tool. From the Protein Data Bank (PDB) database we compared the secondary structure of BchE with those
having 65% or more similarity. |
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| Results: We obtained 13 sequences: Acetylcholinesterase (EC 3.1.1.7, PDB 1gqr; score 72.134), Fasciculin 2
mouse acetylcholinesterase complex 1MAH3, PDB 1mah; score 71.806), AT sulfurase from penicillium chrysogenum,
1i2d; score 67.9727), pyruvate kinase (1a3w; score 67.5503), thronine synthase from Arabidopsis thaliana (1e5x;
score 67.426), DNA repair UVRB in complex with ATP (1d9z; score 66.778), hyperthermophilic tungstopterin
enzyme (1aor; score 66.28), xanthine oxidase from bovine milk (1fiq; score 66.147), alpha D-glucoronidase from
Bacillus stearothermophius (1k9d; score 65.959), ribonuclease inhibitor-angiogenin complex (1a4y; score 65.913),
hemochromatosis protein HFE complexed with transferrin receptor (1de4; score 65.723), K217e variant of Klebsiella
aerogenes urease (1a5k; score 65.667), phosphoenolpyruvase carboxykinase in complex with ADP, A1F3 and
pyruvate (1k3c; score 65.5233). Their functions ranged from catalyzing acetylcholine to sulfate asimilation, glycolysis,
nucleic acid binding, oxidoreductase activity, iron sulfur cluster binding, xanthine oxidation, cation binding, urease
activity and phosphoenolpyruvate carboxykinase activity. They are present in both the cytoplasm, extracellular
compartment and cytoplasmic membranes. |
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| Conclusion: We compared the predicted secondary structure of butyrylcholinesterase and obtained 13 proteins
with at least 65% similarity that are found in the cytoplasm and extracellular regions, with catabolic, synthetic,
electron transport and immune processing. |
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| Keywords |
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| In silico; Protein Data Bank (PDB) |
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| Introduction |
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| Proteins are key components in communication, metabolism and
structure in biological processes. The structure of proteins is conventionally
obtained by eleborate and complex methods such as X-ray
crystallography, NMR and Raman spectroscopy. Though difficult to
execute, they form the gold standard for comparison. |
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| The omics revolution has provided an abundance of publicly available
data. It is not practical to apply traditional biological methods to
classify and annotate them structurally and functionally. |
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| More rapid, automated in silico methods have therefore been developed
to derive meaning from the sea of data. Given that the amino
acid sequences are known and the force character of each molecule is
available, physical and chemical computational methods should be able
to predict the protein structure based on the amino acid sequences. |
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| Butyrylcholinesterase is an enzyme that is involved in the phenotypic
expression of insulin resistance and metabolic syndrome [2]. It
belongs to the esterase family of enzymes, in which acetylcholinesterase (AChE) is an important regulator of neuromuscular activity. The
two members share structural similarity, although the functional significance
of BChE is not as well characterized as it is for AChE. Other
than its specific role in hydrolyzing succinylcholine, a muscle relaxant
given in general anesthesia, the other functions generally relate to hydrolysis
of cocaine, of pesticides and as a prophylactic agent in future
exposure to biochemical warfare agents [3-5]. Because it is produced in
the liver, circulates in the blood stream, and is present at higher levels
than AChE, a toxicological role for BChe has been attributed. |
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| In addition it is affected by dietary lipids, changes in body weight
and in diabetes mellitus [2,3,6,7]. The development of succinylcholine
induced apnea in individuals with variant forms of the enzyme is the
only well established phenotypic expression of the enzyme [6]. Despite
its functional relationship to the neuromusclular enzyme acetylcholinesterase,
the physiological roles of BchE are not well established. The
advent of the genomics era allowed in silico studies to compare the re-lationship of proteins with other proteins with known functions, and
infer their possible physiological roles. Using phylogenetic analysis, we
had shown that BchE exists in life forms across the spectrum, implying
it could have an evolutionarily conserved role [1]. We also showed
that it could play a role in the etiology of insulin resistance and the
coexistence of Alzheimer’s disease and type 2 diabetes mellitus through
oxidative stress [8,9]. |
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| In this presentation we predict the secondary structure of BchE; by
using bioinformatics tools to compare the structure with other proteins
in Protein Databank (PDB) and ascertain its possible role vis a vis other
proteins with similar structure(s). |
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| Methods and Results |
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| Secondary structure prediction |
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| BChE protein information and its sequence is retrieved from the
UniProtKB/Swiss-Prot with entry P06276. Figure 1 shows the BChE
sequence and its information. FASTA formatted BChE human protein
sequence was entered into self-optimized prediction method (SOPM)
to obtain the secondary structure. Figure 2 shows the secondary structure
of BChE along with its protein sequence. |
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Figure 1: UniPortKB/Swiss-prot entry for BChE Human. |
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Figure 2: BChE Secondary Structure as well as its sequence. |
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| The following sequence of BChE (i.e P06276)/ Structure (PDB id:
2pm8) was shown to interact with ApoE (PDB id: 1nfn), PON1 (PDB
id: 1v04) and ATP (sequence id: Q9Y487): |
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| >sp|P06276|CHLE_HUMAN Cholinesterase OS=Homo sapiens
GN=BCHE PE=1 SV=1 |
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| MHSKVTIICIRFLFWFLLLCMLIGKSHTEDDIIIATKNGKVRGMNLTVFGGTVTAFLGIP |
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| YAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDC |
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| LYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALG |
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| FLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPG |
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| SHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEI |
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| LLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVY |
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| GAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDV |
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| VGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLER |
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| RDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMT |
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| KLRAQQCRFWTSFFPKVLEMTGNIDEAEWEWKAGFHRWNNYMMDWKNQFNDYTSKKESCV |
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| GL |
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| Comparison of secondary structure |
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| In the current presentation we have compared the secondary structure
of BChE with other proteins to impute a common biological function,
considering the similarity of secondary structures. However, the
authors realize this is a hypothesis-generating proof of concept in silico study, which is to our knowledge, is the first comparison published for
this purpose. This must be further studied both in silico by comparison
of tertiary and quarternary structures, as well as pathway analysis and
protein-protein interaction to further refine the possible functional role
that can be verified by biological methods. |
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| By using secondary structure of BChE to search for similar structures
in PDB library, thirteen structures with different species have been
identified. To infer the functionality for assigning BChE protein, in accordance
with the similarity and Z-score values, pair-wise alignment
has been implemented between BChe structure with all these thirteen
structures. Figure 3 shows the pair wise alignment of BChE secondary
structure with 1gqr secondary structure and their structure similarity. |
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Figure 3: Pair wise alignment of BChE with 1gdr. |
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Table 1: Protein with similar secondary structures. |
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| >1gqr ACETYLCHOLINESTERASE (E.C. 3.1.1.7) COMPLEXED
WITH RIVASTIGM... |
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| Z-Score: 2.20 |
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| Normalized score: 72.134 |
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| Experimental residue alignment: |
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| Length 602 |
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| Length 532 |
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| By using the literature survey, the functionalities of thirteen species
have been collected, analyzed and given in tabular form. The Table gives
information about functionalities of these species. |
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| Discussion |
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| Our approach to secondary structure prediction is based on using
the sequence of proteins as an interlingua between the different identifiers.
This strategy allows, our secondary structure prediction platform
to integrate data from multiple sources into a single structure, while
allowing the user to control which sequences are used in the prediction. |
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| Genomic data from sequencing projects can be used for biological
and clinical research only if the functional information can be extracted
from them and biological data can be converted into ‘knowledge of biological
systems’ [10]. Butyrylcholinesterase lends itself as a prototype
for such analysis. |
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| Here we have shown that the secondary structure of butyrylcholinesterase
had similar structures distributed across the biological spectrum
ranging from plants to fish, bacteria, fungi and mammals [11-20].
This is consonant with our earlier report where BchE related sequences
were shown to be present in a similar wide spectrum of life forms [1]. |
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| The known functional roles of proteins ranged across a broad sweep
of physiological processes including the catalysis of final steps in glycolysis
[17], threonine formation [11], urate formation [19] and the binding
of a key protein in angiogenesis [20]. The active sites of proteins
also ranged from acetylcholinesterase with a deep narrow gorge [12] to
that of hyperthermophilic aldehyde ferredoxin oxidoreductase, which
shares the properties of multicentric redox proteins [13]. |
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| Evolutionarily, a study of related proteins shows they are conserved
from bacteria to humans and have homologous structure across various
sources [19], and have vestigial features of bifunctional ancestor of
fungal sulfurylase [16]. Divergence of active site is suggested, as well as
sequence identify at the erythroid cells compared to others [18]. |
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| Structural similarities among proteins are associated with functional
relationship and with being part of the same functional network
[21]. Earlier we showed that butyrylcholinesterase formed a network
with related proteins including dehydrogenases (ALDH9A1, PDHX),
ATPase (ATP6VOA2) and peraoxanase (PON1), besides acetylcholinesterases
[19]. Based on their similarity, butyrylcholinesterase may have
putative roles in maintaining cell growth and a supplementary role to
acetylcholinesterase in neural function [22,8]. |
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| Evidence is available for the modulatory role of butyrylcholinesterase
in different components of the metabolic syndrome [23]. The current
study provides further leads to understanding its relation to other
proteins similar in their secondary structure. A confluence of in silico
and in vitro methods will be able to increase possibly new indications
for therapeutic use of the protein [2]. |
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| The information has been annotated from published biological investigations.
The purpose of this in silico work is to provide proof-ofcon
[7,8] and that it may be applied for the study of other proteins with
poorly characterized functions. |
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| In summary proteins present in the cytoplasm, extracellular compartment
and cytoplasmic membranes share secondary structure simi-larity with butyrylcholinesterase and participate in catabolic, synthetic,
electron transport and immune processing. |
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| References |
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