Received date May 14, 2012; Accepted date June 20, 2012; Published date June 25, 2012
Citation: Srinivas K, Sridhar GR, Allam AR (2012) Secondary Structure of Butyrylcholinesterase. J Diabetes Metab 3:199. doi:10.4172/2155-6156.1000199
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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In silico; Protein Data Bank (PDB)
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.
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.
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.
Butyrylcholinesterase is an enzyme that is involved in the phenotypic expression of insulin resistance and metabolic syndrome . 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 pesticidesand 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.
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 . 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 . 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].
In this presentation we predict the secondary structure of BchE; by using bioinformaticstools 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).
Secondary structure prediction
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.
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):
>sp|P06276|CHLE_HUMAN Cholinesterase OS=Homo sapiens GN=BCHE PE=1 SV=1
Comparison of secondary structure
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.
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.
>1gqr ACETYLCHOLINESTERASE (E.C. 220.127.116.11) COMPLEXED WITH RIVASTIGM...
Normalized score: 72.134
Experimental residue alignment:
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.
|PDB id||Species Name||Score||Z-score||Biological Functions||Molecular Functions||Cellular Components|
|1gqr||species of electric ray||72.134||2.20||acetylcholinesterase activity cholinesterase activity||acetylcholine catabolic process in synaptic cleft|
|1mah||Mouse||71.8062||2.18||cholinesterase activity||Extracellular region|
|1i2d||CRYSTAL STRUCTURE OF ATP SULFURYLASE FROM PENICILLIUM CHRYSOGENUM||67.9727||1.92||Sulfate adenylyltransferase (ATP) activity ATP binding kinase activity transferase activity, transferring phosphorus-containing groups||sulfate assimilation|
|1a3w||PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH FBP, PG, MN2+ AND K+||67.5503||1.89||magnesium ion binding pyruvate kinase activity potassium ion binding||glycolysis|
|1e5x||STRUCTURE OF THREONINE SYNTHASE FROM ARABIDOPSIS THALIANA||67.4264||1.89||catalytic activity threonine synthase activity pyridoxal phosphate binding||amino acid metabolic process metabolic process threonine biosynthetic process|
|1d9z||CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP||66.7785||1.84||nucleic acid binding
DNA binding helicase activity
ATP binding excinuclease ABC activity hydrolase activity
excinuclease repair complex
|1aor||STRUCTURE OF A HYPERTHERMOPHILIC TUNGSTOPTERIN ENZYME, ALDEHYDE FERREDOXIN OXIDOREDUCTASE||66.28||1.81||oxidoreductase activity, acting on the aldehyde or oxo group of donors,
iron-sulfur protein as acceptor iron-sulfur cluster binding
|1fiq||CRYSTAL STRUCTURE OF XANTHINE OXIDASE FROM BOVINE MILK||66.147||1.80||xanthine dehydrogenase activity xanthine oxidase activity electron carrier activity oxidoreductase activity
metal ion binding
FAD binding iron-sulfur cluster binding
|1k9d||A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1||65.9591||1.79||catalytic activity cation binding alpha-glucuronidase activity||carbohydrate metabolic process xylan catabolic process||extracellular region|
|1a4y||RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX||65.9134||1.79||protein binding
nucleic acid binding
pancreatic ribonuclease activity
|1de4||HEMOCHROMATOSIS PROTEIN HFE COMPLEXED WITH TRANSFERRIN RECEPTOR||65.7235||1.77||immune response
antigen processing and presentation
MHC class I protein complex
|1a5k||K217E VARIANT OF KLEBSIELLA AEROGENES UREASE||65.6678||1.77||urease activity nickel ion binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds||nitrogen compound metabolic process urea metabolic process|
|1k3c||Phosphoenolpyruvate carboxykinase in complex with ADP, AlF3 and Pyruvate||65.5233||1.76||phosphoenolpyruvate carboxykinase activity
phosphoenolpyruvate carboxykinase (ATP) activity ATP binding
purine nucleotide binding
Table 1: Protein with similar secondary structures.
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.
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’ . Butyrylcholinesterase lends itself as a prototype for such analysis.
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 .
The known functional roles of proteins ranged across a broad sweep of physiological processes including the catalysis of final steps in glycolysis , threonine formation , urate formation  and the binding of a key protein in angiogenesis . The active sites of proteins also ranged from acetylcholinesterase with a deep narrow gorge  to that of hyperthermophilic aldehyde ferredoxin oxidoreductase, which shares the properties of multicentric redox proteins .
Evolutionarily, a study of related proteins shows they are conserved from bacteria to humans and have homologous structure across various sources , and have vestigial features of bifunctional ancestor of fungal sulfurylase . Divergence of active site is suggested, as well as sequence identify at the erythroid cells compared to others .
Structural similarities among proteins are associated with functional relationship and with being part of the same functional network . Earlier we showed that butyrylcholinesterase formed a network with related proteins including dehydrogenases (ALDH9A1, PDHX), ATPase (ATP6VOA2) and peraoxanase (PON1), besides acetylcholinesterases . Based on their similarity, butyrylcholinesterase may have putative roles in maintaining cell growth and a supplementary role to acetylcholinesterase in neural function [22,8].
Evidence is available for the modulatory role of butyrylcholinesterase in different components of the metabolic syndrome . 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 .
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.
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.