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Occurrence and Identification of Emeria Species in Broiler Rearing Tran et al. Journal of Animal Science and Technology (2015) 57:44 DOI 10.1186/s40781-015-0077-x RESEARCH Open Access In silico characterisation, homology modelling and structure-based functional annotation of blunt snout bream (Megalobrama amblycephala) Hsp70 and Hsc70 proteins Ngoc Tuan Tran1,3, Ivan Jakovlić1 and Wei-Min Wang1,2* Abstract Background: Heat shock proteins play an important role in protection from stress stimuli and metabolic insults in almost all organisms. Methods: In this study, computational tools were used to deeply analyse the physicochemical characteristics and, using homology modelling, reliably predict the tertiary structure of the blunt snout bream (Ma-) Hsp70 and Hsc70 proteins. Derived three-dimensional models were then used to predict the function of the proteins. Results: Previously published predictions regarding the protein length, molecular weight, theoretical isoelectric point and total number of positive and negative residues were corroborated. Among the new findings are: the extinction coefficient (33725/33350 and 35090/34840 - Ma-Hsp70/ Ma-Hsc70, respectively), instability index (33.68/35.56 – both stable), aliphatic index (83.44/80.23 – both very stable), half-life estimates (both relatively stable), grand average of hydropathicity (−0.431/-0.473 – both hydrophilic) and amino acid composition (alanine-lysine-glycine/glycine-lysine-aspartic acid were the most abundant, no disulphide bonds, the N-terminal of both proteins was methionine). Homology modelling was performed by SWISS-MODEL program and the proposed model was evaluated as highly reliable based on PROCHECK’s Ramachandran plot, ERRAT, PROVE, Verify 3D, ProQ and ProSA analyses. Conclusions: The research revealed a high structural similarity to Hsp70 and Hsc70 proteins from several taxonomically distant animal species, corroborating a remarkably high level of evolutionary conservation among the members of this protein family. Functional annotation based on structural similarity provides a reliable additional indirect evidence for a high level of functional conservation of these two genes/proteins in blunt snout bream, but it is not sensitive enough to functionally distinguish the two isoforms. Keywords: Hsp70, Hsc70, Physicochemical characteristics, Homology modelling, Structural similarity, Functional annotation * Correspondence: [email protected] 1College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China 2Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 41500, China Full list of author information is available at the end of the article © 2015 Tran et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Tran et al. Journal of Animal Science and Technology (2015) 57:44 Page 2 of 9 Background of the blunt snout bream aquaculture industry reached Heat shock (or stress) proteins (HSPs) are a family of 652 215 tons in 2010 [21–23]. Previously, Ming, Xie [7] highly conserved cellular proteins that play an important used bioinformatics tools to analyse some physicochemical role in protection from stress stimuli and metabolic in- characteristics of the two Ma-Hsp70 family proteins, sults in almost all organisms [1–4]. They include three such as molecular weight, isoelectric point, solubility major families: Hsp90 (85–90 kDa), Hsp70 (68–73 kDa) (as hydrophilic property) and richness in B cells antigenic and low molecular-weight Hsps (16–47 kDa) [3]. The sites. Their results indicated that Ma-Hsp70 shares more Hsp70 family is encoded by two different genes: a consti- than 85 % identity with its homologs in other vertebrates, tutive, “housekeeping” heat shock cognate (hsc) 70 gene, has no signal peptide or transmembrane region, con- which is predominantly associated with physiological pro- tains many protein kinase C phosphorylation sites, N- cesses, and stress-inducible hsp70. Hsc70 protein plays a myristoylation sites, casein kinase II phosphorylation key role as molecular chaperone in a wide range of cellular sites and N-glycosylation sites, while the predominant processes, such as protein assembly, folding, transport elements of the secondary structure are α-helix and through membrane channels, translocation and denatur- random coil. However, as the previous study left many ation [4–7]. Hsp70 protein is mainly responsible for the questions regarding the physicochemical and structural maintenance of cellular homeostasis during the stress re- properties (particularly regarding the tertiary structure) sponse, thus protecting cells from the damage caused by open, this study, as a successive work, aims to fill this environmental stress agents, such as heat shock, chemical gap. Several different computational tools and available web exposure and UV or γ-irradiation [4, 8, 9]. Hsp70 is also a servers were used to deeply analyse the physicochemical potential activator of the innate immune system mecha- characteristics and, using homology modelling, reliably pre- nisms [10–12]. Hsp70 is considered to be by far the most dict the tertiary structure of the blunt snout bream Hsp70 evolutionary conserved protein, found in all organisms and Hsc70 proteins. Additionally, rapidly increasing num- from archaebacteria and plants to humans [13]. Both ber of known gene sequences in many organisms has proteins have a modular structure consisting of a highly prompted the need for new procedures and techniques for conserved N-terminal ATPase domain, an adjacent the high-throughput functional annotation of genes. While well-conserved substrate-binding domain (SBD) that most of those traditionally used remain rather costly and contains a hydrophobic pocket with a lid-like structure work-intensive, with rapidly growing number of protein over it, and a conserved but more variable C-terminal structures deposited in the Protein Data Bank (PDB), com- domain, which plays an important role in Hsp70 func- putational structural genomics is becoming an increasingly tions required for cell growth. In the ATP-bound state, promising tool for fast and cheap insight into protein struc- the substrate-binding pocket is open and rapidly exchanges tures, functions and interactions [24–27]. As Ming, Xie [7] substrate. ATP hydrolysis induces closing of the lid over analysed the expression of Ma-hsp70 and Ma-hsc70 genes the pocket, which stabilises substrate binding. Return to in order to gain insight into their functions, this study fur- theATP-boundstaterestores the open conformation, ther aims to provide a supplementary evidence for con- facilitating substrate release [14, 15]. served function of these two genes by in-deep structure In aquaculture, fish are often exposed to stressful situa- analysis and functional annotation of their polypeptide tions, such as sudden temperature changes, high stocking products on the basis of the similarity of their tertiary struc- density, trauma, hypoxia, as well as viral and bacterial infec- tures to the available templates from other organisms. As tions, which often results in high fish mortality. Both genes structure-based functional annotation has seldom been have been identified and their expression characterised used in study of fish proteins, the aim of this study is also in many fish species, e.g., rainbow trout (Oncorhynchus to test the applicability of this approach for functional mykiss), zebrafish (Danio rerio), Korean rockfish (Sebastes annotation of fish gene sequences. schlegeli), Nile tilapia (Oreochromis niloticus), mandarin fish (Siniperca chuatsi)[16–20] and both are known to Methods have a crucial role in response to heat shock, hypoxia, Physicochemical characterisation crowding stress and bacterial pathogens in fish [3, 4, 7, 19]. Amino acid sequences of the blunt snout bream Hsp70 (Ac- However, according to our best knowledge, a three- cession number: ACG63706.2) and Hsc70 (Accession num- dimensional (3-D) model of any fish Hsp70 family protein ber: GQ214528.1) [7] were obtained from the NCBI protein has not been published so far. database (http://www.ncbi.nlm.nih.gov/) in FASTA format Blunt snout bream (Megalobrama amblycephala Yih, as the target template and used for further analyses. Physi- 1955), native to the middle portions of the Yangtze River cochemical properties of the proteins, including molecular basin, is becoming an increasingly important freshwater weight, amino acid composition, theoretical isoelectric point aquaculture species in China. Due to its successful artifi- (pI), the total number of positive and negative residues, cial propagation and high economic value, the total output extinction coefficient (EC), instability index (II), aliphatic Tran et al. Journal of Animal Science and Technology (2015) 57:44 Page 3 of 9 Table 1 Amino acid composition of Ma-Hsp70 and Ma-Hsc70 Amino acid Ma-Hsp70 Ma-Hsc70 Amino acid Ma-Hsp70 Ma-Hsc70 N%N%
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