The S proteins of majority of coronaviruses are cleaved into two functional subunits, S1 and S2. viral and cellular membrane, hence S protein determines the specificity of host and virulence of coronavirus [2]. Similarly, there are two non-valently associated subunits in the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein, gp120 and gp41, gp120 directs target-cell recognition and viral tropism through interaction with the cell-surface receptor CD4, while the membrane-spanning gp41 promotes fusion of the viral and cellular membranes so that viral contents are released into the host cell [3]. Sequence analysis revealed that there are some similar motifs in HIV-1 gp41 and SARS-CoV S2 proteins. Gallaher and Garry [4] identified an N-terminal leucine/isoleucine zipper-like sequence and an aromatic-rich region. Kliger and Levanon [5] reported a C-terminal heptad repeat in the upstream of an aromatic-rich region. These discoveries probably lead to development of new therapeutic strategy against SARS-CoV. The goal of this study is to probe whether any similarity exists in the 3D structure of HIV-1 gp41 and SARS-CoV S2 proteins and identification of possible inhibitor-binding sites. 2.?Materials and methods The core structure of HIV-1 gp41 was downloaded from Protein Data Bank (1AIK). The sequence of spike protein was downloaded from GenBank (“type”:”entrez-protein”,”attrs”:”text”:”NP_828851″,”term_id”:”29836496″,”term_text”:”NP_828851″NP_828851). Liu et al. [1] found that the region 641C1247 of SARS-CoV S protein matches to conserved coronavirus S2 domain PF01601 in HMM database, which is subsequently used in the fold prediction of S2 subunit by 3D Jury meta predictor [6]. The proteins with significant high 3D score were used as templates to construct 3D models of S2 by modeller program [7]. The quality of 3D model was evaluated by proq program [8] and correct models were chosen for structure comparison with gp41 by LGA program [9]. The visualization of 3D structure was generated by PROTEIN EXPLORER (http://www.proteinexplorer.org). 3.?Results and discussion Meta-predictor (3D Jury) revealed that there are three significant hits (3D score 50) for S2 subunit of SARS-CoV: 1dg3_A (Human guanylate binding Protein (signaling protein), 3D score 117, threading server ShotGun on 3), 1f5n_A (Human guanylate binding Protein (signaling protein), 3D score 95, threading server mGenTHREADER) and 1ezf_A (Human squalene synthase (transferase), 3D score 82, threading server INBGU). Three templates were used to generate 3D model of S2. The quality evaluation of these models was conducted by proq program in which two measurements (ProQ-LG and ProQ-MX) were used. The NU6300 corresponding scores are below: ProQ-LG=0.583 and ProQ-MX=0.026 for 1dg3_A, ProQ-LG=1.409 and ProQ-MX=0.034 for 1f5n_A, ProQ-LG=2.503 and ProQ-MX=0.106 for 1ezf_A. In view of the fact that cutoffs for correct model are ProQ-LG 1.5 or ProQ-MX 0.1, so the correct model for S2 is the model built on template 1ezf_A, although other templates obtained marginally higher 3D scores. The alignment between S2 and template 1ezf_A with ClustalW [10] and secondary structure of S2 predicted by PsiPred v2.3 [11] are displayed in Table 1 . Fig. 1 shows that the 3D model of S2 subunit is primarily consisted of helices. In fact, Liu et al. [1] predicted the secondary structure of S protein by eight techniques and found that there are nine successive alpha-helices in S2. Based on the presence of hydrophilic and hydrophobic amino acids alternately, they speculated that these helices could be the amphipathic alpha-helices, which collapse into coiled-coils, bring a fusion peptide back toward the transmembrane domain and lead to the fusion of cellular and viral membranes [2]. Table 1 Alignment between SARS-CoV S2 protein and template 1EZF_A and secondary structure of S2 hr / Open in a separate window Open in a NU6300 separate window Open in a separate window Fig. 1 3D model of SARS-CoV S2. The LGA method is designed to compare protein structures or fragments of protein structures in sequence dependent and sequence independent modes. We superimposed the protein structure of S2 into the core structure of gp41 (1aik) by LGA. Surprisingly we found that the N chain and C chain of gp41 are well overlapped with two helices in the 3D model of S2 subunit (Fig. 2). For SARS-CoV S2 subunit, the corresponding residues include P879-N942, for HIV-1 gp41, the corresponding residues cover S546-G572 (N chain) and W628-L661 (C chain), each of residue pairs has a distance 5?? (Table 2). Open in a separate window Fig. 2 Comparison between gp41 from HIV-1 and SARS-CoV S2. N and C chains of gp41 are colored blue and yellow, respectively. S2 is.This suggests GGL and D-peptide inhibitors from HIV-1 gp41 could be used as potential inhibitors for SARS-CoV entry. Open in a separate window Fig. of coronaviruses are cleaved into two functional subunits, S1 and S2. Liu et al. [1] indicated that the S protein of SARS-associated coronavirus (SARS-CoV) also forms S1 and S2 domains. The peripheral S1 portion is responsible for cellular receptor recognition, while the membrane-spanning S2 portion mediates the fusion of viral and cellular membrane, hence S protein determines the specificity of host and virulence of coronavirus [2]. Similarly, there are two non-valently associated subunits in the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein, gp120 and gp41, gp120 directs target-cell recognition NU6300 and viral tropism through interaction with the cell-surface receptor CD4, while the membrane-spanning gp41 promotes fusion of the viral and cellular membranes so that viral contents are released into the host cell [3]. Sequence analysis revealed that there are some similar motifs in HIV-1 gp41 and SARS-CoV S2 proteins. Gallaher and Garry [4] identified an N-terminal leucine/isoleucine zipper-like sequence and an aromatic-rich region. Kliger and Levanon [5] reported a C-terminal heptad repeat in the upstream of an aromatic-rich region. These discoveries probably lead to development of new therapeutic strategy against SARS-CoV. The goal of this study is to probe whether any similarity exists in the 3D structure of HIV-1 gp41 and SARS-CoV S2 proteins and identification of possible inhibitor-binding sites. 2.?Materials and methods The core structure of HIV-1 gp41 was downloaded from Protein Data Bank (1AIK). The sequence of spike protein was downloaded from GenBank (“type”:”entrez-protein”,”attrs”:”text”:”NP_828851″,”term_id”:”29836496″,”term_text”:”NP_828851″NP_828851). Liu et al. [1] discovered that the spot 641C1247 of SARS-CoV S proteins fits to conserved coronavirus S2 site PF01601 in HMM data source, which can be subsequently found in the collapse prediction of S2 subunit by 3D Jury meta predictor [6]. The proteins with significant high 3D rating were utilized as templates to create 3D types of S2 by modeller system [7]. The grade of 3D model was examined by proq system [8] and right models were selected for structure assessment with gp41 by LGA system [9]. The visualization of 3D framework was generated by Proteins EXPLORER (http://www.proteinexplorer.org). 3.?Outcomes and dialogue Meta-predictor (3D Jury) revealed that we now have three significant strikes (3D rating 50) for S2 CD4 subunit of SARS-CoV: 1dg3_A (Human being guanylate binding Proteins (signaling proteins), 3D rating 117, threading server ShotGun on 3), 1f5n_A (Human being guanylate binding Proteins (signaling proteins), 3D rating 95, threading server mGenTHREADER) and 1ezf_A (Human being squalene synthase (transferase), 3D rating 82, threading server INBGU). Three web templates were used to create 3D style of S2. The product quality evaluation of the models was carried out by proq system where two measurements (ProQ-LG and ProQ-MX) had been used. The related ratings are below: ProQ-LG=0.583 and ProQ-MX=0.026 for 1dg3_A, ProQ-LG=1.409 and ProQ-MX=0.034 for 1f5n_A, ProQ-LG=2.503 and ProQ-MX=0.106 for 1ezf_A. Because to the fact that cutoffs for right model are ProQ-LG 1.5 or ProQ-MX 0.1, therefore the correct magic size for S2 may be the magic size built on design template 1ezf_A, although additional templates acquired marginally higher 3D ratings. The alignment between S2 and template 1ezf_A with ClustalW [10] and supplementary framework of S2 expected by PsiPred v2.3 [11] are displayed in Desk 1 . Fig. 1 demonstrates the 3D style of S2 subunit can be primarily contains helices. Actually, Liu et al. [1] expected the secondary framework of S proteins by eight methods and discovered that you can find nine successive NU6300 alpha-helices in S2. Predicated on the current presence of hydrophilic and hydrophobic proteins alternately, they speculated these helices may be the amphipathic alpha-helices, which collapse into coiled-coils, provide a fusion peptide back again toward the transmembrane site and result in the fusion of mobile and viral membranes [2]. Desk 1 Positioning between SARS-CoV S2 proteins and template 1EZF_A and supplementary framework of S2 hr / Open up in another window Open up in another window Open up in another windowpane Fig. 1 3D style of SARS-CoV S2. The LGA technique was created to evaluate protein constructions or fragments of proteins structures in series dependent and series independent settings. We superimposed the proteins framework of S2 in to the primary framework of gp41 (1aik) by LGA. Remarkably we discovered that the N string and C string of gp41 are well overlapped with two helices in the 3D style of S2 subunit (Fig. 2). For SARS-CoV S2 subunit, the corresponding residues consist of P879-N942, for HIV-1 gp41, the corresponding residues.