Functional genomics based prioritization of potential nsSNPs in EPHX1, GSTT1, GSTM1 and GSTP1 genes for breast cancer susceptibility studies

In the present study, nsSNPs in EPHX1, GSTT1, GSTM1 and GSTP1 genes were screened for their functional impact on concerned proteins and their plausible role in breast cancer susceptibility. Initially, SNPs were retrieved from dbSNP, followed by identification of potentially deleterious nsSNPs using PolyPhen and SIFT. Functional analysis was done with SNPs3D, SNPs&GO and MutPred methods. Prediction and evaluation of the functional impact on the 3D structure of proteins were performed with Swiss PDB viewer and NOMAD-Ref servers. On analysis, 13 nsSNPs were found to be highly deleterious and damaging to the protein structure, of which 6 nsSNPs, rs45549733, rs45506591 and rs4986949 of GSTP1, rs72549341 and rs148240980 of EPHX1 and rs17856199 of GSTT1 were predicted to be potentially polymorphic. It is therefore hypothesized that the 6 identified nsSNPs may alter the detoxification process and elevate carcinogenic metabolite accumulation thus modifies the risk of breast cancer susceptibility in a group of women.     

hRFT2基因单核苷酸多态性的生物信息学分析

旨在筛选可能与人类疾病有关的hRFT2基因单核苷酸多态性(single nucleotide polymorphisms,nsSNPs)和突变位点,从SNP数据库中检索并筛选出395个有效的hRFT2基因SNPs,其中包括30个同义SNPs(synonymous SNPs,sSNPs)和31个非同义SNPs(non-synonymous single nucleotide polymorphisms,nsSNPs)。分别采用SIFT、SNPs3D和PolyPhen-2方法分析nsSNPs引起的氨基酸替换是否可能影响hRFT2的功能。结果表明,5个nsSNPs(rs11477762、rs146302587、rs146492942、rs76947760和rs145431028)可能严重影响hRFT2蛋白的功能,其中rs76947760和rs145431028的影响已得到临床证明,另外3个nsSNPs(rs148387972、rs140391358和rs3746802)也可能对hRFT2有较大的影响。     

Exploration of deleterious single nucleotide polymorphisms in late-onset Alzheimer disease susceptibility genes

Non-synonymous single nucleotide polymorphisms (nsSNPs) are considered as biomarkers to disease susceptibility. In the present study, nsSNPs in CLU, PICALM and BIN1 genes were screened for their functional impact on concerned proteins and their plausible role in Alzheimer disease (AD) susceptibility. Initially, SNPs were retrieved from dbSNP database, followed by identification of potentially deleterious nsSNPs and prediction of their effect on proteins by PolyPhen and SIFT. Protein stability and the probability of mutation occurrence were predicted using I-Mutant and PANTHER respectively. SNPs3D and FASTSNP were used for the functional analysis of nsSNPs. The functional impact on the 3D structure of proteins was evaluated by SWISSPDB viewer and NOMAD-Ref server. On analysis, 3 nsSNPs with IDs rs12800974 (T158P) of PICALM and rs11554585 (R397C) and rs11554585 (N106D) of BIN1 were predicted to be functionally significant with higher scores of I-Mutant, SIFT, PolyPhen, PANTHER, FASTSNP and SNPs3D. The mutant models of these nsSNPs also showed very high energies and RMSD values compared to their native structures. Current study proposes that the three nsSNPs identified in this study constitute a unique resource of potential genetic factors for AD susceptibility.     

Improving a consensus approach for protein structure selection by removing redundancy

In protein tertiary structure prediction, a crucial step is to select near-native structures from a large number of predicted structural models. Over the years, extensive research has been conducted for the protein structure selection problem with most approaches focusing on developing more accurate energy or scoring functions. Despite significant advances in this area, the discerning power of current approaches is still unsatisfactory. In this paper, we propose a novel consensus-based algorithm for the selection of predicted protein structures. Given a set of predicted models, our method first removes redundant structures to derive a subset of reference models. Then, a structure is ranked based on its average pairwise similarity to the reference models. Using the CASP8 data set containing a large collection of predicted models for 122 targets, we compared our method with the best CASP8 quality assessment (QA) servers, which are all consensus based, and showed that our QA scores correlate better with the GDT-TSs than those of the CASP8 QA servers. We also compared our method with the state-of-the-art scoring functions and showed its improved performance for near-native model selection. The GDT-TSs of the top models picked by our method are on average more than 8 percent better than the ones selected by the best performing scoring function.     

The effect of granulocyte colony stimulating factor receptor gene missense single nucleotide polymorphisms on peripheral blood stem cell enrichment

Granulocyte-colony stimulating factor (G-CSF) has become the most effective agent supporting hematopoietic stem cell transplantation (HSCT). The cognate interaction between G-CSF and its specific receptor, G-CSFR, induces the mobilization of HSCs and increases their pool in the peripheral blood. G-CSFR has a highly conserved structure which may be functionally modulated by the presence of missense single nucleotide polymorphisms (SNPs). In this study, we asked whether the missense SNPs in G-CSFR could affect the response to G-CSF in HSCT patients and donors. Here, for the first time, G-CSFR missense SNPs were screened and minor allele frequencies were determined in a specific population with Turkish racial background. Five (rs3917991, rs3918001, rs3918018, rs3918019, and rs146617729) out of 16 missense SNPs screened were determined with minor allele frequencies lower than 0.04. Subsequent association analyses indicated potential impact of rs3918001, rs3918018, and rs3918019 minor alleles on peripheral blood CD34⁺ cell enrichment. Although their frequency is rather low, certain missense SNPs, especially which are placed in the conserved regions of G-CSFR may possess the capacity to influence the response to G-CSF treatment.     

Screening and structural evaluation of deleterious Non-Synonymous SNPs of ePHA2 gene involved in susceptibility to cataract formation

Age-related cataract is clinically and genetically heterogeneous disorder affecting the ocular lens, and the leading cause of vision loss and blindness worldwide. Here we screened nonsynonymous single nucleotide polymorphisms (nsSNPs) of a novel gene, EPHA2 responsible for age related cataracts. The SNPs were retrieved from dbSNP. Using I-Mutant, protein stability change was calculated. The potentially functional nsSNPs and their effect on protein was predicted by PolyPhen and SIFT respectively. FASTSNP was used for functional analysis and estimation of risk score. The functional impact on the EPHA2 protein was evaluated by using SWISSPDB viewer and NOMAD-Ref server. Our analysis revealed 16 SNPs as nonsynonymous out of which 6 nsSNPs, namely rs11543934, rs2291806, rs1058371, rs1058370, rs79100278 and rs113882203 were found to be least stable by I-Mutant 2.0 with DDG value of > -1.0. nsSNPs, namely rs35903225, rs2291806, rs1058372, rs1058370, rs79100278 and rs113882203 showed a highly deleterious tolerance index score of 0.00 by SIFT server. Four nsSNPs namely rs11543934, rs2291806, rs1058370 and rs113882203 were found to be probably damaging with PSIC score of ≥ 2. 0 by Polyp hen server. Three nsSNPs namely, rs11543934, rs2291806 and rs1058370 were found to be highly polymorphic with a risk score of 3-4 with a possible effect of Non-conservative change and splicing regulation by FASTSNP. The total energy and RMSD value was higher for the mutant-type structure compared to the native type structure. We concluded that the nsSNP namely rs2291806 as the potential functional polymorphic that is likely to have functional impact on the EPHA2 gene.     

Computational detection of deleterious SNPs and their effect on sequence and structural level of the <Emphasis Type="Italic">VHL</Emphasis> gene

In this work we have analyzed the genetic variation that can alter the expression and the function of the VHL gene using computational methods. Of 110 single nucleotide polymorphisms (SNPs), 33 were found to be nonsynonymous (nsSNPs) and 23 SNPs were found in untranslated regions. Of the 33 nsSNPs investigated, 36.3% were found to be deleterious by both SIFT and PolyPhen servers. An untranslated region (UTR) resource tool suggested that two SNPs in the 5' UTR region and six SNPs in the 3' UTR region might change the protein expression levels. It was found by both SIFT and PolyPhen servers that a mutation from histidine to arginine at position 115 of the native protein of the VHL gene was most deleterious. A structural analysis of this mutated protein and the native protein was performed and had a root mean square deviation (RMSD) of 2.78 A. Based on this work, we propose that the nsSNP with a SNPid of rs5030812 is an important candidate for the cause of von Hippel-Lindau syndrome via the VHL gene.     

新型冠状病毒相关TMPRSS2蛋白结构特征和抗原表位分析

采用生物信息学方法分析预测新型冠状病毒(Severe acute respiratory syndrome coronavirus 2, SARS-CoV-2)跨膜蛋白酶丝氨酸2(transmembrane protease serine 2, TMPRSS2)的理化特性、结构特征和抗原表位,为抗SARS-CoV-2药物研发提供参考。利用ProtParam、ProtScale分析预测TMPRSS2蛋白酶的理化特性;利用COILS Server、SignalP、TMPred、TargetP Server、NetPhos Server、NetNGlyc Server服务器对TMPRSS2蛋白酶结构进行功能结构的分析预测;利用SOPMA、Pfam、SWISS-MODEL分析预测TMPRSS2蛋白酶高级结构;利用IEBD分析预测TMPRSS2蛋白酶B细胞、T细胞表位。TMPRSS2蛋白酶氨基酸组成数为492个,其中丝氨酸占比最高;亲水性较高,含10个跨膜螺旋区;具有4个磷酸化位点,3个糖基化修饰点;二级结构中无规则卷曲占据主导地位,三级结构能与已知的5ce.1.1.A(SMTL ID)模型同源建模;存在13个潜在的B细胞表位,12个得分较高的T细胞表位。     

Homology modeling of the central catalytic domain of insertion sequence ISLC3 isolated from Lactobacillus casei ATCC 393

The tertiary structure of the central catalytic domain of insertion sequence ISLC3 isolated from Lactobacillus casei ATCC 393 was predicted using the homology modeling approach. The novel insertion sequence was isolated by us from the template bacteriophage phiA3 of L.casei ATCC 393. The number of amino acid residues of the ISLC3 central catalytic domain was 116 and was treated as the query sequence. There were five Web-available threading methods used to find some primary structure templates for the query sequence. These primary templates were further screened using the SWISS-MODEL Protein Modeling Server and the default parameter settings therein to give six final structure templates. All of these final structure templates were the integrase (IN) protein of retroviruses. Multiple sequence alignment using these IN sequences against the query one revealed the signature DDE motif. Based on the structures of these final templates, the structure of the query sequence was constructed using the InsightII/Discover/Homology programs. A metal ion, Mg(2+), was inserted into the center of the putative catalytic pocket formed by the DDE residues of the predicted structure in the final rounds of refinement by molecular dynamics (MD) simulations. The structure with a metal ion included was designated with Mg and that without a metal ion was designated free Mg. The average exposed surface area of some hydrophobic residues of both the predicted free Mg and with Mg structures were computed and compared with those computed for the six structure templates. Whereas the predicted with Mg structure was slightly more exposed than the predicted free Mg structure, the former appeared to be more stable than the latter, as revealed by the lower conformation energy recorded for the former during the structure refinement by MD simulations. To verify further the predicted structures, the coordinates of both predicted structures were fed into the ERRAT Protein Verification Server. It was found that the quality of the predicted with Mg structure was much better than that of the free Mg structure. The validation results also indicated that regions of the predicted with Mg structure that can be rejected at the 95% confidence level were approximately 20% whereas those which can be rejected at the same level for the six structure templates were approximately 10%. The predicted with Mg structure was also docked into a short oligonucleotide representing the substrate of the ISLC3 transposase using the DOCK_4.0.2 program. It was found that both Glu140 and Asp68 residues of the DDE motif of the predicted with Mg structure were able to form hydrogen bonds with the DNA substrate, which was similar to what was observed in a docking study using the retrovirus IN 1asu and its DNA substrate.     

Thioredoxin reductase 1 haplotypes modify familial amyotrophic lateral sclerosis onset

Thioredoxin reductase 1 is a key enzyme in cellular redox processes, which are known to play a role in the pathogenesis of familial amyotrophic lateral sclerosis (FALS). The gene TXNRD1 was therefore screened for association with FALS. Resequencing of the exons and flanking regions identified 19 single-nucleotide polymorphisms (SNPs) of which 2, the intronic SNPs rs6539137 and rs4630362, were significantly associated with FALS. However, no association of rs6539137 with sporadic ALS was detected. The TXNRD1 haplotypes were reconstructed using the EH and PHASE 2.1 programs and also showed an association with FALS. Bayesian analysis of these SNP combinations, carried out using the BIMBAM program, indicated that rs10861192 strongly augmented this association. Indeed the haplotypes with minor alleles at both rs10861192 and rs6539137, although present in FALS, were totally absent from controls. Patients with the minor allele of rs6539137 were also associated with an early age at onset, which was decreased by 8 years. Furthermore the shift of onset was more pronounced in males and not significant in females. These results show that TXNRD1 may act as an important modifier gene of FALS and indicate that the additional thiol-redox system genes, thioredoxin and the peroxiredoxins, should also be investigated in FALS and other neurological disorders.     

Modeling the tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin.

The tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin (Hbm) was modeled using computer tools and the known tertiary structure of rice Hb1 as a template. This method was tested by predicting the tertiary structure of soybean leghemoglobin a (Lba) using rice Hb1 as a template. The tertiary structures of the predicted and native Lba were similar, indicating that our computer methods could reliably predict the tertiary structures of plant Hbs. We next predicted the tertiary structure of Hbm. Hbm appears to have a long pre-helix A and a large CD-loop. The positions of the distal and proximal His are identical in Hbm and rice Hb1, which suggests that heme-Fe is hexacoordinate in Hbm and that the kinetic properties of Hbm and rice Hb1 are expected to be very similar, i.e. that Hbm has a high O2-affinity. Thermostability analysis showed that Hbm CD-loop is unstable and may provide mobility to amino acids located at the heme pocket for both ligand binding and stabilization and heme-Fe coordination. Analysis of the C-terminal half of Hbm showed the existence of a pocket-like region (the N/C cavity) where interactions with organic molecules or proteins could be possible. Lys K94 protrudes into the N/C cavity, suggesting that K94 may sense the binding of molecules to the N/C cavity. Thus, it is likely that the instability of the CD-loop and the possibility of binding molecules to the N/C cavity are essential for positioning amino acids in the heme pocket and in regulating Hbm activity and function.     

Identification and in silico analysis of functional SNPs of the BRCA1 gene

Single-nucleotide polymorphisms (SNPs) play a major role in the understanding of the genetic basis of many complex human diseases. Also, the genetics of human phenotype variation could be understood by knowing the functions of these SNPs. It is still a major challenge to identify the functional SNPs in a disease-related gene. In this work, we have analyzed the genetic variation that can alter the expression and the function of the BRCA1 gene using computational methods. Of the total 477 SNPs, 65 were found to be nonsynonymous (ns) SNPs. Among the 14 SNPs in the untranslated region, 4 were found in the 5' and 10 were found in the 3' untranslated region (UTR). It was found that 16.9% of the nsSNPs were damaging, by both the SIFT and the PolyPhen servers. The UTR Resource tool suggested that 2 of 4 SNPs in the 5' UTR and 3 of 10 SNPs in the 3' UTR might change the protein expression levels. We identified major mutations from proline to serine at positions 1776 and 1812 of the native protein of the BRCA1 gene. From a comparison of the stabilizing residues of the native and mutant proteins, we propose that an nsSNP (rs1800751) could be an important candidate for the breast cancer caused by the BRCA1 gene.     

Identification of functional single nucleotide polymorphisms in the branchpoint site

Background

The human genome contains millions of single nucleotide polymorphisms (SNPs); many of these SNPs are intronic and have unknown functional significance. SNPs occurring within intron branchpoint sites, especially at the adenine (A), would presumably affect splicing; however, this has not been systematically studied. We employed a splicing prediction tool to identify human intron branchpoint sites and screened dbSNP for identifying SNPs located in the predicted sites to generate a genome-wide branchpoint site SNP database.

Results

We identified 600 SNPs located within branchpoint sites; among which, 216 showed a change in A. After scoring the SNPs by counting the As in the ±?10 nucleotide region, only four SNPs were identified without additional As (rs13296170, rs12769205, rs75434223, and rs67785924). Using minigene constructs, we examined the effects of these SNPs on splicing. The three SNPs (rs13296170, rs12769205, and rs75434223) with nucleotide substitution at the A position resulted in abnormal splicing (exon skipping and/or intron inclusion). However, rs67785924, a 5-bp deletion that abolished the branchpoint A nucleotide, exhibited normal RNA splicing pattern, presumably using two of the downstream As as alternative branchpoints. The influence of additional As on splicing was further confirmed by studying rs2733532, which contains three additional As in the ±?10 nucleotide region.

Conclusions

We generated a high-confidence genome-wide branchpoint site SNP database, experimentally verified the importance of A in the branchpoint, and suggested that other nearby As can protect branchpoint A substitution from abnormal splicing.

     

Customized multiplexing SNP panel for Korean-specific DNA phenotyping in forensic applications

Due to the recent growth of the alien population in Korea, tracking the ethnic origin of human specimens has gained importance in genetic forensics. To address this issue, we developed a method to analyze single nucleotide polymorphisms (SNPs) based on next-generation sequencing (NGS) technology, which is now being used for personal identification in forensics. We designed a panel of 153 Korean-specific high-performance multiplexed SNPs and performed NGS using 233 DNA samples collected from eight different ethnic groups around the world. Eight Korean-specific genetic markers (rs28777, rs1010872, rs6043841, rs6034433, rs885479, rs2503107, rs4530059, and rs214955) that were screened showed significant variability among the ethnic groups. Three markers were novel SNPs that were absent from our multiplexed SNP panel, and two markers were associated with specific phenotypes. Our high-performance multiplexed SNP panel allows efficient screening of Korean-specific SNP alleles in populations that are genetically similar to the Korean population (e.g., Japanese and northeast Asians including Chinese and Eurasians), which will be useful for personal identification, paternity testing, and forensic investigations.     

植物炭疽病真菌金属硫蛋白的三级结构预测

根据实验测定的Ⅰ类金属硫蛋白(metallothionein, MT)三级结构的实验数据,给出该类蛋白质的两种特征结构(CXC、CXXC一级结构,半胱氨酸-金属络合簇三级结构)的原子间距离约束条件,然后运用距离几何算法计算出一系列可能的构象.从这些构象中经统计分析筛选出目标函数值显著较小的结构作为所预测蛋白质的三级结构模型.用已知结构的蓝蟹MT对方法进行检验证实其可行性后,对植物炭疽病真菌金属硫蛋白CAP3进行了三级结构预测.     

LOMETS: a local meta-threading-server for protein structure prediction

We developed LOMETS, a local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. Nine state-of-the-art threading programs are installed and run in a local computer cluster, which ensure the quick generation of initial threading alignments compared with traditional remote-server-based meta-servers. Consensus models are generated from the top predictions of the component-threading servers, which are at least 7% more accurate than the best individual servers based on TM-score at a t-test significance level of 0.1%. Moreover, side-chain and C-alpha (C(alpha)) contacts of 42 and 61% accuracy respectively, as well as long- and short-range distant maps, are automatically constructed from the threading alignments. These data can be easily used as constraints to guide the ab initio procedures such as TASSER for further protein tertiary structure modeling. The LOMETS server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/LOMETS.