"Brefeldin a-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type alpha-helical structure." has been published in BMC Research Notes. (2014-7-11)

Brefeldin a-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type alpha-helical structure.

Chen YA, Murakami Y, Ahmad S, Yoshimaru T, Katagri T, Mizuguchi K.
PubMed:24997568

Abstract
BACKGROUND: Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) has been identified recently as a novel regulator of estrogen signalling in breast cancer cells. Despite being a potential target for new breast cancer treatment, its amino acid sequence suggests no association with any well-characterized protein family and provides little clues as to its molecular function. In this paper, we predicted the structure, function and interactions of BIG3 using a range of bioinformatic tools.

RESULTS: Homology search results showed that BIG3 had distinct features from its paralogues, BIG1 and BIG2, with a unique region between the two shared domains, Sec7 and DUF1981. Although BIG3 contains Sec7 domain, the lack of the conserved motif and the critical glutamate residue suggested no potential guaninyl-exchange factor (GEF) activity. Fold recognition tools predicted BIG3 to adopt an alpha-helical repeat structure similar to that of the armadillo (ARM) family. Using state-of-the-art methods, we predicted interaction sites between BIG3 and its partner PHB2.

CONCLUSIONS: The combined results of the structure and interaction prediction led to a novel hypothesis that one of the predicted helices of BIG3 might play an important role in binding to PHB2 and thereby preventing its translocation to the nucleus. This hypothesis has been subsequently verified experimentally.

2014-07-11 | Category : Research | Author : bioinfoadmin

"Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators." has been published in BMC Bioinformatics. (2014-7-1)

Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.

Murakami Y, Mizuguchi K.
PubMed:24953126

Abstract
BACKGROUND:
Identification of protein-protein interactions (PPIs) is essential for a better understanding of biological processes, pathways and functions. However, experimental identification of the complete set of PPIs in a cell/organism (“an interactome”) is still a difficult task. To circumvent limitations of current high-throughput experimental techniques, it is necessary to develop high-performance computational methods for predicting PPIs.

RESULTS:
In this article, we propose a new computational method to predict interaction between a given pair of protein sequences using features derived from known homologous PPIs. The proposed method is capable of predicting interaction between two proteins (of unknown structure) using Averaged One-Dependence Estimators (AODE) and three features calculated for the protein pair: (a) sequence similarities to a known interacting protein pair (FSeq), (b) statistical propensities of domain pairs observed in interacting proteins (FDom) and (c) a sum of edge weights along the shortest path between homologous proteins in a PPI network (FNet). Feature vectors were defined to lie in a half-space of the symmetrical high-dimensional feature space to make them independent of the protein order. The predictability of the method was assessed by a 10-fold cross validation on a recently created human PPI dataset with randomly sampled negative data, and the best model achieved an Area Under the Curve of 0.79 (pAUC0.5% = 0.16). In addition, the AODE trained on all three features (named PSOPIA) showed better prediction performance on a separate independent data set than a recently reported homology-based method.

CONCLUSIONS:
Our results suggest that FNet, a feature representing proximity in a known PPI network between two proteins that are homologous to a target protein pair, contributes to the prediction of whether the target proteins interact or not. PSOPIA will help identify novel PPIs and estimate complete PPI networks. The method proposed in this article is freely available on the web at http://mizuguchilab.org/PSOPIA.

2014-07-01 | Category : Research | Author : bioinfoadmin

"Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation." has been published in PLOS ONE. (2014-6-17)

Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation.

Chen YA, Tripathi LP, Dessailly BH, Nyström-Persson J, Ahmad S, Mizuguchi K.
PubMed:24918583

Abstract
Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.

2014-06-17 | Category : Research | Author : bioinfoadmin

"Prediction of detailed enzyme functions and identification of specificity determining residues by random forests." has been published in PLOS ONE. (2014-1-16)

Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.

Nagao C, Nagano N, Mizuguchi K.

PubMed:24416252

Abstract
Determining enzyme functions is essential for a thorough understanding of cellular processes. Although many prediction methods have been developed, it remains a significant challenge to predict enzyme functions at the fourth-digit level of the Enzyme Commission numbers. Functional specificity of enzymes often changes drastically by mutations of a small number of residues and therefore, information about these critical residues can potentially help discriminate detailed functions. However, because these residues must be identified by mutagenesis experiments, the available information is limited, and the lack of experimentally verified specificity determining residues (SDRs) has hindered the development of detailed function prediction methods and computational identification of SDRs. Here we present a novel method for predicting enzyme functions by random forests, EFPrf, along with a set of putative SDRs, the random forests derived SDRs (rf-SDRs). EFPrf consists of a set of binary predictors for enzymes in each CATH superfamily and the rf-SDRs are the residue positions corresponding to the most highly contributing attributes obtained from each predictor. EFPrf showed a precision of 0.98 and a recall of 0.89 in a cross-validated benchmark assessment. The rf-SDRs included many residues, whose importance for specificity had been validated experimentally. The analysis of the rf-SDRs revealed both a general tendency that functionally diverged superfamilies tend to include more active site residues in their rf-SDRs than in less diverged superfamilies, and superfamily-specific conservation patterns of each functional residue. EFPrf and the rf-SDRs will be an effective tool for annotating enzyme functions and for understanding how enzyme functions have diverged within each superfamily.

2014-01-16 | Category : Research | Author : bioinfoadmin

"Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability." has been published in Proteins. (2014-1-7)

Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability.

Andrabi M, Mizuguchi K, Ahmad S.

PubMed:24265157

Abstract
Both Proteins and DNA undergo conformational changes in order to form functional complexes and also to facilitate interactions with other molecules. These changes have direct implications for the stability and specificity of the complex, as well as the cooperativity of interactions between multiple entities. In this work, we have extensively analyzed conformational changes in DNA-binding proteins by superimposing DNA-bound and unbound pairs of protein structures in a curated database of 90 proteins. We manually examined each of these pairs, unified the authors’ annotations, and summarized our observations by classifying conformational changes into six structural categories. We explored a relationship between conformational changes and functional classes, binding motifs, target specificity, biophysical features of unbound proteins, and stability of the complex. In addition, we have also investigated the degree to which the intrinsic flexibility can explain conformational changes in a subset of 52 proteins with high quality coordinate data. Our results indicate that conformational changes in DNA-binding proteins contribute significantly to both the stability of the complex and the specificity of targets recognized by them. We also conclude that most conformational changes occur in proteins interacting with specific DNA targets, even though unbound protein structures may have sufficient information to interact with DNA in a nonspecific manner.

2014-01-07 | Category : Research | Author : bioinfoadmin

“Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells.” has been published in Nature Communications. (2013-9-20)

Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells.

Yoshimaru T.,Komatsu M.,Matsuo T.,Chen YA.,Murakami Y.,Mizuguchi K.,Mizohata E.,Inoue T.,Akiyama M.,Yamaguchi R.,Imoto S.,Miyano S.,Miyoshi Y.,Sasa M.,Nakamura Y.,Katagiri T.

PubMed

Abstract
The acquisition of endocrine resistance is a common obstacle in endocrine therapy of patients with oestrogen receptor-α (ERα)-positive breast tumours. We previously demonstrated that the BIG3–PHB2 complex has a crucial role in the modulation of oestrogen/ERα signalling in breast cancer cells. Here we report a cell-permeable peptide inhibitor, called ERAP, that regulates multiple ERα-signalling pathways associated with tamoxifen resistance in breast cancer cells by inhibiting the interaction between BIG3 and PHB2. Intrinsic PHB2 released from BIG3 by ERAP directly binds to both nuclear- and membrane-associated ERα, which leads to the inhibition of multiple ERα-signalling pathways, including genomic and non-genomic ERα activation and ERα phosphorylation, and the growth of ERα-positive breast cancer cells both in vitro and in vivo. More importantly, ERAP treatment suppresses tamoxifen resistance and enhances tamoxifen responsiveness in ERα-positive breast cancer cells. These findings suggest inhibiting the interaction between BIG3 and PHB2 may be a new therapeutic strategy for the treatment of luminal-type breast cancer.

2013-10-02 | Category : Research | Author : bioinfoadmin