JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis.

SUMMARY: JUCHMME is an open-source software package designed to fit arbitrary custom Hidden Markov Models (HMMs) with a discrete alphabet of symbols. We incorporate a large collection of standard algorithms for HMMs as well as a number of extensions and evaluate the software on various biological problems. Importantly, the JUCHMME toolkit includes several additional features that allow for easy building and evaluation of custom HMMs, which could be a useful resource for the research community. AVAILABILITY AND IMPLEMENTATION: http://www.compgen.org/tools/juchmme, https://github.com/pbagos/juchmme. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Analysis of Single-Nucleotide Polymorphisms in Human Voltage-Gated Ion Channels.

Voltage-gated ion channels (VGICs) are one of the largest groups of transmembrane proteins. Due to their major role in the generation and propagation of electrical signals, VGICs are considered important from a medical viewpoint, and their dysfunction is often associated with Channelopathies. We identified disease-associated mutations and polymorphisms in these proteins through mapping missense single-nucleotide polymorphisms from the UniProt and ClinVar databases on their amino acid sequence, considering their special topological and functional characteristics. Statistical analysis revealed that disease-associated SNPs are mostly found in the voltage sensor domain and the pore loop. Both of these regions are extremely important for the activation and ion conductivity of VGICs. Moreover, among the most frequently observed mutations are those of arginine to glutamine, to histidine or to cysteine, which can probably be attributed to the extremely important role of arginine residues in the regulation of membrane potential in these proteins. We suggest that topological information in combination with genetic variation data can contribute toward a better evaluation of the effect of currently unclassified mutations in VGICs. It is hoped that potential associations with certain disease phenotypes will be revealed in the future with the use of similar approaches.

CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea.

Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED's superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http://195.251.108.230/apps.compgen.org/CW-PRED/ and as standalone software.

Proteome-Wide Detection and Annotation of Receptor Tyrosine Kinases (RTKs): RTK-PRED and the TyReK Database.

Receptor tyrosine kinases (RTKs) form a highly important group of protein receptors of the eukaryotic cell membrane. They control many vital cellular functions and are involved in the regulation of complex signaling networks. Mutations in RTKs have been associated with different types of cancers and other diseases. Although they are very important for proper cell function, they have been experimentally studied in a limited range of eukaryotic species. Currently, there is no available database for RTKs providing information about their function, expression, and interactions. Therefore, the identification of RTKs in multiple organisms, the documentation of their characteristics, and the collection of related information would be very useful. In this paper, we present a novel RTK detection pipeline (RTK-PRED) and the Receptor Tyrosine Kinases Database (TyReK-DB). RTK-PRED combines profile HMMs with transmembrane topology prediction to identify and classify potential RTKs. Proteins of all eukaryotic reference proteomes of the UniProt database were used as input in RTK-PRED leading to a filtered dataset of 20,478 RTKs. Based on the information collected for these RTKs from multiple databases, the relational TyReK database was created.

NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions.

The nuclear envelope (NE) is a double-membrane system surrounding the nucleus of eukaryotic cells. A large number of proteins are localized in the NE, performing a wide variety of functions, from the bidirectional exchange of molecules between the cytoplasm and the nucleus to chromatin tethering, genome organization, regulation of signaling cascades, and many others. Despite its importance, several aspects of the NE, including its protein-protein interactions, remain understudied. In this work, we present NucEnvDB, a publicly available database of NE proteins and their interactions. Each database entry contains useful annotation including a description of its position in the NE, its interactions with other proteins, and cross-references to major biological repositories. In addition, the database provides users with a number of visualization and analysis tools, including the ability to construct and visualize protein-protein interaction networks and perform functional enrichment analysis for clusters of NE proteins and their interaction partners. The capabilities of NucEnvDB and its analysis tools are showcased by two informative case studies, exploring protein-protein interactions in Hutchinson-Gilford progeria and during SARS-CoV-2 infection at the level of the nuclear envelope.

LiGIoNs: A computational method for the detection and classification of ligand-gated ion channels.

Ligand-Gated Ion Channels (LGICs) is one of the largest groups of transmembrane proteins. Due to their major role in synaptic transmission, both in the nervous system and the somatic neuromuscular junction, LGICs present attractive therapeutic targets. During the last few years, several computational methods for the detection of LGICs have been developed. These methods are based on machine learning approaches utilizing features extracted solely from the amino acid composition. Here we report the development of LiGIoNs, a profile Hidden Markov Model (pHMM) method for the prediction and ligand-based classification of LGICs. The method consists of a library of 10 pHMMs, one per LGIC subfamily, built from the alignment of representative LGIC sequences. In addition, 14 Pfam pHMMs are used to further annotate and classify unknown protein sequences into one of the 10 LGIC subfamilies. Evaluation of the method showed that it outperforms existing methods in the detection of LGICs. On top of that, LiGIoNs is the only currently available method that classifies LGICs into subfamilies. The method is available online at http://bioinformatics.biol.uoa.gr/ligions/.

AmyCo: the amyloidoses collection.

Amyloid fibrils are formed when soluble proteins misfold into highly ordered insoluble fibrillar aggregates and affect various organs and tissues. The deposition of amyloid fibrils is the main hallmark of a group of disorders, called amyloidoses. Curiously, fibril deposition has been also recorded as a complication in a number of other pathological conditions, including well-known neurodegenerative or endocrine diseases. To date, amyloidoses are roughly classified, owing to their tremendous heterogeneity. In this work, we introduce AmyCo, a freely available collection of amyloidoses and clinical disorders related to amyloid deposition. AmyCo classifies 75 diseases associated with amyloid deposition into two distinct categories, namely 1) amyloidosis and 2) clinical conditions associated with amyloidosis. Each database entry is annotated with the major protein component (causative protein), other components of amyloid deposits and affected tissues or organs. Database entries are also supplemented with appropriate detailed annotation and are referenced to ICD-10, MeSH, OMIM, PubMed, AmyPro and UniProtKB databases. To our knowledge, AmyCo is the first attempt towards the creation of a complete and an up-to-date repository, containing information about amyloidoses and diseases related to amyloid deposition. The AmyCo web interface is available at http://bioinformatics.biol.uoa.gr/amyco .

Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes.

Surface proteins in Gram-positive bacteria are frequently implicated in virulence. We have focused on a group of extracellular cell wall-attached proteins (CWPs), containing an LPXTG motif for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A hidden Markov model (HMM) approach for predicting the LPXTG-anchored cell wall proteins of Gram-positive bacteria was developed and compared against existing methods. The HMM model is parsimonious in terms of the number of freely estimated parameters, and it has proved to be very sensitive and specific in a training set of 55 experimentally verified LPXTG-anchored cell wall proteins as well as in reliable data sets of globular and transmembrane proteins. In order to identify such proteins in Gram-positive bacteria, a comprehensive analysis of 94 completely sequenced genomes has been performed. We identified, in total, 860 LPXTG-anchored cell wall proteins, a number that is significantly higher compared to those obtained by other available methods. Of these proteins, 237 are hypothetical proteins according to the annotation of SwissProt, and 88 had no homologs in the SwissProt database--this might be evidence that they are members of newly identified families of CWPs. The prediction tool, the database with the proteins identified in the genomes, and supplementary material are available online at http://bioinformatics.biol.uoa.gr/CW-PRED/.

Deep-proteome mapping of WM-266-4 human metastatic melanoma cells: From oncogenic addiction to druggable targets.

Cutaneous melanoma is a malignant tumor of skin melanocytes that are pigment-producing cells located in the basal layer (stratum basale) of epidermis. Accumulation of genetic mutations within their oncogenes or tumor-suppressor genes compels melanocytes to aberrant proliferation and spread to distant organs of the body, thereby resulting in severe and/or lethal malignancy. Metastatic melanoma's heavy mutational load, molecular heterogeneity and resistance to therapy necessitate the development of novel biomarkers and drug-based protocols that target key proteins involved in perpetuation of the disease. To this direction, we have herein employed a nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) proteomics technology to profile the deep-proteome landscape of WM-266-4 human metastatic melanoma cells. Our advanced melanoma-specific catalogue proved to contain 6,681 unique proteins, which likely constitute the hitherto largest single cell-line-derived proteomic collection of the disease. Through engagement of UNIPROT, DAVID, KEGG, PANTHER, INTACT, CYTOSCAPE, dbEMT and GAD bioinformatics resources, WM-266-4 melanoma proteins were categorized according to their sub-cellular compartmentalization, function and tumorigenicity, and successfully reassembled in molecular networks and interactomes. The obtained data dictate the presence of plastically inter-converted sub-populations of non-cancer and cancer stem cells, and also indicate the oncoproteomic resemblance of melanoma to glioma and lung cancer. Intriguingly, WM-266-4 cells seem to be subjected to both epithelial-to-mesenchymal (EMT) and mesenchymal-to-epithelial (MET) programs, with 1433G and ADT3 proteins being identified in the EMT/MET molecular interface. Oncogenic addiction of WM-266-4 cells to autocrine/paracrine signaling of IL17-, DLL3-, FGF(2/13)- and OSTP-dependent sub-routines suggests their critical contribution to the metastatic melanoma chemotherapeutic refractoriness. Interestingly, the 1433G family member that is shared between the BRAF- and EMT/MET-specific interactomes likely emerges as a novel and promising druggable target for the malignancy. Derailed proliferation and metastatic capacity of WM-266-4 cells could also derive from their metabolic addiction to pathways associated with glutamate/ammonia, propanoate and sulfur homeostasis, whose successful targeting may prove beneficial for advanced melanoma-affected patients.

PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization.

The ability to predict the subcellular localization of a protein from its sequence is of great importance, as it provides information about the protein's function. We present a computational tool, PredSL, which utilizes neural networks, Markov chains, profile hidden Markov models, and scoring matrices for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence. It aims to classify proteins into five groups: chloroplast, thylakoid, mitochondrion, secretory pathway, and "other". When tested in a five-fold cross-validation procedure, PredSL demonstrates 86.7% and 87.1% overall accuracy for the plant and non-plant datasets, respectively. Compared with TargetP, which is the most widely used method to date, and LumenP, the results of PredSL are comparable in most cases. When tested on the experimentally verified proteins of the Saccharomyces cerevisiae genome, PredSL performs comparably if not better than any available algorithm for the same task. Furthermore, PredSL is the only method capable for the prediction of these subcellular localizations that is available as a stand-alone application through the URL:http://bioinformatics.biol.uoa.gr/PredSL/.

The human plasma membrane peripherome: visualization and analysis of interactions.

A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with noncovalent interactions. The aim of this study was to construct and analyze the interactions of the human plasma membrane peripheral proteins (peripherome hereinafter). For this purpose, we collected a dataset of peripheral proteins of the human plasma membrane. We also collected a dataset of experimentally verified interactions for these proteins. The interaction network created from this dataset has been visualized using Cytoscape. We grouped the proteins based on their subcellular location and clustered them using the MCL algorithm in order to detect functional modules. Moreover, functional and graph theory based analyses have been performed to assess biological features of the network. Interaction data with drug molecules show that ~10% of peripheral membrane proteins are targets for approved drugs, suggesting their potential implications in disease. In conclusion, we reveal novel features and properties regarding the protein-protein interaction network created by peripheral proteins of the human plasma membrane.

Estimation of membrane proteins in the human proteome.

Genomics and proteomics have added valuable information to our knowledgebase of the human biological system including the discovery of therapeutic targets and disease biomarkers. However, molecular profiling studies commonly result in the identification of novel proteins of unknown localization. A class of proteins of special interest is membrane proteins, in particular plasma membrane proteins. Despite their biological and medical significance, the 3-dimensional structures of less than 1% of plasma membrane proteins have been determined. In order to aid in identification of membrane proteins, a number of computational methods have been developed. These tools operate by predicting the presence of transmembrane segments. Here, we utilized five topology prediction methods (TMHMM, SOSUI, waveTM, HMMTOP, and TopPred II) in order to estimate the ratio of integral membrane proteins in the human proteome. These methods employ different algorithms and include a newly-developed method (waveTM) that has yet to be tested on a large proteome database. Since these tools are prone for error mainly as a result of falsely predicting signal peptides as transmembrane segments, we have utilized an additional method, SignalP. Based on our analyses, the ratio of human proteins with transmembrane segments is estimated to fall between 15% and 39% with a consensus of 13%. Agreement among the programs is reduced further when both a positive identification of a membrane protein and the number of transmembrane segments per protein are considered. Such a broad range of prediction depends on the selectivity of the individual method in predicting integral membrane proteins. These methods can play a critical role in determining protein structure and, hence, identifying suitable drug targets in humans.

waveTM: wavelet-based transmembrane segment prediction.

waveTM is a web tool for the prediction of transmembrane segments in alpha-helical membrane proteins. Prediction is performed by a dynamic programming algorithm on wavelet-denoised 'hydropathy' signals. Users submit a protein sequence and receive interactively the results. Topology prediction can also be obtained in conjunction with the algorithm OrienTM. A web server that implements the waveTM algorithm is freely available at http://bioinformatics.biol.uoa.gr/waveTM.