Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems

A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains elusive. One of the reasons is that proteins are not acting alone, but are specifically interacting with other proteins and biomolecules, forming intricate interaction networks that are essential for the majority of cell processes and pathological conditions. Thus, characterizing such interaction networks is an important step in understanding how information flows from gene to phenotype. Indeed, structural characterization of protein–protein interactions at atomic resolution has many applications in biomedicine, from diagnosis and vaccine design, to drug discovery. However, despite the advances of experimental structural determination, the number of interactions for which there is available structural data is still very small. In this context, a complementary approach is computational modeling of protein interactions by docking, which is usually composed of two major phases: (i) sampling of the possible binding modes between the interacting molecules and (ii) scoring for the identification of the correct orientations. In addition, prediction of interface and hot-spot residues is very useful in order to guide and interpret mutagenesis experiments, as well as to understand functional and mechanistic aspects of the interaction. Computational docking is already being applied to specific biomedical problems within the context of personalized medicine, for instance, helping to interpret pathological mutations involved in protein–protein interactions, or providing modeled structural data for drug discovery targeting protein–protein interactions.Spanish Ministry of Economy grant number BIO2016-79960-R; D.B.B. is supported by a predoctoral fellowship from CONACyT; M.R. is supported by an FPI fellowship from the Severo Ochoa program. We are grateful to the Joint BSC-CRG-IRB Programme in Computational Biology.Peer ReviewedPostprint (author's final draft

FAST : a fault detection and identification software tool

The aim of this work is to improve the reliability and safety of complex critical control systems by contributing to the systematic application of fault diagnosis. In order to ease the utilization of fault detection and isolation (FDI) tools in the industry, a systematic approach is required to allow the process engineers to analyze a system from this perspective. In this way, it should be possible to analyze this system to find if it provides the required fault diagnosis and redundancy according to the process criticality. In addition, it should be possible to evaluate what-if scenarios by slightly modifying the process (f.i. adding sensors or changing their placement) and evaluating the impact in terms of the fault diagnosis and redundancy possibilities. Hence, this work proposes an approach to analyze a process from the FDI perspective and for this purpose provides the tool FAST which covers from the analysis and design phase until the final FDI supervisor implementation in a real process. To synthesize the process information, a very simple format has been defined based on XML. This format provides the needed information to systematically perform the Structural Analysis of that process. Any process can be analyzed, the only restriction is that the models of the process components need to be available in the FAST tool. The processes are described in FAST in terms of process variables, components and relations and the tool performs the structural analysis of the process obtaining: (i) the structural matrix, (ii) the perfect matching, (iii) the analytical redundancy relations (if any) and (iv) the fault signature matrix. To aid in the analysis process, FAST can operate stand alone in simulation mode allowing the process engineer to evaluate the faults, its detectability and implement changes in the process components and topology to improve the diagnosis and redundancy capabilities. On the other hand, FAST can operate on-line connected to the process plant through an OPC interface. The OPC interface enables the possibility to connect to almost any process which features a SCADA system for supervisory control. When running in on-line mode, the process is monitored by a software agent known as the Supervisor Agent. FAST has also the capability of implementing distributed FDI using its multi-agent architecture. The tool is able to partition complex industrial processes into subsystems, identify which process variables need to be shared by each subsystem and instantiate a Supervision Agent for each of the partitioned subsystems. The Supervision Agents once instantiated will start diagnosing their local components and handle the requests to provide the variable values which FAST has identified as shared with other agents to support the distributed FDI process.Per tal de facilitar la utilització d'eines per la detecció i identificació de fallades (FDI) en la indústria, es requereix un enfocament sistemàtic per permetre als enginyers de processos analitzar un sistema des d'aquesta perspectiva. D'aquesta forma, hauria de ser possible analitzar aquest sistema per determinar si proporciona el diagnosi de fallades i la redundància d'acord amb la seva criticitat. A més, hauria de ser possible avaluar escenaris de casos modificant lleugerament el procés (per exemple afegint sensors o canviant la seva localització) i avaluant l'impacte en quant a les possibilitats de diagnosi de fallades i redundància. Per tant, aquest projecte proposa un enfocament per analitzar un procés des de la perspectiva FDI i per tal d'implementar-ho proporciona l'eina FAST la qual cobreix des de la fase d'anàlisi i disseny fins a la implementació final d'un supervisor FDI en un procés real. Per sintetitzar la informació del procés s'ha definit un format simple basat en XML. Aquest format proporciona la informació necessària per realitzar de forma sistemàtica l'Anàlisi Estructural del procés. Qualsevol procés pot ser analitzat, només hi ha la restricció de que els models dels components han d'estar disponibles en l'eina FAST. Els processos es descriuen en termes de variables de procés, components i relacions i l'eina realitza l'anàlisi estructural obtenint: (i) la matriu estructural, (ii) el Perfect Matching, (iii) les relacions de redundància analítica, si n'hi ha, i (iv) la matriu signatura de fallades. Per ajudar durant el procés d'anàlisi, FAST pot operar aïlladament en mode de simulació permetent a l'enginyer de procés avaluar fallades, la seva detectabilitat i implementar canvis en els components del procés i la topologia per tal de millorar les capacitats de diagnosi i redundància. Per altra banda, FAST pot operar en línia connectat al procés de la planta per mitjà d'una interfície OPC. La interfície OPC permet la possibilitat de connectar gairebé a qualsevol procés que inclogui un sistema SCADA per la seva supervisió. Quan funciona en mode en línia, el procés està monitoritzat per un agent software anomenat l'Agent Supervisor. Addicionalment, FAST té la capacitat d'implementar FDI de forma distribuïda utilitzant la seva arquitectura multi-agent. L'eina permet dividir sistemes industrials complexes en subsistemes, identificar quines variables de procés han de ser compartides per cada subsistema i generar una instància d'Agent Supervisor per cadascun dels subsistemes identificats. Els Agents Supervisor un cop activats, començaran diagnosticant els components locals i despatxant les peticions de valors per les variables que FAST ha identificat com compartides amb altres agents, per tal d'implementar el procés FDI de forma distribuïda.Postprint (published version

Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline

Molecular analysis of BRCA1 (MIM# 604370) and BRCA2 (MIM #600185) genes is essential for familial breast and ovarian cancer prevention and treatment. An efficient, rapid, cost-effective accurate strategy for the detection of pathogenic variants is crucial. Mutations detection of BRCA1/2 genes includes screening for single nucleotide variants (SNVs), small insertions or deletions (indels), and Copy Number Variations (CNVs). Sanger sequencing is unable to identify CNVs and therefore Multiplex Ligation Probe amplification (MLPA) or Multiplex Amplicon Quantification (MAQ) is used to complete the BRCA1/2 genes analysis. The rapid evolution of Next Generation Sequencing (NGS) technologies allows the search for point mutations and CNVs with a single platform and workflow. In this study we test the possibilities of NGS technology to simultaneously detect point mutations and CNVs in BRCA1/2 genes, using the OncomineTM BRCA Research Assay on Personal Genome Machine (PGM) Platform with Ion Reporter Software for sequencing data analysis (Thermo Fisher Scientific). Comparison between the NGS-CNVs, MLPA and MAQ results shows how the NGS approach is the most complete and fast method for the simultaneous detection of all BRCA mutations, avoiding the usual time consuming multistep approach in the routine diagnostic testing of hereditary breast and ovarian cancers

miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential.

We have shown that antagomiR inhibition of miRNA miR-21 and miR-196b activity is sufficient to ablate MLL-AF9 leukemia stem cells (LSC) in vivo. Here, we used an shRNA screening approach to mimic miRNA activity on experimentally verified miR-196b targets to identify functionally important and therapeutically relevant pathways downstream of oncogenic miRNA in MLL-r AML. We found Cdkn1b (p27Kip1) is a direct miR-196b target whose repression enhanced an embryonic stem cell–like signature associated with decreased leukemia latency and increased numbers of leukemia stem cells in vivo. Conversely, elevation of p27Kip1 significantly reduced MLL-r leukemia self-renewal, promoted monocytic differentiation of leukemic blasts, and induced cell death. Antagonism of miR-196b activity or pharmacologic inhibition of the Cks1-Skp2–containing SCF E3-ubiquitin ligase complex increased p27Kip1 and inhibited human AML growth. This work illustrates that understanding oncogenic miRNA target pathways can identify actionable targets in leukemia

Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics

The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple-species consortium that synergistically degrades and grows on the phenylurea herbicide linuron. To acquire a better insight into the interactions between the consortium members and the underlying molecular mechanisms, we compared the transcriptomes of the key biodegrading strains WDL7 and WDL1 grown as biofilms in either isolation or consortium conditions by differential RNAseq analysis. Differentially expressed pathways and cellular systems were inferred using the network-based algorithm PheNetic. Coculturing affected mainly metabolism in WDL1. Significantly enhanced expression of hylA encoding linuron hydrolase was observed. Moreover, differential expression of several pathways involved in carbohydrate, amino acid, nitrogen, and sulfur metabolism was observed indicating that WDL1 gains carbon and energy from linuron indirectly by consuming excretion products from WDL7 and/or WDL6. Moreover, in consortium conditions, WDL1 showed a pronounced stress response and overexpression of cell to cell interaction systems such as quorum sensing, contact-dependent inhibition, and Type VI secretion. Since the latter two systems can mediate interference competition, it prompts the question if synergistic linuron degradation is the result of true adaptive cooperation or rather a facultative interaction between bacteria that coincidentally occupy complementary metabolic niches

Protein Expression, Characterization and Activity Comparisons of Wild Type and Mutant DUSP5 Proteins

Background The mitogen-activated protein kinases (MAPKs) pathway is critical for cellular signaling, and proteins such as phosphatases that regulate this pathway are important for normal tissue development. Based on our previous work on dual specificity phosphatase-5 (DUSP5), and its role in embryonic vascular development and disease, we hypothesized that mutations in DUSP5 will affect its function. Results In this study, we tested this hypothesis by generating full-length glutathione-S-transferase-tagged DUSP5 and serine 147 proline mutant (S147P) proteins from bacteria. Light scattering analysis, circular dichroism, enzymatic assays and molecular modeling approaches have been performed to extensively characterize the protein form and function. We demonstrate that both proteins are active and, interestingly, the S147P protein is hypoactive as compared to the DUSP5 WT protein in two distinct biochemical substrate assays. Furthermore, due to the novel positioning of the S147P mutation, we utilize computational modeling to reconstruct full-length DUSP5 and S147P to predict a possible mechanism for the reduced activity of S147P. Conclusion Taken together, this is the first evidence of the generation and characterization of an active, full-length, mutant DUSP5 protein which will facilitate future structure-function and drug development-based studies

Rigidity and flexibility of biological networks

The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of protein structures, as well as local flexibility measures of proteins and their applications in explaining allostery and thermostability is given. We also briefly discuss the network aspects of cytoskeletal tensegrity. Finally, we show the importance of the balance between functional flexibility and rigidity in protein-protein interaction, metabolic, gene regulatory and neuronal networks. Our summary raises the possibility that the concepts of flexibility and rigidity can be generalized to all networks.Comment: 21 pages, 4 figures, 1 tabl