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Protein Interaction Networks in Health and Disease

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199822 Year: Pages: 89 DOI: 10.3389/978-2-88919-982-2 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2016-01-19 14:05:46
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The identification and mapping of protein-protein interactions (PPIs) is a major goal in systems biology. Experimental data are currently produced in large scale using a variety of high-throughput assays in yeast or mammalian systems. Analysis of these data using computational tools leads to the construction of large protein interaction networks, which help researchers identify novel protein functions.However, our current view of protein interaction networks is still limited and there is an active field of research trying to further develop this concept to include important processes: the topology of interactions and their changes in real time, the effects of competition for binding to the same protein region, PPI variation due to alternative splicing or post-translational modifications, etc.In particular, a clinically relevant topic for development of the concept of protein interactions networks is the consideration of mutant isoforms, which may be responsible for a pathological condition. Mutations in proteins may result in loss of normal interactions and appearance of novel abnormal interactions that may affect a protein’s function and biological cycle.This Research Topic presents novel findings and recent achievements in the field of protein interaction networks with a focus on disease. Authors describe methods for the identification and quantification of PPIs, the annotation and analysis of networks, considering PPIs and protein complexes formed by mutant proteins associated with pathological conditions or genetic diseases.

Function and Flexibility: Friend or Foe?

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199723 Year: Pages: 102 DOI: 10.3389/978-2-88919-972-3 Language: English
Publisher: Frontiers Media SA
Subject: Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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Louis Sullivan (1856 - 1924) revolutionized architecture by designing the first skyscraper and he became famous by proclaiming that “form follows function”. When x-ray crystallographers visualized the structures of proteins for the first time, the structural biology field embraced the view that “function follows form” as the 3D-architecture of proteins could unveil various aspects of their function. Despite the original “1 gene - 1 protein structure - 1 function” relationship, nowadays a far more complicated picture emerges where the flexibility and dynamics of a protein can play a central role in a multitude of functions. The ultimate form(s) that a protein adopt when interacting with (a) partner molecule(s) are the most biologically relevant and in this context Sullivan’s quote is still appropriate: the conformation that the protein adopts follows from the function of that protein. Despite the fact that many well-characterized proteins have a well-folded structure, there is a growing interest in the conformational flexibility within proteins. This flexibility is also a balanced phenomenon: excess of flexibility can be detrimental for protein behaviour, as well as the lack thereof. Notwithstanding its importance, studying intrinsically disordered protein regions or conformational rearrangements can be a very challenging. Therefore, flexibility can be perceived as a friend or a foe, depending on the context. This e-book showcases the impact of the study of protein flexibility on the structural biology field and presents protein flexibility in the context of disease as well as its benign aspects. As detailed knowledge of the structural aspects of polypeptides remains essential to comprehend protein function, one of the future challenges for structural biology also lies with large macromolecular protein complexes. Also there the dynamics and flexibility are essential for proper functioning and molecular movement, which is an important aspect of living matter. This challenge stimulated the development of advanced techniques to study protein flexibility and the use of those techniques to address fundamental biological and biomedical problems. Those innovations should help us to unravel the intimate link between protein function and flexibility and explore new horizons.

Protein Solubility and Aggregation in Bacteria

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199761 Year: Pages: 127 DOI: 10.3389/978-2-88919-976-1 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2016-01-19 14:05:46
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Proteins suffer many conformational changes and interactions through their life, from their synthesis at ribosomes to their controlled degradation. Only folded and soluble proteins are functional. Thus, protein folding and solubility are controlled genetically, transcriptionally, and at the protein sequence level. In addition, a well-conserved cellular machinery assists the folding of polypeptides to avoid misfolding and ensure the attainment of soluble and functional structures. When these redundant protective strategies are overcome, misfolded proteins are recruited into aggregates. Recombinant protein production is an essential tool for the biotechnology industry and also supports expanding areas of basic and biomedical research, including structural genomics and proteomics. Although bacteria still represent a convenient production system, many recombinant polypeptides produced in prokaryotic hosts undergo irregular or incomplete folding processes that usually result in their accumulation as insoluble aggregates, narrowing thus the spectrum of protein-based drugs that are available in the biotechnology market. In fact, the solubility of bacterially produced proteins is of major concern in production processes, and many orthogonal strategies have been exploited to try to increase soluble protein yields. Importantly, contrary to the usual assumption that the bacterial aggregates formed during protein production are totally inactive, the presence of a fraction of molecules in a native-like structure in these assemblies endorse them with a certain degree of biological activity, a property that is allowing the use of bacteria as factories to produce new functional materials and catalysts. The protein embedded in intracellular bacterial deposits might display different conformations, but they are usually enriched in beta-sheet-rich assemblies resembling the amyloid fibrils characteristic of several human neurodegenerative diseases. This makes bacterial cells simple, but biologically relevant model systems to address the mechanisms behind amyloid formation and the cellular impact of protein aggregates. Interestingly, bacteria also exploit the structural principles behind amyloid formation for functional purposes such as adhesion or cytotoxicity. In the present research topic we collect papers addressing all the issues mentioned above from both the experimental and computational point of view.

Molecular Chaperones and Neurodegeneration

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453429 Year: Pages: 180 DOI: 10.3389/978-2-88945-342-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2018-02-27 16:16:45
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Molecular chaperones or heat-shock proteins (HSPs) play essential roles in safeguarding structural stability and preventing misfolding and aggregation of proteins, and maintaining the proteome functionality in the cell. For over two decades until the present time, new functions have been discovered and several molecular mechanisms have been elucidated for many chaperones, while the field is being continuously challenged by new open questions. Probably as a consequence of the increasing research on the molecular bases of neurodegenerative diseases, and the realisation that many such disorders are linked to protein misfolding processes, unleashing the roles and mechanisms of chaperones in the context of neurodegeneration has become a prime scientific goal. This e-book contains a diversity of reviews, perspective and original research articles highlighting the importance and potential of this emerging subject.

Ribosome Inactivating Toxins

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ISBN: 9783038972488 / 9783038972495 Year: Pages: 329 DOI: 10.3390/books978-3-03897-249-5 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Therapeutics --- Public Health
Added to DOAB on : 2019-01-17 10:21:23
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Ribosome inactivating proteins (RIPs) form a vast family of hundreds of toxins from plants, fungi, algae and bacteria. RIP activities have also been detected in animal tissues. They target a single adenine of a ribosomal RNA, thereby blocking protein synthesis and leading intoxicated cells to apoptosis. The role of plant RIPs may be related to plant defense against predators and viruses, plant senescence or bacterial pathogenesis. Most RIPs are no threat to human or animal health. However, several bacterial RIPs are major virulence factors involved in severe epidemic diseases such as dysentery or the hemolytic uremic syndrome that may occur in patients suffering from Shiga toxin-producing entero-hemorrhagic Escherichia coli infection. Several plant RIPs such as ricin toxin, abrin or sarcin have been, or may be involved in accidental or criminal poisonings, political intimidation or bio-suicides. Health crisis, biosafety and biosecurity issues became a major concern and many efforts are made to develop treatments. Finally, RIPs can be engineered into immunotoxins to destroy cancer cells or cells chronically infected by viruses.This book presents the most recent data on all aspects of RIPs including function, diversity and evolution, mechanism, pathophysiology, medical countermeasures and engineering into anticancer drugs.

Protein Phosphorylation in Health and Disease

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199006 Year: Pages: 122 DOI: 10.3389/978-2-88919-900-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2016-01-19 14:05:46
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Protein phosphorylation is one of the most abundant reversible post-translational modifications in eukaryotes. It is involved in virtually all cellular processes by regulating protein function, localization and stability and by mediating protein-protein interactions. Furthermore, aberrant protein phosphorylation is implicated in the onset and progression of human diseases such as cancer and neurodegenerative disorders. In the last years, tens of thousands of in vivo phosphorylation events have been identified by large-scale quantitative phospho-proteomics experiment suggesting that a large fraction of the proteome might be regulated by phosphorylation. This data explosion is increasingly enabling the development of computational approaches, often combined with experimental validation, aiming at prioritizing phosphosites and assessing their functional relevance. Some computational approaches also address the inference of specificity determinants of protein kinases/phosphatases and the identification of phosphoresidue recognition domains. In this context, several challenging issues are still open regarding phosphorylation, including a better understanding of the interplay between phosphorylation and allosteric regulation, agents and mechanisms disrupting or promoting abnormal phosphorylation in diseases, the identification and modulation of novel phosphorylation inhibitors, and so forth. Furthermore, the determinants of kinase and phosphatase recognition and binding specificity are still unknown in several cases, as well as the impact of disease mutations on phosphorylation-mediated signaling. The articles included in this Research Topic illustrate the very diverse aspects of phosphorylation, ranging from structural changes induced by phosphorylation to the peculiarities of phosphosite evolution. Some also provide a glimpse into the huge complexity of phosphorylation networks and pathways in health and disease, and underscore that a deeper knowledge of such processes is essential to identify disease biomarkers, on one hand, and design more effective therapeutic strategies, on the other.

Molecular Science for Drug Development and Biomedicine

ISBN: 9783906980836 9783906980843 Year: Pages: 356
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2015-10-22 06:15:53
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With the avalanche of biological sequences generated in the postgenomic age, molecular science is facing an unprecedented challenge, i.e., how to timely utilize the huge amount of data to benefit human beings. Stimulated by such a challenge, a rapid development has taken place in molecular science, particularly in the areas associated with drug development and biomedicine, both experimental and theoretical. The current thematic issue was launched with the focus on the topic of “Molecular Science for Drug Development and Biomedicine”, in hopes to further stimulate more useful techniques and findings from various approaches of molecular science for drug development and biomedicine.

Tau oligomers

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192618 Year: Pages: 113 DOI: 10.3389/978-2-88919-261-8 Language: English
Publisher: Frontiers Media SA
Subject: Psychiatry --- Neurology --- Medicine (General) --- Science (General)
Added to DOAB on : 2015-12-03 13:02:24
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Neurofibrillary tangles (NFTs) composed of intracellular aggregates of tau protein are a key neuropathological feature of Alzheimer's Disease (AD) and other neurodegenerative diseases, collectively termed tauopathies. The abundance of NFTs has been reported to correlate positively with the severity of cognitive impairment in AD. However, accumulating evidences derived from studies of experimental models have identified that NFTs themselves may not be neurotoxic. Now, many of tau researchers are seeking a "toxic" form of tau protein. Moreover, it was suggested that a "toxic" tau was capable to seed aggregation of native tau protein and to propagate in a prion-like manner. However, the exact neurotoxic tau species remain unclear. Because mature tangles seem to be non-toxic component, "tau oligomers" as the candidate of “toxic” tau have been investigated for more than one decade. In this topic, we will discuss our consensus of “tau oligomers” because the term of “tau oligomers” [e.g. dimer (disulfide bond-dependent or independent), multimer (more than dimer), granular (definition by EM or AFM) and maybe small filamentous aggregates] has been used by each researchers definition. From a biochemical point of view, tau protein has several unique characteristics such as natively unfolded conformation, thermo-stability, acid-stability, and capability of post-translational modifications. Although tau protein research has been continued for a long time, we are still missing the mechanisms of NFT formation. It is unclear how the conversion is occurred from natively unfolded protein to abnormally mis-folded protein. It remains unknown how tau protein can be formed filaments [e.g. paired helical filament (PHF), straight filament and twisted filament] in cells albeit in vitro studies confirmed tau self-assembly by several inducing factors. Researchers are still debating whether tau oligomerization is primary event rather than tau phosphorylation in the tau pathogenesis. Inhibition of either tau phosphorylation or aggregation has been investigated for the prevention of tauopathies, however, it will make an irrelevant result if we don’t know an exact target of neurotoxicity. It is a time to have a consensus of definition, terminology and methodology for the identification of "tau oligomers".

Biocomputing 2016:Proceedings of the Pacific Symposium

Authors: --- --- --- --- et al.
ISBN: 9789814749411 Year: Pages: 604 DOI: 10.1142/9930 Language: English
Publisher: World Scientific Publishing Co.
Subject: Biology
Added to DOAB on : 2016-01-19 03:27:59
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The Pacific Symposium on Biocomputing (PSB) 2016 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2016 will be held on January 4 – 8, 2016 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2016 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's "hot topics." In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.Contents:Cancer Panomics: Computational Methods and Infrastructure for Integrative Analysis of Cancer High-Throughput "Omics" DataComputational Approaches to Drug Repurposing and PharmacologyDetecting and Characterizing Pleiotropy: New Methods for Uncovering the Connection Between the Complexity of Genomic Architecture and Multiple PhenotypesPersonalized Medicine: From Genotypes and Molecular Phenotypes Towards TherapyText and Data Mining for Biomedical DiscoveryReadership: Academia and industry in the fields of biocomputing, bioinformatics and computational biology.

Biocomputing 2015:Proceedings of the Pacific Symposium

Authors: --- --- --- --- et al.
ISBN: 9789814644730 Year: Pages: 516 DOI: 10.1142/9455 Language: English
Publisher: World Scientific Publishing Co.
Subject: Biology
Added to DOAB on : 2016-01-19 03:42:23
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The Pacific Symposium on Biocomputing (PSB) 2015 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2015 will be held from January 4 – 8, 2015 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2015 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's “hot topics.” In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.Contents:Cancer Panomics: Computational Methods and Infrastructure for Integrative Analysis of Cancer High-Throughput "OMICS" DataCancer Pathways: Automatic Extraction, Representation, and Reasoning in the "Big Data" ERACharacterizing the Importance of Environmental Exposures, Interactions Between the Environment and Genetic Architecture, and Genetic Interactions: New Methods for Understanding the Etiology of Complex Traits and DiseaseCrowdsourcing and Mining Crowd DataPersonalized Medicine: From Genotypes, Molecular Phenotypes and the Quantified Self, Towards Improved MedicineReadership: Academia and industry in the fields of biocomputing, bioinformatics and computational biology.

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