PTEN proteoforms in biology and disease

Proteoforms are specific molecular forms of protein products arising from a single gene that possess different structures and different functions. Therefore, a single gene can produce a large repertoire of proteoforms by means of allelic variations (mutations, indels, SNPs), alternative splicing and other pre-translational mechanisms, post-translational modifications (PTMs), conformational dynamics, and functioning. Resulting proteoforms that have different sizes, alternative splicing patterns, sets of post-translational modifications, protein–protein interactions, and protein–ligand interactions, might dramatically increase the functionality of the encoded protein. Herein, we have interrogated the tumor suppressor PTEN for its proteoforms and find that this protein exists in multiple forms with distinct functions and sub-cellular localizations. Furthermore, the levels of each PTEN proteoform in a given cell may affect its biological function. Indeed, the paradigm of the continuum model of tumor suppression by PTEN can be better explained by the presence of a continuum of PTEN proteoforms, diversity, and levels of which are associated with pathological outcomes than simply by the different roles of mutations in the PTEN gene. Consequently, understanding the mechanisms underlying the dysregulation of PTEN proteoforms by several genomic and non-genomic mechanisms in cancer and other diseases is imperative. We have identified different PTEN proteoforms, which control various aspects of cellular function and grouped them into three categories of intrinsic, function-induced, and inducible proteoforms. A special emphasis is given to the inducible PTEN proteoforms that are produced due to alternative translational initiation. The novel finding that PTEN forms dimers with biological implications supports the notion that PTEN proteoform–proteoform interactions may play hitherto unknown roles in cellular homeostasis and in pathogenic settings, including cancer. These PTEN proteoforms with unique properties and functionalities offer potential novel therapeutic opportunities in the treatment of various cancers and other diseases.     

Technologies of directed protein evolution in vivo

Directed evolution of proteins for improved or modified functionality is an important branch of modern biotechnology. It has traditionally been performed using various in vitro methods, but more recently, methods of in vivo artificial evolution come into play. In this review, we discuss and compare prokaryotic and eukaryotic-based systems of directed protein evolution in vivo, highlighting their benefits and current limitations and focusing on the biotechnological potential of vertebrate immune cells for the generation of protein diversity by means of the immunoglobulin diversification machinery.     

Targeting mitochondria by α-tocopheryl succinate kills neuroblastoma cells irrespective of MycN oncogene expression

Amplification of the MycN oncogene characterizes a subset of highly aggressive neuroblastomas, the most common extracranial solid tumor of childhood. However, the significance of MycN amplification for tumor cell survival is controversial, since down-regulation of MycN was found to decrease markedly neuroblastoma sensitivity towards conventional anticancer drugs, cisplatin, and doxorubicin. Here, we show that a redox-silent analogue of vitamin E, α-tocopheryl succinate (α-TOS), which triggers apoptotic cell death via targeting mitochondria, can kill tumor cells irrespective of their MycN expression level. In cells overexpressing MycN, as well as cells in which MycN was switched off, α-TOS stimulated rapid entry of Ca(2+) into the cytosol, compromised Ca(2+) buffering capacity of the mitochondria and sensitized them towards mitochondrial permeability transition and subsequent apoptotic cell death. Prevention of mitochondrial Ca(2+) accumulation or chelation of cytosolic Ca(2+) rescued the cells. Thus, targeting mitochondria might be advantageous for the elimination of tumor cells with otherwise dormant apoptotic pathways.     

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.     

Review of the genus Bolbonaso Emeljanov with checklist and key to Indian Caliscelidae (Hemiptera: Fulgoroidea)

A list of species of the family Caliscelidae Amyot et Serville known from India with data on distribution and sources for identification and a key to genera are given. The genus Bolbonaso Emeljanov, 2007 is revised. A new species, Bolbonaso chandri sp. nov., is described from Eastern India (Assam and Meghalaya States). Bolbonaso tapirifacies (Parshad, 1981) is redescribed and recorded for the first time from Southern India (Karnataka State). The lectotype is designated for Chirodisca eximia (Stål, 1859) which is recorded for the first time from Pakistan. New faunistic data in Nepal are listed for Delhina eurybrachydoides Distant, 1912.     

Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis

Five structurally and functionally different proteins, an enzyme superoxide dismutase 1 (SOD1), a TAR-DNA binding protein-43 (TDP-43), an RNA-binding protein FUS, a cofilin-binding protein C9orf72, and polypeptides generated as a result of its intronic hexanucleotide expansions, and to lesser degree actin-binding profilin-1 (PFN1), are considered to be the major drivers of amyotrophic lateral sclerosis. One of the features common to these proteins is the presence of significant levels of intrinsic disorder. The goal of this study is to consider these neurodegeneration-related proteins from the intrinsic disorder perspective. To this end, we employed a broad set of computational tools for intrinsic disorder analysis and conducted intensive literature search to gain information on the structural peculiarities of SOD1, TDP-43, FUS, C9orf72, and PFN1 and their intrinsic disorder predispositions, and the roles of intrinsic disorder in their normal and pathological functions.     

The Prospects for Machine Discovery in Linguistics

The article reports the results from the developmentof four data-driven discovery systems, operating inlinguistics. The first mimics the induction methods ofJohn Stuart Mill, the second performs componentialanalysis of kinship vocabularies, the third is ageneral multi-class discrimination program, and thefourth finds logical patterns in data. These systemsare briefly described and some arguments are offeredin favour of machine linguistic discovery. Thearguments refer to the strength of machines incomputationally complex tasks, the guaranteedconsistency of machine results, the portability ofmachine methods to new tasks and domains, and thepotential machines provide for our gaining newinsights.     

A recyclable catalyst that precipitates at the end of the reaction

Homogeneous catalysts--which exist in the same (usually liquid) phase as reactants and products--are usually more selective than heterogeneous catalysts and far less affected by limitations due to slow transport of reactants and products, but their separation from reaction products can be costly and inefficient. This has stimulated the development of strategies that facilitate the recycling of homogeneous catalysts. Some of these methods exploit the preference of a catalyst for one of two solvents with thermoregulated miscibility; others exploit a dramatic decrease in catalyst solubility as one reagent is consumed or temperature changed after completion of the reaction. Here we describe a tungsten catalyst for the solvent-free hydrosilylation of ketones that retains its activity until essentially all of the liquid substrate is converted to liquid products, which we can then simply decant to separate the catalyst that precipitates from the products of the reaction. We attribute the ability of the catalyst to retain its solubility and hence activity until completion of the reaction to the transient formation of liquid clathrate that contains a few molecules of the substrate per molecule of the otherwise solid catalyst. Insights into the fundamental processes controlling the formation of this liquid clathrate might help to tailor other catalysts and substrates, so as to develop efficient and solvent-free schemes for reactions of practical interest.