Abstract:
:It is not surprising that a large number of diseases related to amyloid fibril depositions are formed in various organs. Therefore, it is necessary to understand the transformation of native proteins into amyloid fibrils in order to clarify which key elements of this process determine the pathway of protein misfolding. Significant attention has been directed recently to investigating the mechanism of formation of cross-β structures that have the properties of liquids but can also exist in gel-like forms, thus facilitating the retention of both RNAs and RNA-binding proteins. Proteins that form stress granules are believed to do this rapidly, and they are expected to contain a prion-like domain that can facilitate this process. By analyzing the known yeast prion proteins and 29 RNA-binding proteins with prion-like domains, we demonstrate here that the existence of repeats is one of the general characteristics of prion-like domains. The presence of repeats should help to determine the border of prion domains as in the case of Rnq1: five found repeats shift the border of the prion domain from the 153-rd to at least the 133-th residue. One can suggest that such repeats assist in the rapid initiation of the process of assembly and formation of cross-β structures and such domains most likely should be disordered. These repeats should contain aromatic amino acid residues for the formation of a hydrogel because its amino acid context modulates the strength of interaction. The key factors determined here can be used to control the process of aggregation to prevent the development of pathologies and diseases caused by prion-like domains.
journal_name
Mol Biosystjournal_title
Molecular bioSystemsauthors
Galzitskaya OVdoi
10.1039/c5mb00273gsubject
Has Abstractpub_date
2015-08-01 00:00:00pages
2210-8issue
8eissn
1742-206Xissn
1742-2051journal_volume
11pub_type
杂志文章abstract::This paper describes a sensitive, non-destructive displacement assay, using a fluorescent peptide indicator, for real-time monitoring of the interactions between RNA and RNA binding proteins (RBPs). The developed fluorescent peptide indicators, each containing a mid-sequence fluorophore unit, allowed sensing of target...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25470k
更新日期:2013-05-01 00:00:00
abstract::Integrative pharmacology has been used to identify the key active constituents (KACs) of Buchang Naoxintong capsules (BNCs), a traditional Chinese medical preparation; this approach involves the evaluation of the content profiles and drug-like properties of the BNC constituents and development of an ingredient-target ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00460h
更新日期:2016-01-01 00:00:00
abstract::A growing number of diverse proteins are being identified that moonlight. Moonlighting proteins comprise an interesting subset of multifunctional proteins in which the two functions are found in a single polypeptide chain. They do not include proteins that are multifunctional due to gene fusions, families of homologou...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b900658n
更新日期:2009-04-01 00:00:00
abstract::Protein-protein interactions are important for the majority of biological processes. A significant number of computational methods have been developed to predict protein-protein interactions using protein sequence, structural and genomic data. Vast experimental data is publicly available on the Internet, but it is sca...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70486f
更新日期:2014-04-01 00:00:00
abstract::Epithelial to mesenchymal transition (EMT) is a biological process that plays a crucial role in cancer metastasis. Although studies regarding the EMT mechanisms are usual in terms of gene expression and protein functions, little is known about the involvement of lipids in EMT. In this work, an untargeted lipidomic ana...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00413f
更新日期:2015-12-01 00:00:00
abstract::Major progress in the study of RNase P has resulted from crystallography of bacterial catalytic subunits and the discovery of catalytic activity in eukaryotes. Several new substrates have also been identified, primarily in bacteria but also in yeast. Our current world should be called the "RNA-protein world" rather th...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b707850c
更新日期:2007-09-01 00:00:00
abstract::The interaction of spermine and its analogue, 1-naphthyl acetyl spermine with four double stranded DNA polynucleotides has been studied to understand the structural and thermodynamic basis of the binding. The efficacy and specificity of DNA binding of this analogue has not yet been revealed. The energetics of the inte...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70616h
更新日期:2014-05-01 00:00:00
abstract::Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes. The large size of these webs and their entangled nature make it...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/B904960f
更新日期:2009-12-01 00:00:00
abstract::Regulatory networks are able to process complex signals and respond appropriately to the cellular context. Thus, an increasing effort by systems biology researchers is being focused on understanding which interactions are responsible for a given functional response. When translated into specific mathematical models, h...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25243k
更新日期:2013-02-02 00:00:00
abstract::In order to elucidate the effect of flexible linker length on the catalytic efficiency of fusion proteins, two short flexible peptide linkers of various lengths were fused between Arabidopsis thaliana 4-coumaroyl-CoA ligase (4CL) and Polygonum cuspidatum stilbene synthase (STS) to generate fusion proteins 4CL-(GSG)n-S...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00563b
更新日期:2017-02-28 00:00:00
abstract::Lovastatin and other statins inhibit HMG-CoA reductase, which carries out an early step in the sterol biosynthesis pathway. Statins lower cholesterol and are widely prescribed to prevent heart disease, but like many drugs, they can interact with nutritionally acquired metabolites. To probe these interactions, we explo...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00166j
更新日期:2011-02-01 00:00:00
abstract::Information on extracellular signals and conditions is often transduced by biological systems using cascades of protein phosphorylation that affect the activity of enzymes, the localization of proteins and gene expression. A model to study signal transduction is the response of the yeast Saccharomyces cerevisiae to os...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b902256b
更新日期:2009-11-01 00:00:00
abstract::Sequence specific binding of DNA and RNA is of fundamental importance in the regulation of cellular gene expression. Because of their modular structure repeat domain proteins are particularly well suited for these processes and have been widely adopted throughout evolution. Detailed biochemical and structural data has...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/c2mb05392f
更新日期:2012-03-01 00:00:00
abstract::The heterogeneity of genetic alterations in human cancer genomes presents a major challenge to advancing our understanding of cancer mechanisms and identifying cancer driver genes. To tackle this heterogeneity problem, many approaches have been proposed to investigate genetic alterations and predict driver genes at th...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25528f
更新日期:2013-03-01 00:00:00
abstract::The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally impor...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00246f
更新日期:2014-07-01 00:00:00
abstract::Calcium (Ca(2+)) is used as a signaling molecule to regulate many cellular processes. Calcium signaling generally involves transient elevations of the concentration of free Ca(2+) in the cytosol. More pronounced and sustained elevations of intracellular Ca(2+) concentrations are observed during apoptosis (programmed c...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b920805d
更新日期:2010-05-01 00:00:00
abstract::Complex signalling systems have evolved in multicellular organisms to enable cell-to-cell communication during growth and development. In plants, cell communication via the extracellular matrix (apoplast) controls many processes vital for plant survival. Secretion of ATP into the extracellular matrix is now recognised...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/c1mb05278k
更新日期:2012-02-01 00:00:00
abstract::Protein splicing technology harnesses the ability of inteins to ligate protein fragments, forming a mature protein. This report describes our effort to engineer rapamycin-dependent protein splicing of a ribotoxin, called α-sarcin. Engineering this system required the investigation of important splicing parameters, inc...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70387h
更新日期:2014-04-01 00:00:00
abstract::Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Consid...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00026f
更新日期:2016-04-01 00:00:00
abstract::Stochastic fluctuations (noise) in gene expression can cause members of otherwise genetically identical populations to display drastically different phenotypes. An understanding of the sources of noise and the strategies cells employ to function reliably despite noise is proving to be increasingly important in describ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b801245h
更新日期:2008-07-01 00:00:00
abstract::At the intersection between artificial intelligence and statistics, supervised learning allows algorithms to automatically build predictive models from just observations of a system. During the last twenty years, supervised learning has been a tool of choice to analyze the always increasing and complexifying data gene...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b907946g
更新日期:2009-12-01 00:00:00
abstract::Naphthalene, a polycyclic aromatic hydrocarbon, is a ubiquitous environmental pollutant capable of causing illness. In this study, we deconvoluted the metabolites related to naphthalene intervention in various organs by using nuclear magnetic resonance (NMR) and liquid chromatography-tandem mass spectrometry (LC-MS/MS...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00090k
更新日期:2014-07-01 00:00:00
abstract::Drug combinations have been widely applied to treat complex diseases, like cancer, HIV and cardiovascular diseases. One of the most important characteristics for drug combinations is the synergistic effects among different drugs, that is to say, the combination effects are larger than the sum of individual effects. Al...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00599j
更新日期:2016-02-01 00:00:00
abstract::In this review we bring together recent results from our group focused towards the development of biosensors from single conically-shaped artificial nanopores. The nanopores, used in the work presented here, were prepared using the track-etch process. The fabrication of track-etched conical nanopores has been optimize...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b708725j
更新日期:2007-10-01 00:00:00
abstract::The effect of aging and development in male Wistar-derived rats on the profile of endogenous metabolites excreted in the urine was investigated using both (1)H NMR spectroscopy and HPLC-TOF MS using electrospray ionisation (ESI). The endogenous metabolites were profiled in samples collected from male rats every two we...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b500852b
更新日期:2005-07-01 00:00:00
abstract::We employed high-temperature classical molecular dynamics (MD) simulations to investigate the unfolding process of the wild-type (WT) and F508del-NBD1 domains of CFTR protein, with and without second-site mutations. To rationalize the in vitro behavior of F508del-NBD1, namely its lower folding yield and higher aggrega...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00193a
更新日期:2016-08-16 00:00:00
abstract::Diabetic retinopathy (DR) is a serious microvascular syndrome of diabetes, and is one of the most frequent causes of blindness in the world. It has three progressive stages with complex metabolic deregulations in the holistic system of Western medicine. Chinese medicine classifies DR into two different syndrome types;...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00341g
更新日期:2011-07-01 00:00:00
abstract::The major obstacle for the development of targeted therapies is the lack of pharmacodynamic (PD) biomarkers to provide an early readout of biological activities. As the modulation of metabolites may reflect the biological changes occurring in the targets, metabolomics is promising to be an efficient way to explore PD ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c7mb00093f
更新日期:2017-07-25 00:00:00
abstract::The ectonucleotide phosphodiesterase/pyrophosphatase-1 (NPP1) is a type II transmembrane glycoprotein that regulates extracellular inorganic purine nucleotide and inorganic diphosphate levels through the hydrolysis of ATP into AMP and diphosphate. NPP1 is a promising drug target as it plays a role in several disorders...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c7mb00095b
更新日期:2017-05-30 00:00:00
abstract::The recognition and association between the Ca2+/calmodulin-activated protein kinase II-α (CaMKIIα) and the multi-PDZ domain protein 1 (MUPP1) plays an important role in the sperm acrosome reaction and human fertilization. Previously, we have demonstrated that the MUPP1 PDZ11 domain is the primary binding partner of t...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c7mb00379j
更新日期:2017-09-26 00:00:00