Results for 'Proteins'

996 found
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  1. Section A. membranes.Protein Synthesis as A. Membrane-Oriented & Richard W. Hendler - 1968 - In Peter Koestenbaum, Proceedings. [San Jose? Calif.,: [San Jose? Calif.. pp. 37.
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  2. Protein-centric connection of biomedical knowledge: Protein Ontology research and annotation tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Landgrebe Jobst & Smith Barry, Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR, vol. 833. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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  3.  35
    G protein‐coupled receptors: the inside story.Kees Jalink & Wouter H. Moolenaar - 2010 - Bioessays 32 (1):13-16.
    Recent findings necessitate revision of the traditional view of G protein‐coupled receptor (GPCR) signaling and expand the diversity of mechanisms by which receptor signaling influences cell behavior in general. GPCRs elicit signals at the plasma membrane and are then rapidly removed from the cell surface by endocytosis. Internalization of GPCRs has long been thought to serve as a mechanism to terminate the production of second messengers such as cAMP. However, recent studies show that internalized GPCRs can continue to either stimulate (...)
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  4.  33
    Protein disulfide isomerase is regulated in multiple ways: Consequences for conformation, activities, and pathophysiological functions.Lei Wang, Jiaojiao Yu & Chih-Chen Wang - 2021 - Bioessays 43 (3):2000147.
    Protein disulfide isomerase (PDI) is one of the most abundant and critical protein folding catalysts in the endoplasmic reticulum of eukaryotic cells. PDI consists of four thioredoxin domains and interacts with a wide range of substrate and partner proteins due to its intrinsic conformational flexibility. PDI plays multifunctional roles in a variety of pathophysiological events, both as an oxidoreductase and a molecular chaperone. Recent studies have revealed that the conformation and activity of PDI can be regulated in multiple ways, (...)
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  5.  26
    Replication protein A prevents promiscuous annealing between short sequence homologies: Implications for genome integrity.Sarah K. Deng, Huan Chen & Lorraine S. Symington - 2015 - Bioessays 37 (3):305-313.
    Replication protein A (RPA) is the main eukaryotic single‐stranded DNA (ssDNA) binding protein, having essential roles in all DNA metabolic reactions involving ssDNA. RPA binds ssDNA with high affinity, thereby preventing the formation of secondary structures and protecting ssDNA from the action of nucleases, and directly interacts with other DNA processing proteins. Here, we discuss recent results supporting the idea that one function of RPA is to prevent annealing between short repeats that can lead to chromosome rearrangements by microhomology‐mediated (...)
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  6.  30
    Replication protein A: Single‐stranded DNA's first responder.Ran Chen & Marc S. Wold - 2014 - Bioessays 36 (12):1156-1161.
    Replication protein A (RPA), the major single‐stranded DNA‐binding protein in eukaryotic cells, is required for processing of single‐stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high‐affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule studies showed that (...)
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  7. Protein Analysis Meets Visual Word Recognition: A Case for String Kernels in the Brain.Thomas Hannagan & Jonathan Grainger - 2012 - Cognitive Science 36 (4):575-606.
    It has been recently argued that some machine learning techniques known as Kernel methods could be relevant for capturing cognitive and neural mechanisms (Jäkel, Schölkopf, & Wichmann, 2009). We point out that ‘‘String kernels,’’ initially designed for protein function prediction and spam detection, are virtually identical to one contending proposal for how the brain encodes orthographic information during reading. We suggest some reasons for this connection and we derive new ideas for visual word recognition that are successfully put to the (...)
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  8.  33
    RGS proteins as targets in the treatment of intestinal inflammation and visceral pain: New insights and future perspectives.Maciej Salaga, Martin Storr, Kirill A. Martemyanov & Jakub Fichna - 2016 - Bioessays 38 (4).
    Regulators of G protein signaling (RGS) proteins provide timely termination of G protein‐coupled receptor (GPCR) responses. Serving as a central control point in GPCR signaling cascades, RGS proteins are promising targets for drug development. In this review, we discuss the involvement of RGS proteins in the pathophysiology of the gastrointestinal inflammation and their potential to become a target for anti‐inflammatory drugs. Specifically, we evaluate the emerging evidence for modulation of selected receptor families: opioid, cannabinoid and serotonin by (...)
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  9. Protein Ontology: A controlled structured network of protein entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...)
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  10. The Protein Ontology: A structured representation of protein forms and complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of (...)
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  11.  18
    Ribosomal protein uS3 in cell biology and human disease: Latest insights and prospects.Dmitri Graifer & Galina Karpova - 2020 - Bioessays 42 (12):2000124.
    The conserved ribosomal protein uS3 in eukaryotes has long been known as one of the essential components of the small (40S) ribosomal subunit, which is involved in the structure of the 40S mRNA entry pore, ensuring the functioning of the 40S subunit during translation initiation. Besides, uS3, being outside the ribosome, is engaged in various cellular processes related to DNA repair, NF‐kB signaling pathway and regulation of apoptosis. This review is devoted to recent data opening new horizons in understanding the (...)
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  12.  27
    RNA‐protein interactions: Central players in coordination of regulatory networks.Alexandros Armaos, Elsa Zacco, Natalia Sanchez de Groot & Gian Gaetano Tartaglia - 2021 - Bioessays 43 (2):2000118.
    Changes in the abundance of protein and RNA molecules can impair the formation of complexes in the cell leading to toxicity and death. Here we exploit the information contained in protein, RNA and DNA interaction networks to provide a comprehensive view of the regulation layers controlling the concentration‐dependent formation of assemblies in the cell. We present the emerging concept that RNAs can act as scaffolds to promote the formation ribonucleoprotein complexes and coordinate the post‐transcriptional layer of gene regulation. We describe (...)
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  13.  18
    Multifaceted targeted protein degradation systems for different cellular compartments.Cornelia E. Zorca, Armaan Fallahi, Sophie Luo & Mohamed A. Eldeeb - 2022 - Bioessays 44 (6):2200008.
    Selective protein degradation maintains cellular homeostasis, but this process is disrupted in many diseases. Targeted protein degradation (TPD) approaches, built upon existing cellular mechanisms, are promising methods for therapeutically regulating protein levels. Here, we review the diverse palette of tools that are now available for doing so throughout the gene expression pathway and in specific cellular compartments. These include methods for directly removing targeted proteins via the ubiquitin proteasome system with proteolysis targeting chimeras (PROTACs) or dephosphorylation targeting chimeras (DEPTACs). (...)
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  14.  14
    Mitochondrial protein import machinery conveys stress signals to the cytosol and beyond.Eirini Lionaki, Ilias Gkikas & Nektarios Tavernarakis - 2023 - Bioessays 45 (3):2200160.
    Mitochondria hold diverse and pivotal roles in fundamental processes that govern cell survival, differentiation, and death, in addition to organismal growth, maintenance, and aging. The mitochondrial protein import system is a major contributor to mitochondrial biogenesis and lies at the crossroads between mitochondrial and cellular homeostasis. Recent findings highlight the mitochondrial protein import system as a signaling hub, receiving inputs from other cellular compartments and adjusting its function accordingly. Impairment of protein import, in a physiological, or disease context, elicits adaptive (...)
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  15.  65
    G protein‐coupled receptors engage the mammalian Hippo pathway through F‐actin.Laura Regué, Fan Mou & Joseph Avruch - 2013 - Bioessays 35 (5):430-435.
    The Hippo pathway, a cascade of protein kinases that inhibits the oncogenic transcriptional coactivators YAP and TAZ, was discovered in Drosophila as a major determinant of organ size in development. Known modes of regulation involve surface proteins that mediate cell‐cell contact or determine epithelial cell polarity which, in a tissue‐specific manner, use intracellular complexes containing FERM domain and actin‐binding proteins to modulate the kinase activities or directly sequester YAP. Unexpectedly, recent work demonstrates that GPCRs, especially those signaling through (...)
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  16.  10
    C2H2 proteins: Evolutionary aspects of domain architecture and diversification.Artem N. Bonchuk & Pavel G. Georgiev - 2024 - Bioessays 46 (8):2400052.
    The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2‐type zinc finger domains that specifically bind to DNA. Few well‐studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has (...)
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  17.  24
    Quinary protein structure and the consequences of crowding in living cells: Leaving the test‐tube behind.Anna Jean Wirth & Martin Gruebele - 2013 - Bioessays 35 (11):984-993.
    Although the importance of weak protein‐protein interactions has been understood since the 1980s, scant attention has been paid to this “quinary structure”. The transient nature of quinary structure facilitates dynamic sub‐cellular organization through loose grouping of proteins with multiple binding partners. Despite our growing appreciation of the quinary structure paradigm in cell biology, we do not yet understand how the many forces inside the cell – the excluded volume effect, the “stickiness” of the cytoplasm, and hydrodynamic interactions – perturb (...)
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  18.  22
    Peptidylprolylisomerases, Protein Folders, or Scaffolders? The Example of FKBP51 and FKBP52.Theo Rein - 2020 - Bioessays 42 (7):1900250.
    Peptidylprolyl‐isomerases (PPIases) comprise of the protein families of FK506 binding proteins (FKBPs), cyclophilins, and parvulins. Their common feature is their ability to expedite the transition of peptidylprolyl bonds between the cis and the trans conformation. Thus, it seemed highly plausible that PPIase enzymatic activity is crucial for protein folding. However, this has been difficult to prove over the decades since their discovery. In parallel, more and more studies have discovered scaffolding functions of PPIases. This essay discusses the hypothesis that (...)
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  19.  27
    The Protein‐Coding Human Genome: Annotating High‐Hanging Fruits.Klas Hatje, Stefanie Mühlhausen, Dominic Simm & Martin Kollmar - 2019 - Bioessays 41 (11):1900066.
    The major transcript variants of human protein‐coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes—they can be protein‐coding, noncoding, or pseudogenes—and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro‐exons and (...)
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  20.  31
    Fluorogenic Protein‐Based Strategies for Detection, Actuation, and Sensing.Arnaud Gautier & Alison G. Tebo - 2018 - Bioessays 40 (10):1800118.
    Fluorescence imaging has become an indispensable tool in cell and molecular biology. GFP‐like fluorescent proteins have revolutionized fluorescence microscopy, giving experimenters exquisite control over the localization and specificity of tagged constructs. However, these systems present certain drawbacks and as such, alternative systems based on a fluorogenic interaction between a chromophore and a protein have been developed. While these systems are initially designed as fluorescent labels, they also present new opportunities for the development of novel labeling and detection strategies. This (...)
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  21.  50
    Protein transport into peroxisomes: Knowns and unknowns.Tânia Francisco, Tony A. Rodrigues, Ana F. Dias, Aurora Barros-Barbosa, Diana Bicho & Jorge E. Azevedo - 2017 - Bioessays 39 (10):1700047.
    Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and rapidly transported into the organelle by a complex machinery. The data gathered in recent years suggest that this machinery operates through a syringe-like mechanism, in which the shuttling receptor PEX5 − the “plunger” − pushes a newly synthesized protein all the way through a peroxisomal transmembrane protein complex − the “barrel” − into the matrix of the organelle. Notably, insertion of cargo-loaded receptor into the “barrel” is an ATP-independent process, whereas (...)
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  22.  30
    Ribosomal Proteins Control Tumor Suppressor Pathways in Response to Nucleolar Stress.Frédéric Lessard, Léa Brakier-Gingras & Gerardo Ferbeyre - 2019 - Bioessays 41 (3):1800183.
    Ribosome biogenesis includes the making and processing of ribosomal RNAs, the biosynthesis of ribosomal proteins from their mRNAs in the cytosol and their transport to the nucleolus to assemble pre‐ribosomal particles. Several stresses including cellular senescence reduce nucleolar rRNA synthesis and maturation increasing the availability of ribosome‐free ribosomal proteins. Several ribosomal proteins can activate the p53 tumor suppressor pathway but cells without p53 can still arrest their proliferation in response to an imbalance between ribosomal proteins and (...)
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  23.  20
    Protein translocation across mitochondrial membranes.Ulla Wienhues & Walter Neupert - 1992 - Bioessays 14 (1):17-23.
    Protein translocation across biological membranes is of fundamental importance for the biogenesis of organelles and in protein secretion. We will give an overview of the recent achievements in the understanding of protein translocation across mitochondrial membranes(1‐5). In particular we will focus on recently identified components of the mitochondrial import apparatus.
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  24.  63
    Fluorescent proteins for FRET microscopy: Monitoring protein interactions in living cells.Richard N. Day & Michael W. Davidson - 2012 - Bioessays 34 (5):341-350.
    The discovery and engineering of novel fluorescent proteins (FPs) from diverse organisms is yielding fluorophores with exceptional characteristics for live‐cell imaging. In particular, the development of FPs for fluorescence (or Förster) resonance energy transfer (FRET) microscopy is providing important tools for monitoring dynamic protein interactions inside living cells. The increased interest in FRET microscopy has driven the development of many different methods to measure FRET. However, the interpretation of FRET measurements is complicated by several factors including the high fluorescence (...)
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  25.  33
    Protein-protein interactions: Making sense of networks via graph-theoretic modeling.Nataša Pržulj - 2011 - Bioessays 33 (2):115-123.
    The emerging area of network biology is seeking to provide insights into organizational principles of life. However, despite significant collaborative efforts, there is still typically a weak link between biological and computational scientists and a lack of understanding of the research issues across the disciplines. This results in the use of simple computational techniques of limited potential that are incapable of explaining these complex data. Hence, the danger is that the community might begin to view the topological properties of network (...)
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  26.  40
    Protein folding and evolution are driven by the Maxwell demon activity of proteins.Alejandro Balbín & Eugenio Andrade - 2004 - Acta Biotheoretica 52 (3):173-200.
    In this paper we propose a theoretical model of protein folding and protein evolution in which a polypeptide (sequence/structure) is assumed to behave as a Maxwell Demon or Information Gathering and Using System (IGUS) that performs measurements aiming at the construction of the native structure. Our model proposes that a physical meaning to Shannon information (H) and Chaitin's algorithmic information (K) parameters can be both defined and referred from the IGUS standpoint. Our hypothesis accounts for the interdependence of protein folding (...)
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  27. The representation of protein complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and (...)
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  28.  24
    S100 protein and down syndrome.Alexander Marks & Robert Allore - 1990 - Bioessays 12 (8):381-383.
    S100 protein is a low molecular weight calcium‐binding protein widely distributed in the central nervous system of vertebrates. Recent evidence suggests that S100 protein may play a role in the regulation of glial proliferation and neuronal differentiation. The gene for S100 protein has been mapped to the 21q22 region, a chromosomal locus whose duplication has been implicated in the generation of Down Syndrome (DS). This raises the possibility that abnormalities in S100 protein gene dosage at a critical period during development (...)
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  29.  15
    Fluid protein fold space and its implications.Lauren L. Porter - 2023 - Bioessays 45 (9):2300057.
    Fold‐switching proteins, which remodel their secondary and tertiary structures in response to cellular stimuli, suggest a new view of protein fold space. For decades, experimental evidence has indicated that protein fold space is discrete: dissimilar folds are encoded by dissimilar amino acid sequences. Challenging this assumption, fold‐switching proteins interconnect discrete groups of dissimilar protein folds, making protein fold space fluid. Three recent observations support the concept of fluid fold space: (1) some amino acid sequences interconvert between folds with (...)
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  30.  20
    Protein tyrosine kinases as new potential targets against human schistosomiasis.Colette Dissous, Arnaud Ahier & Naji Khayath - 2007 - Bioessays 29 (12):1281-1288.
    In spite of the numerous efforts made to control their transmission, parasite schistosomes still represent a serious public health concern and a major economic problem in many developing countries. Praziquantel (PZQ) is the drug of choice for the treatment of schistosomiasis and the only one that is available for mass chemotherapy. However, its widespread use and its inefficacy on juvenile parasites raise fears that schistosomes will develop drug resistance, and make the development of alternative drugs highly desirable. Protein tyrosine kinases (...)
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  31.  36
    PRDM proteins: Important players in differentiation and disease.Cathrine K. Fog, Giorgio G. Galli & Anders H. Lund - 2012 - Bioessays 34 (1):50-60.
    The PRDM family has recently spawned considerable interest as it has been implicated in fundamental aspects of cellular differentiation and exhibits expanding ties to human diseases. The PRDMs belong to the SET domain family of histone methyltransferases, however, enzymatic activity has been determined for only few PRDMs suggesting that they act by recruiting co‐factors or, more speculatively, confer methylation of non‐histone targets. Several PRDM family members are deregulated in human diseases, most prominently in hematological malignancies and solid cancers, where they (...)
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  32.  35
    LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell-cell communication.Federico Abascal & Rafael Zardoya - 2012 - Bioessays 34 (7):551-560.
  33.  16
    NIPSNAP protein family emerges as a sensor of mitochondrial health.Esmat Fathi, Jay M. Yarbro & Ramin Homayouni - 2021 - Bioessays 43 (6):2100014.
    Since their discovery over two decades ago, the molecular and cellular functions of the NIPSNAP family of proteins (NIPSNAPs) have remained elusive until recently. NIPSNAPs interact with a variety of mitochondrial and cytoplasmic proteins. They have been implicated in multiple cellular processes and associated with different physiologic and pathologic conditions, including pain transmission, Parkinson's disease, and cancer. Recent evidence demonstrated a direct role for NIPSNAP1 and NIPSNAP2 proteins in regulation of mitophagy, a process that is critical for (...)
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  34.  13
    G proteins, chemosensory perception, and the C. elegans genome project: An attractive story.Thomas M. Wilkie - 1999 - Bioessays 21 (9):713-717.
    Heterotrimeric G proteins, consisting of α, β, and γ subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al.(1) (...)
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  35.  25
    The Protein Side of the Central Dogma: Permanence and Change.Michel Morange - 2006 - History and Philosophy of the Life Sciences 28 (4):513 - 524.
    There are two facets to the central dogma proposed by Francis Crick in 1957. One concerns the relation between the sequence of nucleotides and the sequence of amino acids, the second is devoted to the relation between the sequence of amino acids and the native three-dimensional structure of proteins. 'Folding is simply a function of the order of the amino acids,' i.e. no information is required for the proper folding of a protein other than the information contained in its (...)
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  36.  12
    How Small Proteins Adjust the Metabolism of Cyanobacteria Under Stress.Alexander Kraus & Wolfgang R. Hess - forthcoming - Bioessays:e202400245.
    Several recently discovered small proteins of less than 100 amino acids control important, but sometimes surprising, steps in the metabolism of cyanobacteria. There is mounting evidence that a large number of small protein genes have also been overlooked in the genome annotation of many other microorganisms. Although too short for enzymatic activity, their functional characterization has frequently revealed the involvement in processes such as signaling and sensing, interspecies communication, stress responses, metabolism, regulation of transcription and translation, and in the (...)
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  37.  30
    Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.Joseph A. Marsh & Sarah A. Teichmann - 2014 - Bioessays 36 (2):209-218.
    Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often closely related (...)
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  38.  18
    Linking the unfolded protein response to bioactive lipid metabolism and signalling in the cell non‐autonomous extracellular communication of ER stress.Nicole T. Watt, Anna McGrane & Lee D. Roberts - 2023 - Bioessays 45 (8):2300029.
    The endoplasmic reticulum (ER) organelle is the key intracellular site of both protein and lipid biosynthesis. ER dysfunction, termed ER stress, can result in protein accretion within the ER and cell death; a pathophysiological process contributing to a range of metabolic diseases and cancers. ER stress leads to the activation of a protective signalling cascade termed the Unfolded Protein Response (UPR). However, chronic UPR activation can ultimately result in cellular apoptosis. Emerging evidence suggests that cells undergoing ER stress and UPR (...)
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  39.  50
    Glycosaminoglycan-protein interactions: definition of consensus sites in glycosaminoglycan binding proteins.Ronald E. Hileman, Jonathan R. Fromm, John M. Weiler & Robert J. Linhardt - 1998 - Bioessays 20 (2):156-167.
    Although interactions of proteins with glycosaminoglycans (GAGs), such as heparin and heparan sulphate, are of great biological importance, structural requirements for protein‐GAG binding have not been well‐characterised. Ionic interactions are important in promoting protein‐GAG binding. Polyelectrolyte theory suggests that much of the free energy of binding comes from entropically favourable release of cations from GAG chains. Despite their identical charges, arginine residues bind more tightly to GAGs than lysine residues. The spacing of these residues may determine protein‐GAG affinity and (...)
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  40.  5
    G proteins, chemosensory perception, and the C. elegans genome project: An attractive story.H. Georg Kuhn & Clive N. Svendsen - 1999 - Bioessays 21 (9):713-717.
    Heterotrimeric G proteins, consisting of α, β, and γ subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al.(1) (...)
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  41.  31
    Rnd proteins: Multifunctional regulators of the cytoskeleton and cell cycle progression.Philippe Riou, Priam Villalonga & Anne J. Ridley - 2010 - Bioessays 32 (11):986-992.
    Rnd3/RhoE has two distinct functions, regulating the actin cytoskeleton and cell proliferation. This might explain why its expression is often altered in cancer and by multiple stimuli during development and disease. Rnd3 together with its relatives Rnd1 and Rnd2 are atypical members of the Rho GTPase family in that they do not hydrolyse GTP. Rnd3 and Rnd1 both antagonise RhoA/ROCK‐mediated actomyosin contractility, thereby regulating cell migration, smooth muscle contractility and neurite extension. In addition, Rnd3 has been shown to have a (...)
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  42.  30
    Reovirus protein σ1: From cell attachment to protein oligomerization and folding mechanisms.Patrick W. K. Lee & Gustavo Leone - 1994 - Bioessays 16 (3):199-206.
    The reovirus cell attachment protein σ1 is a lollipopshaped structure with the fibrous tail anchored to the virion. Since it interacts with the cell receptor, σ1 is a major determinant of reovirus infectivity and tissue tropism. Studies on its structure‐function relationships have been facilitated by the fact that protein σ1 produced in any expression system is capable of binding to cell receptors. The use of site‐specific and deletion mutants has led to the identification and characterization of its virion anchorage and (...)
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  43.  18
    Palmitoylated Proteins in Plasmodium falciparum‐Infected Erythrocytes: Investigation with Click Chemistry and Metabolic Labeling.Nicole Kilian, Yongdeng Zhang, Lauren LaMonica, Giles Hooker, Derek Toomre, Choukri Ben Mamoun & Andreas M. Ernst - 2020 - Bioessays 42 (6):1900145.
    The examination of the complex cell biology of the human malaria parasite Plasmodium falciparum usually relies on the time‐consuming generation of transgenic parasites. Here, metabolic labeling and click chemistry are employed as a fast transfection‐independent method for the microscopic examination of protein S‐palmitoylation, an important post‐translational modification during the asexual intraerythrocytic replication of P. falciparum. Applying various microscopy approaches such as confocal, single‐molecule switching, and electron microscopy, differences in the extent of labeling within the different asexual developmental stages of P. (...)
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  44.  12
    Revisiting poly(A)‐binding proteins: Multifaceted regulators during gametogenesis and early embryogenesis.Long-Wen Zhao & Heng-Yu Fan - 2021 - Bioessays 43 (6):2000335.
    Post‐transcriptional regulation faces a distinctive challenge in gametes. Transcription is limited when the germ cells enter the division phase due to condensed chromatin, while gene expression during gamete maturation, fertilization, and early cleavage depends on existing mRNA post‐transcriptional coordination. The dynamics of the 3ʹ‐poly(A) tail play crucial roles in defining mRNA fate. The 3ʹ‐poly(A) tail is covered with poly(A)‐binding proteins (PABPs) that help to mediate mRNA metabolism and recent work has shed light on the number and function of germ (...)
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  45.  14
    Protein Phosphorylation Dynamics: Unexplored Because of Current Methodological Limitations.Alain Robichon - 2020 - Bioessays 42 (4):1900149.
    The study of intrinsic phosphorylation dynamics and kinetics in the context of complex protein architecture in vivo has been challenging: Method limitations have prevented significant advances in the understanding of the highly variable turnover of phosphate groups, synergy, and cooperativity between P‐sites. However, over the last decade, powerful analytical technologies have been developed to determine the full catalog of the phosphoproteome for many species. The curated databases of phospho sites found by mass spectrometry analysis and the computationally predicted sites based (...)
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    AraC protein: A love–hate relationship.Robert Schleif - 2003 - Bioessays 25 (3):274-282.
    In the bacterium Escherichia coli, the AraC protein positively and negatively regulates expression of the proteins required for the uptake and catabolism of the sugar L‐arabinose. This essay describes how work from my laboratory on this system spanning more than thirty years has aided our understanding of positive regulation, revealed DNA looping (a mechanism that explains many action‐at‐a‐distance phenomena) and, more recently, has uncovered the mechanism by which arabinose shifts AraC from a state where it prefers to bind to (...)
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    Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae.Uri Weill, Nir Cohen, Amir Fadel, Shifra Ben-Dor & Maya Schuldiner - 2019 - Bioessays 41 (8):1800252.
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    A protein‐lipid complex that detoxifies free fatty acids.Shaojie Cui & Jin Ye - 2023 - Bioessays 45 (3):2200210.
    Fatty acids (FAs) are well known to serve as substrates for reactions that provide cells with membranes and energy. In contrast to these metabolic reactions, the physiological importance of FAs themselves known as free FAs (FFAs) in cells remains obscure. Since accumulation of FFAs in cells is toxic, cells must develop mechanisms to detoxify FFAs. One such mechanism is to sequester free polyunsaturated FAs (PUFAs) into a droplet‐like structure assembled by Fas‐Associated Factor 1 (FAF1), a cytosolic protein. This sequestration limits (...)
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    Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors.Ekaterina S. Marakasova, Birgit Eisenhaber, Sebastian Maurer-Stroh, Frank Eisenhaber & Ancha Baranova - 2017 - Bioessays 39 (10):1700014.
    Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 and few other proteins encoded by Herpesviridae, Nef, E1A, NS5A, (...)
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  50.  46
    Motor protein control of ion flux is an early step in embryonic left–right asymmetry.Michael Levin - 2003 - Bioessays 25 (10):1002-1010.
    The invariant left–right asymmetry of animal body plans raises fascinating questions in cell, developmental, evolutionary, and neuro‐biology. While intermediate mechanisms (e.g., asymmetric gene expression) have been well‐characterized, very early steps remain elusive. Recent studies suggested a candidate for the origins of asymmetry: rotary movement of extracellular morphogens by cilia during gastrulation. This model is intellectually satisfying, because it bootstraps asymmetry from the intrinsic biochemical chirality of cilia. However, conceptual and practical problems remain with this hypothesis, and the genetic data is (...)
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