scholarly journals Rings in the Extreme: PCNA Interactions and Adaptations in the Archaea

Archaea ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Jody A. Winter ◽  
Karen A. Bunting
Keyword(s):  
Structural Analysis ◽  
Protein Binding ◽  
Protein Interactions ◽  
Extreme Environments ◽  
Binding Partners ◽  
Great Insight ◽  
Dna Replication And Repair ◽  
Evolution Of Proteins ◽  
Insight Into

Biochemical and structural analysis of archaeal proteins has enabled us to gain great insight into many eukaryotic processes, simultaneously offering fascinating glimpses into the adaptation and evolution of proteins at the extremes of life. The archaeal PCNAs, central to DNA replication and repair, are no exception. Characterisation of the proteins alone, and in complex with both peptides and protein binding partners, has demonstrated the diversity and subtlety in the regulatory role of these sliding clamps. Equally, studies have provided valuable detailed insight into the adaptation of protein interactions and mechanisms that are necessary for life in extreme environments.

scholarly journals Behavioral Strategy and the COVID-19 Disruption

2020 ◽  
Vol 46 (8) ◽  
pp. 1322-1329
Author(s):  
Nicolai J. Foss
Keyword(s):  
Decision Making ◽  
Strategic Decision ◽  
Strategic Decision Making ◽  
Behavioral Strategy ◽  
Management Research ◽  
Strategy Research ◽  
Great Insight ◽  
Fundamental Uncertainty ◽  
Insight Into

What can strategic management research do to help to make sense of the COVID-19 disruption, and what are the implications of the disruption for the strategy field? I argue that among the streams in strategy research, behavioral strategy is uniquely situated in terms of providing a psychologically based interpretive lens that could lend great insight into decision making in extreme conditions. However, the disruption also points to weakness in current behavioral strategy thinking, notably with respect to the role of models vis-à-vis judgment in strategic decision making, the deeply social (political, institutional) nature of strategy making, and the treatment of fundamental uncertainty.

Regulation of the water channel aquaporin-2 by posttranslational modification

2011 ◽  
Vol 300 (5) ◽  
pp. F1062-F1073 ◽  
Author(s):  
Hanne B. Moeller ◽  
Emma T. B. Olesen ◽  
Robert A. Fenton
Keyword(s):  
Membrane Proteins ◽  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Posttranslational Modification ◽  
Water Channel ◽  
Cellular Functions ◽  
Aquaporin 2 ◽  
Eukaryotic Membrane Proteins ◽  
Insight Into

The cellular functions of many eukaryotic membrane proteins, including the vasopressin-regulated water channel aquaporin-2 (AQP2), are regulated by posttranslational modifications. In this article, we discuss the experimental discoveries that have advanced our understanding of how posttranslational modifications affect AQP2 function, especially as they relate to the role of AQP2 in the kidney. We review the most recent data demonstrating that glycosylation and, in particular, phosphorylation and ubiquitination are mechanisms that regulate AQP2 activity, subcellular sorting and distribution, degradation, and protein interactions. From a clinical perspective, posttranslational modification resulting in protein misrouting or degradation may explain certain forms of nephrogenic diabetes insipidus. In addition to providing major insight into the function and dynamics of renal AQP2 regulation, the analysis of AQP2 posttranslational modification may provide general clues as to the role of posttranslational modification for regulation of other membrane proteins.

Dewey’s Criticisms of Traditional Philosophy

1998 ◽  
pp. 13-19
Author(s):  
Charles Lowney
Keyword(s):  
Natural World ◽  
Error Characteristic ◽  
Traditional Philosophy ◽  
Relevant Today ◽  
Great Insight ◽  
History Of ◽  
Philosophic Tradition ◽  
Insight Into ◽  
Modern Thinking

In this paper I address some of John Dewey’s more generally applicable criticisms of the philosophic "tradition," and show how his criticisms stem from his naturalistic approach to philosophy. This topic is important because Dewey gives great insight into discussions that are relevant today regarding the role of philosophy. In 1935 he anticipated many of the criticisms of the "later" Wittgenstein regarding the establishment of post facto standards as a cause, the separation of language from behavior and the privatization of mind—yet Dewey still finds use for metaphysics or "thinking at large." I believe the essence of Dewey’s criticisms are found in a few key distinctions. Therefore, I cover the history of philosophy with blanket criticisms of the blanket categories of "classical" and of "modern" thought. For Dewey, the fundamental error characteristic of both Greek and Modern thinking is the artificial bifurcation of our thoughts, feelings and actions from the natural world. As I see it, the heart of this metaphysical mistake is captured by the distinctions he draws between the "instrumental" and "consummatory," and between the "precarious" and "stable."

scholarly journals Getting into position: the catalytic mechanisms of protein ubiquitylation

2004 ◽  
Vol 379 (3) ◽  
pp. 513-525 ◽  
Author(s):  
Lori A. PASSMORE ◽  
David BARFORD
Keyword(s):  
Protein Interactions ◽  
Regulatory Elements ◽  
Substrate Selection ◽  
Protein Protein Interactions ◽  
Different Types ◽  
Catalytic Mechanisms ◽  
Cellular Pathways ◽  
Ubiquitin Conjugating Enzymes ◽  
Insight Into

The role of protein ubiquitylation in the control of diverse cellular pathways has recently gained widespread attention. Ubiquitylation not only directs the targeted destruction of tagged proteins by the 26 S proteasome, but it also modulates protein activities, protein–protein interactions and subcellular localization. An understanding of the components involved in protein ubiquitylation (E1s, E2s and E3s) is essential to understand how specificity and regulation are conferred upon these pathways. Much of what we know about the catalytic mechanisms of protein ubiquitylation comes from structural studies of the proteins involved in this process. Indeed, structures of ubiquitin-activating enzymes (E1s) and ubiquitin-conjugating enzymes (E2s) have provided insight into their mechanistic details. E3s (ubiquitin ligases) contain most of the substrate specificity and regulatory elements required for protein ubiquitylation. Although several E3 structures are available, the specific mechanistic role of E3s is still unclear. This review will discuss the different types of ubiquitin signals and how they are generated. Recent advances in the field of protein ubiquitylation will be examined, including the mechanisms of E1, E2 and E3. In particular, we discuss the complexity of molecular recognition required to impose selectivity on substrate selection and topology of poly-ubiquitin chains.

The AGO proteins: an overview

2018 ◽  
Vol 399 (6) ◽  
pp. 525-547 ◽  
Author(s):  
Saife Niaz
Keyword(s):  
Protein Binding ◽  
Structure Function ◽  
Small Rnas ◽  
Biological Process ◽  
Biochemical Properties ◽  
The Core ◽  
Binding Partners

AbstractSmall RNAs govern almost every biological process in eukaryotes associating with the Argonaute (AGO) proteins to form the RNA-induced silencing complex (mRISC). AGO proteins constitute the core of RISCs with different members having variety of protein-binding partners and biochemical properties. This review focuses on the AGO subfamily of the AGOs that are ubiquitously expressed and are associated with small RNAs. The structure, function and role of the AGO proteins in the cell is discussed in detail.

scholarly journals Role of Organic/Sulfide Ratios On DNRA Cultivation And The Microbial Community Structure of A Co-Driven Sequencing Biofilm Batch Reactor

2021 ◽  
Author(s):  
Xiaoling Li ◽  
Jianqiang Zhao ◽  
Yuhao Zhang ◽  
Jiaojie He ◽  
Kaili Ma ◽  
...  
Keyword(s):  
Batch Reactor ◽  
Electron System ◽  
High Electron ◽  
16S Rna ◽  
Functional Bacteria ◽  
Great Insight ◽  
Nitrogen Conversion ◽  
Insight Into ◽  
Competing Pathways

Abstract Denitrification and dissimilatory nitrate reduction to ammonium (DNRA), are two competing pathways in nitrate reducing process. In this study, a series of C/S ratios from 8:1 to 2:4 was investigated in a sequencing biofilm batch reactor (SBBR) to determine the role of reducers (sulfide and acetate) on their competition. The results showed the proportion of DNRA increased in high electron system, either in organic rich or in sulfide rich system. The highest DNRA ratio increased to 16.7% at the C/S ratio of 2:3. Excess electron donors, particularly sulfide, were favorable for DNRA in a limited nitrate environment. Moreover, a higher reductive environment (ORP <-400 mV) can be used as an indicator for the occurrence of DNRA. 16s RNA analysis demonstrated that Grobacter was the main functional bacteria of DNRA in the organic rich system, while Alphaproteobacteria and Desulfomicrobium were dominant DNRA bacteria in the sulfide rich system. DNRA cultivation could enrich nitrogen conversion pathways in conventional denitrification systems. This provides the great insight into nitrogen removal in high nitrogen containing sewage with low C/N.

scholarly journals The face of TSR revealed

2002 ◽  
Vol 159 (2) ◽  
pp. 203-206 ◽  
Author(s):  
Roy L. Silverstein
Keyword(s):  
Structural Information ◽  
Structural Data ◽  
Type I ◽  
The Novel ◽  
Multifunctional Protein ◽  
Binding Partners ◽  
Multiple Binding ◽  
Great Insight ◽  
The Face ◽  
Insight Into

In this issue, Tan et al. (2002) report the first high resolution (1.9 Å) structural data for thrombospondin (TSP)-1, a large multifunctional protein that regulates cell adhesion, angiogenesis, cell proliferation and survival, TGFβ activation, and protease function (for review see Chen et al., 2000). Because TSP-1 has multiple binding partners and many functions, precise structural information is crucial to understanding its biology. The structure now reported, derived from crystals of the second and third type I repeats of TSP-1 is of particular interest because of the specific functions attributed to these repeats and because domains homologous to the repeats appear in many other proteins in nature. The novel layered fold motif described brings great insight into how the complicated functions of TSP-1 and related molecules are affected.

Relationships between EEA1 binding partners and their role in endosome fusion

2001 ◽  
Vol 114 (10) ◽  
pp. 1959-1965 ◽  
Author(s):  
I.G. Mills ◽  
S. Urbe ◽  
M.J. Clague
Keyword(s):  
Protein Binding ◽  
Complex Network ◽  
Vital Role ◽  
Early Endosome ◽  
Stable Complex ◽  
Baby Hamster Kidney ◽  
Bhk Cells ◽  
Binding Partners ◽  
Early Endosomes

Homotypic fusion between early endosomes requires the phosphatidylinositol 3-phosphate (PI3P)-binding protein, Early Endosomal Autoantigen 1 (EEA1). We have investigated the role of other proteins that interact with EEA1 in the fusion of early endosomes derived from Baby Hamster Kidney (BHK) cells. We confirm a requirement for syntaxin 13, but additionally show that the assay is equally sensitive to reagents specifically targeted against syntaxin 6. Binding of EEA1 to immobilised GST-syntaxin 6 and 13 was directly compared; only syntaxin 6 formed a stable complex with EEA1. Early endosome fusion requires the release of intravesicular calcium, and calmodulin plays a vital role in the fusion pathway, as judged by sensitivity to antagonists. We demonstrate that both EEA1 and syntaxin 13 interact with calmodulin. In the case of EEA1, binding to calmodulin requires an IQ domain, which is adjacent to a C-terminal FYVE domain that specifically binds to PI3P. We have assessed the influence of protein binding partners on EEA1 interaction with PI3P and find that both calmodulin and rab5-GTP are antagonistic to PI3P binding, whilst syntaxins 6 and 13 have no effect. These studies reveal a complex network of interactions between the proteins required for endosome fusion.

Role of small nuclear RNAs in eukaryotic gene expression

2013 ◽  
Vol 54 ◽  
pp. 79-90 ◽  
Author(s):  
Saba Valadkhan ◽  
Lalith S. Gunawardane
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Stability ◽  
Splice Sites ◽  
Branch Site ◽  
Small Nuclear Rnas ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

Sign in / Sign up

Export Citation Format

Share Document