scholarly journals Role of the nucleotidyl cyclase helical domain in catalytically active dimer formation

2017 ◽  
Vol 114 (46) ◽  
pp. E9821-E9828 ◽  
Author(s):  
Irene Vercellino ◽  
Lenka Rezabkova ◽  
Vincent Olieric ◽  
Yevhen Polyhach ◽  
Tobias Weinert ◽  
...  
Keyword(s):  
Adenylyl Cyclase ◽  
Genetic Diseases ◽  
Bound State ◽  
Catalytic Domains ◽  
Helical Domain ◽  
Wide Range ◽  
Catalytically Active ◽  
Human Proteins ◽  
Retinal Guanylyl Cyclase

Nucleotidyl cyclases, including membrane-integral and soluble adenylyl and guanylyl cyclases, are central components in a wide range of signaling pathways. These proteins are architecturally diverse, yet many of them share a conserved feature, a helical region that precedes the catalytic cyclase domain. The role of this region in cyclase dimerization has been a subject of debate. Although mutations within this region in various cyclases have been linked to genetic diseases, the molecular details of their effects on the enzymes remain unknown. Here, we report an X-ray structure of the cytosolic portion of the membrane-integral adenylyl cyclase Cya from Mycobacterium intracellulare in a nucleotide-bound state. The helical domains of each Cya monomer form a tight hairpin, bringing the two catalytic domains into an active dimerized state. Mutations in the helical domain of Cya mimic the disease-related mutations in human proteins, recapitulating the profiles of the corresponding mutated enzymes, adenylyl cyclase-5 and retinal guanylyl cyclase-1. Our experiments with full-length Cya and its cytosolic domain link the mutations to protein stability, and the ability to induce an active dimeric conformation of the catalytic domains. Sequence conservation indicates that this domain is an integral part of cyclase machinery across protein families and species. Our study provides evidence for a role of the helical domain in establishing a catalytically competent dimeric cyclase conformation. Our results also suggest that the disease-associated mutations in the corresponding regions of human nucleotidyl cyclases disrupt the normal helical domain structure.

scholarly journals Structural states of a RNA aptamer, molecular dynamics simulation study

2016 ◽  
Author(s):  
Ida Autiero ◽  
Luigi Vitagliano ◽  
Roberto Improta ◽  
Menotti - Ruvo
Keyword(s):  
Rna Folding ◽  
Physiological Role ◽  
Bound State ◽  
Dynamics Simulation ◽  
Free State ◽  
Rna Aptamer ◽  
Dynamic Features ◽  
Structural Arrangement ◽  
Wide Range

Motivation RNA, which adopts a wide range of secondary structures is involved in several kind of chemical interactions and shows a notable structural plasticity. Due to remarkable chemical properties and an important physiological role of RNAs, there is a growing interest in development of RNA-based drugs and ligands of clinical relevance. However, RNAs structural and dynamic features as well as the main RNA-protein recognition effects remain largely unaddressed. We have studied the conformational behaviour and the dynamic of two different structural arrangements of an aptamer binding the bacillus anthracis ribosomal protein S8. This RNA aptamer has experimentally shown two different topologies in free state and in protein-bound state, although sequences differ for just few residues beyond the common internal loop. The role of the interacting protein on the RNA folding, stabilizing or inducing a particular conformation will be discussed. Methods Three molecular dynamic simulations of 300 ns each have been performed starting from three distinct aptamer structures: i) the aptamer free-state, using a representative model of a NMR ensemble of structures (pdb 2lun); ii) a similar aptamer bound to its target protein (4pdb) iii); an aptamer model built using the sequence of the RNA in the free state but with the structural arrangement of the bound-state to investigate a possible influence of the sequence on the RNA folding. All the systems under investigations were solvated in a truncated octahedral water box using explicit water models, with a least a 1.1 Å distance to the border, using Na+ counter-ions to neutralize. 6 steps of heating simulation from 50 K to 300K were carried out before to perform the final MD run of 300 ns in NPT conditions without restrains. The trajectories were analysed using the GROMACS utilities and X3DNA program. Results Our data show that both bound-state RNA arrangements are structurally stable, holding all the main interactions since the beginning of the simulations. The free-state RNA is the system with the largest flexibility, reaching an equilibrium after 40 ns of simulation. Although the NMR structure appears less rigid, during the total run it never matches the arrangement of the bound state. Definitely, within our time scale, a convergence of the free state with the bound-state trajectories has never been observed and the two different arrangements show differences in flexibility. Preliminary data suggest a significantly different behaviour of the free- and bound-state structures supporting a preminent role of the interacting partner protein on the RNA overall folding to induce a particular stable structural arrangement.

scholarly journals Structural states of a RNA aptamer, molecular dynamics simulation study

2016 ◽  
Author(s):  
Ida Autiero ◽  
Luigi Vitagliano ◽  
Roberto Improta ◽  
Menotti - Ruvo
Keyword(s):  
Rna Folding ◽  
Physiological Role ◽  
Bound State ◽  
Dynamics Simulation ◽  
Free State ◽  
Rna Aptamer ◽  
Dynamic Features ◽  
Structural Arrangement ◽  
Wide Range

Motivation RNA, which adopts a wide range of secondary structures is involved in several kind of chemical interactions and shows a notable structural plasticity. Due to remarkable chemical properties and an important physiological role of RNAs, there is a growing interest in development of RNA-based drugs and ligands of clinical relevance. However, RNAs structural and dynamic features as well as the main RNA-protein recognition effects remain largely unaddressed. We have studied the conformational behaviour and the dynamic of two different structural arrangements of an aptamer binding the bacillus anthracis ribosomal protein S8. This RNA aptamer has experimentally shown two different topologies in free state and in protein-bound state, although sequences differ for just few residues beyond the common internal loop. The role of the interacting protein on the RNA folding, stabilizing or inducing a particular conformation will be discussed. Methods Three molecular dynamic simulations of 300 ns each have been performed starting from three distinct aptamer structures: i) the aptamer free-state, using a representative model of a NMR ensemble of structures (pdb 2lun); ii) a similar aptamer bound to its target protein (4pdb) iii); an aptamer model built using the sequence of the RNA in the free state but with the structural arrangement of the bound-state to investigate a possible influence of the sequence on the RNA folding. All the systems under investigations were solvated in a truncated octahedral water box using explicit water models, with a least a 1.1 Å distance to the border, using Na+ counter-ions to neutralize. 6 steps of heating simulation from 50 K to 300K were carried out before to perform the final MD run of 300 ns in NPT conditions without restrains. The trajectories were analysed using the GROMACS utilities and X3DNA program. Results Our data show that both bound-state RNA arrangements are structurally stable, holding all the main interactions since the beginning of the simulations. The free-state RNA is the system with the largest flexibility, reaching an equilibrium after 40 ns of simulation. Although the NMR structure appears less rigid, during the total run it never matches the arrangement of the bound state. Definitely, within our time scale, a convergence of the free state with the bound-state trajectories has never been observed and the two different arrangements show differences in flexibility. Preliminary data suggest a significantly different behaviour of the free- and bound-state structures supporting a preminent role of the interacting partner protein on the RNA overall folding to induce a particular stable structural arrangement.

scholarly journals A CPSF-73 Homologue Is Required for Cell Cycle Progression but Not Cell Growth and Interacts with a Protein Having Features of CPSF-100

2005 ◽  
Vol 25 (4) ◽  
pp. 1489-1500 ◽  
Author(s):  
Zbigniew Dominski ◽  
Xiao-cui Yang ◽  
Matthew Purdy ◽  
Eric J. Wagner ◽  
William F. Marzluff
Keyword(s):  
Hela Cells ◽  
Cell Cycle Progression ◽  
Wide Range ◽  
Catalytically Active ◽  
Cellular Mrnas ◽  
Human Proteins ◽  
Cleavage And Polyadenylation ◽  
Specificity Factor ◽  
Processing Event ◽  
Mouse Cells

ABSTRACT Formation of the mature 3′ ends of the vast majority of cellular mRNAs occurs through cleavage and polyadenylation and requires a cleavage and polyadenylation specificity factor (CPSF) containing, among other proteins, CPSF-73 and CPSF-100. These two proteins belong to a superfamily of zinc-dependent β-lactamase fold proteins with catalytic specificity for a wide range of substrates including nucleic acids. CPSF-73 contains a zinc-binding histidine motif involved in catalysis in other members of the β-lactamase superfamily, whereas CPSF-100 has substitutions within the histidine motif and thus is unlikely to be catalytically active. Here we describe two previously unknown human proteins, designated RC-68 and RC-74, which are related to CPSF-73 and CPSF-100 and which form a complex in HeLa and mouse cells. RC-68 contains the intact histidine motif, and hence it might be a functional counterpart of CPSF-73, whereas RC-74 lacks this motif, thus resembling CPSF-100. In HeLa cells RC-68 is present in both the cytoplasm and the nucleus whereas RC-74 is exclusively nuclear. RC-74 does not interact with CPSF-73, and neither RC-68 nor RC-74 is found in a complex with CPSF-160, indicating that these two proteins form a separate entity independent of the CPSF complex and are likely involved in a pre-mRNA processing event other than cleavage and polyadenylation of the vast majority of cellular pre-mRNAs. RNA interference-mediated depletion of RC-68 arrests HeLa cells early in G1 phase, but surprisingly the arrested cells continue growing and reach the size typical of G2 cells. RC-68 is highly conserved from plants to humans and may function in conjunction with RC-74 in the 3′ end processing of a distinct subset of cellular pre-mRNAs encoding proteins required for G1 progression and entry into S phase.

scholarly journals Adenylyl Cyclase G Is Activated by an Intramolecular Osmosensor

2004 ◽  
Vol 15 (3) ◽  
pp. 1479-1486 ◽  
Author(s):  
Shweta Saran ◽  
Pauline Schaap
Keyword(s):  
Adenylyl Cyclase ◽  
Catalytic Domain ◽  
Inducible Promoter ◽  
Null Mutant ◽  
Camp Production ◽  
Size Fractionation ◽  
Catalytic Domains ◽  
High Osmolality ◽  
Uv Induction

Adenylyl cyclase G (ACG) is activated by high osmolality and mediates inhibition of spore germination by this stress factor. The catalytic domains of all eukaryote cyclases are active as dimers and dimerization often mediates activation. To investigate the role of dimerization in ACG activation, we coexpressed ACG with an ACG construct that lacked the catalytic domain (ACGΔcat) and was driven by a UV-inducible promoter. After UV induction of ACGΔcat, cAMP production by ACG was strongly inhibited, but osmostimulation was not reduced. Size fractionation of native ACG showed that dimers were formed between ACG molecules and between ACG and ACGΔcat. However, high osmolality did not alter the dimer/monomer ratio. This indicates that ACG activity requires dimerization via a region outside the catalytic domain but that dimer formation does not mediate activation by high osmolality. To establish whether ACG required auxiliary sensors for osmostimulation, we expressed ACG cDNA in a yeast adenylyl cyclase null mutant. In yeast, cAMP production by ACG was similarly activated by high osmolality as in Dictyostelium. This strongly suggests that the ACG osmosensor is intramolecular, which would define ACG as the first characterized primary osmosensor in eukaryotes.

scholarly journals 2321

2017 ◽  
Vol 1 (S1) ◽  
pp. 7-7
Author(s):  
Koji Ota ◽  
Dalee Zhou ◽  
Jonathan Zippin
Keyword(s):  
Cell Death ◽  
Ultraviolet Radiation ◽  
Adenylyl Cyclase ◽  
Ph Sensor ◽  
Adenylyl Cyclases ◽  
Melanin Content ◽  
Soluble Adenylyl Cyclase ◽  
Wide Range ◽  
Skin Biology

OBJECTIVES/SPECIFIC AIMS: Our objective is to study the role of soluble adenylyl cyclase in the melanocyte regulation of pigment in response to ultraviolet radiation. Melanocytes are specialized cells that produce melanin in organelles called melanosomes, and melanin determines the pigmentation of hair and skin. cAMP is a master regulator of pigmentation and transmembrane class of adenylyl cyclases are essential for expression of important enzymes involved in melanogenesis. However, pigmentation is also controlled by melanosomal pH, which regulates melanogenesis, tyrosinase activity, and melanosome maturation. The relationship between melanosomal pH and cAMP has been elusive. Soluble adenylyl cyclase is a noncanonical source of cAMP that is not responsive to G proteins but rather functions as a pH sensor. We recently demonstrated that loss of soluble adenylyl cyclase (sAC) activity leads to increased melanosomal pH as well as increased pigmentation in cells and hair. We expanded our research to investigate the role of sAC in the intrinsic response of melanocytes to ultraviolet radiation. METHODS/STUDY POPULATION: We utilized sACfl/fl (wild type) and sACKO mouse melanocytes and compared their change in pigmentation in response to ultraviolet radiation. Melanin was used as a measure of pigmentation. We irradiated these cells at differing doses of UVB (0, 1, 2, or 3 mJ/cm2) daily for 3 days. After UVB treatment, cells were observed and the surviving cell numbers were determined. Cells were then analyzed for melanin content using spectroscopy. RESULTS/ANTICIPATED RESULTS: We found that while both sACfl/fl and sACKO cells had increased melanin content in response to UVB, the melanin content of sACKO cells increased more compared with sACfl/fl cells (p=0.001 at daily dose of 3 mJ/cm2). In addition, sACKO cells required less UVB dose to induce a response. We also observed that sACKO cells show increased cell death compared with sACfl/fl cells. DISCUSSION/SIGNIFICANCE OF IMPACT: Although both sACfl/fl and sACKO cells can induce melanin production in response to UV, our results suggest that sACKO cells are more sensitive. We believe that this increased response in sACKO cells is due to increased melanosomal pH. In addition, sACKO cells show increased cell death, suggesting that sAC is important in the damage response secondary to UV exposure. UV plays a wide range of roles in skin biology such as contributing to cancer risk and pigmentation. Since pigmentation is essential for the protection of the skin from UV insult, further investigation of possible mechanisms in which sAC can influence pigmentation in response to UV is warranted.

The Problem of Identifying and Modeling the Relationship between Monetary Factor and Inflation in the Russian Economy

2008 ◽  
pp. 61-76
Author(s):  
A. Porshakov ◽  
A. Ponomarenko
Keyword(s):  
Money Supply ◽  
Money Demand ◽  
Russian Economy ◽  
Long Run ◽  
Complex Approach ◽  
Wide Range ◽  
Long Time ◽  
The Relationship ◽  
Supply Side Factors

The role of monetary factor in generating inflationary processes in Russia has stimulated various debates in social and scientific circles for a relatively long time. The authors show that identification of the specificity of relationship between money and inflation requires a complex approach based on statistical modeling and involving a wide range of indicators relevant for the price changes in the economy. As a result a model of inflation for Russia implying the decomposition of inflation dynamics into demand-side and supply-side factors is suggested. The main conclusion drawn is that during the recent years the volume of inflationary pressures in the Russian economy has been determined by the deviation of money supply from money demand, rather than by money supply alone. At the same time, monetary factor has a long-run spread over time impact on inflation.

Introduction: Emotion, History and the Arts

2018 ◽  
Vol 7 (2) ◽  
pp. 117-128 ◽  
Author(s):  
Erin Sullivan ◽  
Marie Louise Herzfeld-Schild
Keyword(s):  
Historical Change ◽  
Carson Mccullers ◽  
Emotional Life ◽  
Review Section ◽  
The Arts ◽  
Wide Range ◽  
War Correspondents ◽  
History Of ◽  
Johan Huizinga

This introduction surveys the rise of the history of emotions as a field and the role of the arts in such developments. Reflecting on the foundational role of the arts in the early emotion-oriented histories of Johan Huizinga and Jacob Burkhardt, as well as the concerns about methodological impressionism that have sometimes arisen in response to such studies, the introduction considers how intensive engagements with the arts can open up new insights into past emotions while still being historically and theoretically rigorous. Drawing on a wide range of emotionally charged art works from different times and places—including the novels of Carson McCullers and Harriet Beecher-Stowe, the private poetry of neo-Confucian Chinese civil servants, the photojournalism of twentieth-century war correspondents, and music from Igor Stravinsky to the Beatles—the introduction proposes five ways in which art in all its forms contributes to emotional life and consequently to emotional histories: first, by incubating deep emotional experiences that contribute to formations of identity; second, by acting as a place for the expression of private or deviant emotions; third, by functioning as a barometer of wider cultural and attitudinal change; fourth, by serving as an engine of momentous historical change; and fifth, by working as a tool for emotional connection across communities, both within specific time periods but also across them. The introduction finishes by outlining how the special issue's five articles and review section address each of these categories, while also illustrating new methodological possibilities for the field.

Short Films from a Small Nation

2018 ◽  
Author(s):  
C. Claire Thomson
Keyword(s):  
Public Information ◽  
Industrial Process ◽  
Actor Network Theory ◽  
Documentary Films ◽  
Wide Range ◽  
Short Films ◽  
Post War ◽  
The 1960S ◽  
Art And Architecture

The first book-length study in English of a national corpus of state-sponsored informational film, this book traces how Danish shorts on topics including social welfare, industry, art and architecture were commissioned, funded, produced and reviewed from the inter-war period to the 1960s. For three decades, state-sponsored short filmmaking educated Danish citizens, promoted Denmark to the world, and shaped the careers of renowned directors like Carl Th. Dreyer. Examining the life cycle of a representative selection of films, and discussing their preservation and mediation in the digital age, this book presents a detailed case study of how informational cinema is shaped by, and indeed shapes, its cultural, political and technological contexts.The book combines close textual analysis of a broad range of films with detailed accounts of their commissioning, production, distribution and reception in Denmark and abroad, drawing on Actor-Network Theory to emphasise the role of a wide range of entities in these processes. It considers a broad range of genres and sub-genres, including industrial process films, public information films, art films, the city symphony, the essay film, and many more. It also maps international networks of informational and documentary films in the post-war period, and explores the role of informational film in Danish cultural and political history.

Quantitative and Qualitative Methods of Studying the Processes of Socialization of a Modern Teenager

2020 ◽  
pp. 102-109
Author(s):  
Svetlana Alekseevna Raschetina ◽  
Keyword(s):  
Research Methods ◽  
Interpersonal Relations ◽  
Internet Communication ◽  
Socialization Process ◽  
Wide Range ◽  
The Family ◽  
Modern Family ◽  
Making Friends ◽  
Main Support

Relevance and problem statement. Modern unstable society is characterized by narrowing the boundaries of controlled socialization and expanding the boundaries of spontaneous socialization of a teenager based on his immersion in the question arises about the importance of the family in the process of socialization of a teenager in the conditions of expanding the space of socialization. There is a need to study the role of the family in this process, to search, develop and test research methods that allow us to reveal the phenomenon of socialization from the side of its value characteristics. The purpose and methodology of the study: to identify the possibilities of a systematic and anthropological methodology for studying the role of the family in the process of socialization of adolescents in modern conditions, testing research methods: photo research on the topic “Ego – I” (author of the German sociologist H. Abels), profile update reflexive processes (by S. A. Raschetina). Materials and results of the study. The study showed that for all the problems that exist in the family of the perestroika era and in the modern family, it acts for a teenager as a value and the first (main) support in the processes of socialization. The positions well known in psychology about the importance of interpersonal relations in adolescence for the formation of attitudes towards oneself as the basis of socialization are confirmed. Today, the frontiers of making friends have expanded enormously on the basis of Internet communication. The types of activities of interest to a teenager (traditional and new ones related to digitalization) are the third pillar of socialization. Conclusion. The “Ego – I” method of photo research has a wide range of possibilities for quantitative and qualitative analysis of the socialization process to identify the value Pillars of this process.

Victorian Culture and Classical Antiquity

2011 ◽  
Author(s):  
Simon Goldhill
Keyword(s):  
Nineteenth Century ◽  
Roman Empire ◽  
Classical Antiquity ◽  
Victorian Culture ◽  
Wide Range ◽  
Victorian Art ◽  
Victorian Science ◽  
Role Of Religion ◽  
Nineteenth Century Novels

How did the Victorians engage with the ancient world? This book is an exploration of how ancient Greece and Rome influenced Victorian culture. Through Victorian art, opera, and novels, the book examines how sexuality and desire, the politics of culture, and the role of religion in society were considered and debated through the Victorian obsession with antiquity. Looking at Victorian art, it demonstrates how desire and sexuality, particularly anxieties about male desire, were represented and communicated through classical imagery. Probing into operas of the period, the book addresses ideas of citizenship, nationalism, and cultural politics. And through fiction—specifically nineteenth-century novels about the Roman Empire—it discusses religion and the fierce battles over the church as Christianity began to lose dominance over the progressive stance of Victorian science and investigation. Rediscovering some great forgotten works and reframing some more familiar ones, the book offers extraordinary insights into how the Victorian sense of antiquity and our sense of the Victorians came into being. With a wide range of examples and stories, it demonstrates how interest in the classical past shaped nineteenth-century self-expression, giving antiquity a unique place in Victorian culture.

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