Mutational and structural study of RipA, a key enzyme inMycobacterium tuberculosiscell division: evidence for theL-to-Dinversion of configuration of the catalytic cysteine

2014 ◽  
Vol 70 (9) ◽  
pp. 2295-2300 ◽  
Author(s):  
Flavia Squeglia ◽  
Alessia Ruggiero ◽  
Maria Romano ◽  
Luigi Vitagliano ◽  
Rita Berisio
Keyword(s):  
Structural Integrity ◽  
Cysteine Proteases ◽  
Enzyme Inactivation ◽  
Side Chain ◽  
Catalytic Cysteine ◽  
Key Enzyme ◽  
And Function ◽  
The Impact ◽  
Daughter Cell Separation

RipA is a key cysteine protease ofMycobacterium tuberculosisas it is responsible for bacterial daughter-cell separation. Although it is an important target for antimicrobial development, its mechanism of action and its interaction pattern with its substrate are hitherto unknown. By combining crystallographic and mutational studies with functional assays and molecular modelling, it is shown that the catalytic activity of the enzyme relies on a Cys–His–Glu triad and the impact of the mutation of each residue of the triad on the structure and function of RipA is analysed. Unexpectedly, the crystallographic analyses reveal that mutation of the glutamic acid to alanine results in inversion of the configuration of the catalytic cysteine. The consequent burial of the catalytic cysteine side chain explains the enzyme inactivation upon mutation. These data point to a novel role of the acidic residue often present in the triad of cysteine proteases as a supervisor of cysteine configuration through preservation of the local structural integrity.

scholarly journals Codon harmonization reduces amino acid misincorporation in bacterially expressed P. falciparum proteins and improves their immunogenicity

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Neeraja Punde ◽  
Jennifer Kooken ◽  
Dagmar Leary ◽  
Patricia M. Legler ◽  
Evelina Angov
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Codon Usage ◽  
Dna Sequences ◽  
Structural Integrity ◽  
Host Cells ◽  
Loss Of Function ◽  
Species Specific ◽  
And Function ◽  
The Impact

Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.

scholarly journals Irritable bowel syndrome: new insights into symptom mechanisms and advances in treatment

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 780 ◽  
Author(s):  
Robin Spiller
Keyword(s):  
Irritable Bowel Syndrome ◽  
New Agents ◽  
Enteric Nerves ◽  
Inflammatory Bowel ◽  
Magnetic Resonance Imaging Mri ◽  
Irritable Bowel ◽  
Fodmap Diet ◽  
And Function ◽  
The Impact

Despite being one of the most common conditions leading to gastroenterological referral, irritable bowel syndrome (IBS) is poorly understood. However, recent years have seen major advances. These include new understanding of the role of both inflammation and altered microbiota as well as the impact of dietary intolerances as illuminated by magnetic resonance imaging (MRI), which has thrown new light on IBS. This article will review new data on how excessive bile acid secretion mediates diarrhea and evidence from post infectious IBS which has shown how gut inflammation can alter gut microbiota and function. Studies of patients with inflammatory bowel disease (IBD) have also shown that even when inflammation is in remission, the altered enteric nerves and abnormal microbiota can generate IBS-like symptoms. The efficacy of the low FODMAP diet as a treatment for bloating, flatulence, and abdominal discomfort has been demonstrated by randomized controlled trials. MRI studies, which can quantify intestinal volumes, have provided new insights into how FODMAPs cause symptoms. This article will focus on these areas together with recent trials of new agents, which this author believes will alter clinical practice within the foreseeable future.

scholarly journals Peran Pendidikan Etika Kristen dalam Media Sosial di Era Disrupsi

2020 ◽  
Vol 1 (1) ◽  
pp. 38-46
Author(s):  
Mesirawati Waruwu ◽  
Yonatan Alex Arifianto ◽  
Aji Suseno
Keyword(s):  
Social Media ◽  
Ethics Education ◽  
Christian Ethics ◽  
Christian Faith ◽  
Ethical Challenges ◽  
Use Of Social Media ◽  
And Function ◽  
Meaning And Function ◽  
The Impact

The limitless development of social media, its meaning and function have begun to shift, no longer as a means of establishing relationships, communication, but at the stage of losing the role of ethics and morals, even disputes have occurred triggered by debates from communicating in social media. The purpose of this study is to describe the role of Christian ethics education in relation to the impact of social media development in the era of disruption. Using descriptive qualitative methods with literature literature can find solutions for believers in facing moral decadence due to social media abuse by knowing the era of disruption and ethical challenges from the wrong use of social media can affect moral decadence so that Christian ethics education on a biblical basis can bring modern humans. Believers in particular have become bright in social media and their use in accordance with Christian faith in this era of disruption.

scholarly journals Vimentin filaments drive migratory persistence in polyploidal cancer cells

2020 ◽  
Vol 117 (43) ◽  
pp. 26756-26765
Author(s):  
Botai Xuan ◽  
Deepraj Ghosh ◽  
Joy Jiang ◽  
Rachelle Shao ◽  
Michelle R. Dawson
Keyword(s):  
Cancer Cells ◽  
Cancer Progression ◽  
Structural Integrity ◽  
Single Cell Analysis ◽  
Critical Role ◽  
Critical Function ◽  
Rna Knockdown ◽  
Interfering Rna ◽  
The Impact

Polyploidal giant cancer cells (PGCCs) are multinucleated chemoresistant cancer cells found in heterogeneous solid tumors. Due in part to their apparent dormancy, the effect of PGCCs on cancer progression has remained largely unstudied. Recent studies have highlighted the critical role of PGCCs as aggressive and chemoresistant cancer cells, as well as their ability to undergo amitotic budding to escape dormancy. Our recent study demonstrated the unique biophysical properties of PGCCs, as well as their unusual migratory persistence. Here we unveil the critical function of vimentin intermediate filaments (VIFs) in maintaining the structural integrity of PGCCs and enhancing their migratory persistence. We performed in-depth single-cell analysis to examine the distribution of VIFs and their role in migratory persistence. We found that PGCCs rely heavily on their uniquely distributed and polarized VIF network to enhance their transition from a jammed to an unjammed state to allow for directional migration. Both the inhibition of VIFs with acrylamide and small interfering RNA knockdown of vimentin significantly decreased PGCC migration and resulted in a loss of PGCC volume. Because PGCCs rely on their VIF network to direct migration and to maintain their enlarged morphology, targeting vimentin or vimentin cross-linking proteins could provide a therapeutic approach to mitigate the impact of these chemoresistant cells in cancer progression and to improve patient outcomes with chemotherapy.

scholarly journals Contribution of HIV Infection, AIDS, and Antiretroviral Therapy to Exocrine Pathogenesis in Salivary and Lacrimal Glands

2018 ◽  
Vol 19 (9) ◽  
pp. 2747 ◽  
Author(s):  
Imran Nizamuddin ◽  
Peter Koulen ◽  
Carole McArthur
Keyword(s):  
Antiretroviral Therapy ◽  
Hiv Infection ◽  
Immune Deficiency Syndrome ◽  
Deficiency Syndrome ◽  
Exocrine Function ◽  
Lacrimal Glands ◽  
Immunodeficiency Virus ◽  
And Function ◽  
The Impact

The structure and function of exocrine glands are negatively affected by human immunodeficiency virus (HIV) infection and its co-morbidities, including innate and adaptive immune responses. At the same time, exocrine function may also be influenced by pharmacotherapies directed at the infectious agents. Here, we briefly review the role of the salivary glands and lacrimal glands in normal physiology and exocrine pathogenesis within the context of HIV infection and acquired immune deficiency syndrome (AIDS), including the contribution of antiretroviral therapies on both. Subsequently, we discuss the impact of HIV infection and the types of antiretroviral therapy on disease management and therapy development efforts.

scholarly journals The Phosphoglycerate Kinase (PGK) Gene Family of Maize (Zea mays var. B73)

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1639
Author(s):  
Julio A. Massange-Sánchez ◽  
Luz E. Casados-Vázquez ◽  
Sheila Juarez-Colunga ◽  
Ruairidh J. H. Sawers ◽  
Axel Tiessen
Keyword(s):  
Phylogenetic Analysis ◽  
Zea Mays ◽  
Leaf Blade ◽  
Phosphoglycerate Kinase ◽  
Future Studies ◽  
Plant Genomes ◽  
Key Enzyme ◽  
And Function ◽  
Distinct Role

Phosphoglycerate kinase (PGK, E.C. 2.7.2.3) interconverts ADP + 1,3-bisphospho-glycerate (1,3-bPGA) to ATP + 3-phosphoglycerate (3PGA). While most bacteria have a single pgk gene and mammals possess two copies, plant genomes contain three or more PGK genes. In this study, we identified five Pgk genes in the Zea mays var. B73 genome, predicted to encode proteins targeted to different subcellular compartments: ZmPgk1, ZmPgk2, and ZmPgk4 (chloroplast), ZmPgk3 (cytosol), and ZmPgk5 (nucleus). The expression of ZmPgk3 was highest in non-photosynthetic tissues (roots and cobs), where PGK activity was also greatest, consistent with a function in glycolysis. Green tissues (leaf blade and husk leaf) showed intermediate levels of PGK activity, and predominantly expressed ZmPgk1 and ZmPgk2, suggesting involvement in photosynthetic metabolism. ZmPgk5 was weakly expressed and ZmPgk4 was not detected in any tissue. Phylogenetic analysis showed that the photosynthetic and glycolytic isozymes of plants clustered together, but were distinct from PGKs of animals, fungi, protozoa, and bacteria, indicating that photosynthetic and glycolytic isozymes of plants diversified after the divergence of the plant lineage from other groups. These results show the distinct role of each PGK in maize and provide the basis for future studies into the regulation and function of this key enzyme.

A stochastic roadmap method to model protein structural transitions

Robotica ◽  
2015 ◽  
Vol 34 (8) ◽  
pp. 1705-1733 ◽  
Author(s):  
Kevin Molloy ◽  
Rudy Clausen ◽  
Amarda Shehu
Keyword(s):  
Protein Structure ◽  
Molecular Basis ◽  
Structure And Function ◽  
Structural Transitions ◽  
Simulation Framework ◽  
Human Disorders ◽  
Model Protein ◽  
And Function ◽  
The Impact

SUMMARYEvidence is emerging that the role of protein structure in disease needs to be rethought. Sequence mutations in proteins are often found to affect the rate at which a protein switches between structures. Modeling structural transitions in wildtype and variant proteins is central to understanding the molecular basis of disease. This paper investigates an efficient algorithmic realization of the stochastic roadmap simulation framework to model structural transitions in wildtype and variants of proteins implicated in human disorders. Our results indicate that the algorithm is able to extract useful information on the impact of mutations on protein structure and function.

scholarly journals The conformational and mutational landscape of the ubiquitin-like marker for the autophagosome formation in cancer

2019 ◽  
Author(s):  
Burcu Aykac Fas ◽  
Mukesh Kumar ◽  
Valentina Sora ◽  
Maliha Mashkoor ◽  
Matteo Lambrughi ◽  
...  
Keyword(s):  
Physical Models ◽  
Missense Mutations ◽  
Cancer Types ◽  
Neutral Mutations ◽  
And Function ◽  
Cellular Components ◽  
The Impact ◽  
Pan Cancer ◽  
Structural Ensemble

AbstractAutophagy is a cellular process to recycle damaged cellular components and its modulation can be exploited for disease treatments. A key autophagy player is a ubiquitin-like protein, LC3B. Compelling evidence attests the role of autophagy and LC3B in different cancer types. Many LC3B structures have been solved, but a comprehensive study, including dynamics, has not been yet undertaken. To address this knowledge gap, we assessed ten physical models for molecular dynamics for their capabilities to describe the structural ensemble of LC3B in solution using different metrics and comparison with NMR data. With the resulting LC3B ensembles, we characterized the impact of 26 missense mutations from Pan-Cancer studies with different approaches. Our findings shed light on driver or neutral mutations in LC3B, providing an atlas of its modifications in cancer. Our framework could be used to assess the pathogenicity of mutations by accounting for the different aspects of protein structure and function altered by mutational events.

scholarly journals Estradiol Inhibits Human Brain Vascular Pericyte Migration Activity: A Functional and Transcriptomic Analysis

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2314
Author(s):  
Lisa Kurmann ◽  
Michal Okoniewski ◽  
Raghvendra K. Dubey
Keyword(s):  
Endothelial Cells ◽  
Cell Migration ◽  
Human Brain ◽  
Neurovascular Unit ◽  
Active Role ◽  
Migration Activity ◽  
Akt Phosphorylation ◽  
And Function ◽  
The Impact

Stroke is the third leading cause of mortality in women and it kills twice as many women as breast cancer. A key role in the pathophysiology of stroke plays the disruption of the blood–brain barrier (BBB) within the neurovascular unit. While estrogen induces vascular protective actions, its influence on stroke remains unclear. Moreover, experiments assessing its impact on endothelial cells to induce barrier integrity are non-conclusive. Since pericytes play an active role in regulating BBB integrity and function, we hypothesize that estradiol may influence BBB by regulating their activity. In this study using human brain vascular pericytes (HBVPs) we investigated the impact of estradiol on key pericyte functions known to influence BBB integrity. HBVPs expressed estrogen receptors (ER-α, ER-β and GPER) and treatment with estradiol (10 nM) inhibited basal cell migration but not proliferation. Since pericyte migration is a hallmark for BBB disruption following injury, infection and inflammation, we investigated the effects of estradiol on TNFα-induced PC migration. Importantly, estradiol prevented TNFα-induced pericyte migration and this effect was mimicked by PPT (ER-α agonist) and DPN (ER-β agonist), but not by G1 (GPR30 agonist). The modulatory effects of estradiol were abrogated by MPP and PHTPP, selective ER-α and ER-β antagonists, respectively, confirming the role of ER-α and ER-β in mediating the anti-migratory actions of estrogen. To delineate the intracellular mechanisms mediating the inhibitory actions of estradiol on PC migration, we investigated the role of AKT and MAPK activation. While estradiol consistently reduced the TNFα-induced MAPK and Akt phosphorylation, only the inhibition of MAPK, but not Akt, significantly abrogated the migratory actions of TNFα. In transendothelial electrical resistance measurements, estradiol induced barrier function (TEER) in human brain microvascular endothelial cells co-cultured with pericytes, but not in HBMECs cultured alone. Importantly, transcriptomics analysis of genes modulated by estradiol in pericytes showed downregulation of genes known to increase cell migration and upregulation of genes known to inhibit cell migration. Taken together, our findings provide the first evidence that estradiol modulates pericyte activity and thereby improves endothelial integrity.

Liver

2018 ◽  
Author(s):  
Hugh Devlin ◽  
Rebecca Craven
Keyword(s):  
Liver Function ◽  
Dental Care ◽  
Impaired Liver Function ◽  
Drug Products ◽  
Dental Patients ◽  
Dental Patient ◽  
Impaired Liver ◽  
And Function ◽  
The Impact

Liver in relation to dentistry is the topic of this chapter. Structure and function of the liver are discussed: metabolism of nutrients and toxins, exocrine functions, and synthesis of key proteins. Drugs and the liver are then discussed: the role of plasma proteins in transport or binding drugs; the liver’s role in metabolizing drugs; and the liver’s role in excreting some drug products into the bile. The effects of chronic excess alcohol on the liver are described and the role of the dentist in spotting potential liver problems in dental patients. The impact of liver disease on patient physiology is next explored, and the relevance for management of the dental patient. Types of hepatitis are described with relevance to dental care for hepatitis transmission. Key tests of liver function are described. The concluding section deals with the dental care of patients with impaired liver function.

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