RNA-binding is an ancient trait of the Annexin family

Introduction: The regulation of intracellular functions in mammalian cells involves close coordination of cellular processes. During recent years it has become evident that the sorting, trafficking and distribution of transport vesicles and mRNA granules/complexes are closely coordinated to ensure effective simultaneous handling of all components required for a specific function, thereby minimizing the use of cellular energy. Identification of proteins acting at the crossroads of such coordinated transport events will ultimately provide mechanistic details of the processes. Annexins are multifunctional proteins involved in a variety of cellular processes associated with Ca²⁺-regulation and lipid binding, linked to the operation of both the endocytic and exocytic pathways. Furthermore, certain Annexins have been implicated in the regulation of mRNA transport and translation. Since Annexin A2 binds specific mRNAs via its core structure and is also present in mRNP complexes, we speculated whether direct association with RNA could be a common property of the mammalian Annexin family sharing a highly similar core structure. Methods and results: Therefore, we performed spot blot and UV-crosslinking experiments to assess the mRNA binding abilities of the different Annexins, using annexin A2 and c-myc 3'UTRs as well as c-myc 5'UTR as baits. We supplemented the data with immunoblot detection of selected Annexins in mRNP complexes derived from the neuroendocrine rat PC12 cells. Furthermore, biolayer interferometry was used to determine the K_D of selected Annexin-RNA interactions, which indicated distinct affinities. Amongst these Annexins, Annexin A13 and the core structures of Annexin A7, Annexin A11 bind c-myc 3'UTR with K_Ds in the nanomolar range. Of the selected Annexins, only Annexin A2 binds the c-myc 5'UTR indicating some selectivity. Discussion: The oldest members of the mammalian Annexin family share the ability to associate with RNA, suggesting that RNA-binding is an ancient trait of this protein family. Thus, the combined RNA- and lipid-binding properties of the Annexins make them attractive candidates to participate in coordinated long-distance transport of membrane vesicles and mRNAs regulated by Ca²⁺. The present screening results can thus pave the way for studies of the multifunctional Annexins in a novel cellular context.

Fragment-Based Drug Discovery for RNA Targets

Rapid development within the fields of both fragment-based drug discovery (FBDD) and medicinal targeting of RNA provides possibilities for combining technologies and methods in novel ways. This review provides an overview of fragment-based screening (FBS) against RNA targets, including a discussion of the most recently used screening and hit validation methods such as NMR spectroscopy, X-ray crystallography, and virtual screening methods. A discussion of fragment library design based on research from small-molecule RNA binders provides an overview on both the currently limited guidelines within RNA-targeting fragment library design, and future possibilities. Finally, future perspectives are provided on screening and hit validation methods not yet used in combination with both fragment screening and RNA targets.

Riboswitches as Drug Targets for Antibiotics

Riboswitches reside in the untranslated region of RNA and regulate genes involved in the biosynthesis of essential metabolites through binding of small molecules. Since their discovery at the beginning of this century, riboswitches have been regarded as potential antibacterial targets. Using fragment screening, high-throughput screening and rational ligand design guided by X-ray crystallography, lead compounds against various riboswitches have been identified. Here, we review the current status and suitability of the thiamine pyrophosphate (TPP), flavin mononucleotide (FMN), glmS, guanine, and other riboswitches as antibacterial targets and discuss them in a biological context. Further, we highlight challenges in riboswitch drug discovery and emphasis the need to develop riboswitch specific high-throughput screening methods.

Structure analysis of thymidylate synthase from white spot syndrome virus reveals WSSV-specific structural elements

White spot syndrome virus (WSSV), the causative agent of white spot disease (WSD) severely affecting crustacean life forms, is highly contagious and forms the principal cause of massive economic losses in the shrimp aquaculture industry. Previous studies have demonstrated thymidylate synthase as a successful anti-cancer therapeutic drug target, leading to various anti-cancer drugs. The differential utilization of nucleotide precursors between white spot syndrome virus and shrimp encouraged us to analyze WSSV-thymidylate synthase (wTS). Here, we report the crystal structures of wTS in its apo-form and as a ternary complex with deoxyuridine monophosphate (dUMP) and methotrexate at a resolution of 2.35 Å and 2.6 Å, respectively. wTS possesses a fold characteristic to known thymidylate synthase (TS) structures. Like other TS structures, the apo-form of wTS displays an open conformation, whereas the wTS ternary complex attains a closed conformation. While the C-terminal loop maintains a typical distance from methotrexate, the Sγ atom of the catalytic Cys is positioned farther from the C6 atom of dUMP. Altogether, we report the first TS structure from a crustacean virus and highlight its distinction from shrimp and other TS structures.

A novel mutation alters the stability of PapA2 resulting in the complete abrogation of sulfolipids in clinical mycobacterial strains

The analysis of whole genomes has revealed specific geographical distribution of Mycobacterium tuberculosis (Mtb) strains across the globe suggestive of unique niche dependent adaptive mechanisms. We provide an important correlation of a genome-based mutation to a molecular phenotype across two predominant clinical Mtb lineages of the Indian subcontinent. We have identified a distinct lineage specific mutation-G247C, translating into an alanine-proline conversion in the papA2 gene of Indo-oceanic lineage 1 (L1) Mtb strains, and restoration of cell wall sulfolipids by simple genetic complementation of papA2 from lineage 3 (L3) or from H37Rv (lineage 4-L4) attributed the loss of this glycolipid to this specific mutation in Indo-Oceanic L1 Mtb. The investigation of structure of Mtb PapA2 revealed a distinct nonribosomal peptide synthetase (NRPS) C domain conformation with an unconventional presence of a zinc binding motif. Surprisingly, the A83P mutation did not map to either the catalytic center in the N-terminal subdomain or any of the substrate-binding region of the protein. On the contrary, the inherent ability of mutant PapA2 to form insoluble aggregates and molecular simulations with the wild-type/mutant (Wt/mut) PapA2 purports an important role for the surface associated 83rd residue in protein conformation. This study demonstrates the importance of a critical structural residue in the papA2 protein of Mtb and helps establish a link between observed genomic alteration and its molecular consequence in the successful human pathogen Mtb. Significance We demonstrate the effect of a unique SNP in PapA2 gene of Indo-oceanic Mycobacterium tuberculosis (Mtb) strains leading to the loss of sulfolipid from these strains. By X-ray crystallographic analysis and molecular dynamics (MD) simulations, we show the importance of this residue in the global PapA2 structure. The presence of a Zn atom has not been reported before for this class of proteins. Here, we provide an important link between genomic alteration and its molecular consequence in Mtb highlighting one of the many adaptive mechanisms that have contributed to its success as a human pathogen. A high degree of identity with PapA1, 3, or 4 would help in interpreting the structure of these PapA proteins and other acyl transferases of other biological systems.

Comparison of post-operative pain after root canal instrumentation with hand K-files, H-files and rotary Kedo-S files in primary teeth: a randomised clinical trial

PURPOSE

To compare the post-operative pain after root canal instrumentation with hand K-files, H-files and rotary Kedo-S in primary teeth.

METHOD

All 4-6-year-old children were invited and 69 agreed to participate. The participants were randomly divided and distributed for instrumentation with K-file (Group 1), H-file (Group 2) and rotary Kedo-S files (Group 3). After completion of root canal procedure, the post-operative pain was evaluated at intervals of 6, 12, 24, 48, and 72 h using modified Wong-Baker pain scale and compared between the groups.

RESULTS

Post-operative pain between three groups at 6, 12, 24, 48 and 72 h was compared using Chi square test. There was decreased post-operative pain with Kedo-S rotary files as compared to other two groups (P value < 0.001). The post-operative pain decreased after 12 h for all the groups with no pain at 24, 48 and 72 h intervals.

CONCLUSION

Paediatric rotary files Kedo-S showed significantly less post-operative pain as compared to K-file and H-file at 6 h and 12 h intervals. However, follow-up interval of 24, 48 and 72 h showed no significant difference between the rotary and hand file groups.

Phospholipid homeostasis, membrane tenacity and survival of Mtb in lipid rich conditions is determined by MmpL11 function

The mycobacterial cell wall is a chemically complex array of molecular entities that dictate the pathogenesis of Mycobacterium tuberculosis. Biosynthesis and maintenance of this dynamic entity in mycobacterial physiology is still poorly understood. Here we demonstrate a requirement for M. tuberculosis MmpL11 in the maintenance of the cell wall architecture and stability in response to surface stress. In the presence of a detergent like Tyloxapol, a mmpL11 deletion mutant suffered from a severe growth attenuation as a result of altered membrane polarity, permeability and severe architectural damages. This mutant failed to tolerate permissible concentrations of cis-fatty acids suggesting its increased sensitivity to surface stress, evident as smaller colonies of the mutant outgrown from lipid rich macrophage cultures. Additionally, loss of MmpL11 led to an altered cellular fatty acid flux in the mutant: reduced incorporation into membrane cardiolipin was associated with an increased flux into the cellular triglyceride pool. This increase in storage lipids like triacyl glycerol (TAG) was associated with the altered metabolic state of higher dormancy-associated gene expression and decreased sensitivity to frontline TB drugs. This study provides a detailed mechanistic insight into the function of mmpL11 in stress adaptation of mycobacteria.

Tuning epitaxial graphene sensitivity to water by hydrogen intercalation

The effects of humidity on the electronic properties of quasi-free standing one layer graphene (QFS 1LG) are investigated via simultaneous magneto-transport in the van der Pauw geometry and local work function measurements in a controlled environment. QFS 1LG on 4H-SiC(0001) is obtained by hydrogen intercalation of the interfacial layer. In this system, the carrier concentration experiences a two-fold increase in sensitivity to changes in relative humidity as compared to the as-grown epitaxial graphene. This enhanced sensitivity to water is attributed to the lowering of the hydrophobicity of QFS 1LG, which results from spontaneous polarization of 4H-SiC(0001) strongly influencing the graphene. Moreover, the superior carrier mobility of the QFS 1LG system is retained even at the highest humidity. The work function maps constructed from Kelvin probe force microscopy also revealed higher sensitivity to water for 1LG compared to 2LG in both QFS 1LG and as-grown systems. These results point to a new field of applications for QFS 1LG, i.e., as humidity sensors, and the corresponding need for metrology in calibration of graphene-based sensors and devices.

Atypical hemodynamic manifestations of cardiac tamponade

Clinical examination and transthoracic echocardiography play a vital role in the management of patients with pericardial effusion and cardiac tamponade physiology. We report patients in advanced phase 3 cardiac tamponade with variant clinical and hemodynamic presentations. These atypical cardiac tamponade cases include: A patient with severe aortic valve regurgitation who lacked pulsus paradoxus; a patient with systemic sclerosis without hypotension; and a patient with pulmonary hypertension lacking right heart collapse on echocardiography. Recognition of these atypical clinical and hemodynamic manifestations of cardiac tamponade will avoid undue delay in the treatment.

Designing appropriate rehabilitation technology: a mobility device for women with ambulatory disabilities in India

Mobility is an essential requirement for personal independence and social participation. For persons with an ambulatory disability, a lack of mobility creates barriers to the realization of these goals. In developed countries, significant research and development has resulted in the technological advancement of assistive devices. Unfortunately, transfer of these technologies to developing countries has proven difficult. Consequently, effort has been directed at designing appropriate technology in these countries--most often in the form of wheelchairs and hand-driven tricycles. For activities within and around the home, however, especially in cultures where many activities are traditionally performed on the floor, wheelchairs and tricycles are often inappropriate solutions. In response to this, a novel mobility device has been designed for use by women with ambulatory disabilities living in rural and low-income areas of India. The device is intended to assist the user in performing activities of daily living which occur within and near the home, and at ground level. To this end, the device conceptually differs from traditional wheelchair designs in that it physically keeps the rider near to the floor. This paper describes the new device as well as the cross-cultural and cross-professional collaborative methodology used in its design.

The mobility needs of women with physical disabilities in India: a functional perspective

The purpose of this research was to explore the functional mobility needs of women with lower extremity disabilities in Gujarat state, India. Ten women participated in a Mobility Needs Assessment which used multiple data collection methods to gather quantitative and qualitative information in five main areas. The results indicated that the physical environment was diverse, at times unpredictable, and environmental barriers were commonly encountered. The women travelled relatively long distances to perform self-care activities such as bathing and toileting. Furthermore, the women had compensated for their disability by implementing different strategies, such as four methods of locomotion, ten sitting positions, and various methods for carrying objects. Activities of daily living were similar amongst the women, although some women required assistance to complete specific activities successfully. Although the women expressed different views on how they felt about their present level of mobility, all were able to identify activities they wished to perform if they could move more easily. The resulting information contributed towards an area where little has been documented previously.