Conformational ensemble of the poliovirus 3CD precursor observed by MD simulations and confirmed by SAXS: A strategy to expand the viral proteome?

The genomes of RNA viruses are relatively small. To overcome the small-size limitation, RNA viruses assign distinct functions to the processed viral proteins and their precursors. This is exemplified by poliovirus 3CD protein. 3C protein is a protease and RNA-binding protein. 3D protein is an RNA-dependent RNA polymerase (RdRp). 3CD exhibits unique protease and RNA-binding activities relative to 3C and is devoid of RdRp activity. The origin of these differences is unclear, since crystal structure of 3CD revealed “beads-on-a-string” structure with no significant structural differences compared to the fully processed proteins. We performed molecular dynamics (MD) simulations on 3CD to investigate its conformational dynamics. A compact conformation of 3CD was observed that was substantially different from that shown crystallographically. This new conformation explained the unique properties of 3CD relative to the individual proteins. Interestingly, simulations of mutant 3CD showed altered interface. Additionally, accelerated MD simulations uncovered a conformational ensemble of 3CD. When we elucidated the 3CD conformations in solution using small-angle X-ray scattering (SAXS) experiments a range of conformations from extended to compact was revealed, validating the MD simulations. The existence of conformational ensemble of 3CD could be viewed as a way to expand the poliovirus proteome, an observation that may extend to other viruses

BCAT1 controls metabolic reprogramming in activated human macrophages and is associated with inflammatory diseases

This work was supported by the Medical Research Council (MR/M004716/1 and MR/N01121X/1 to J.B.) and by Kidney Research UK (RP9/2013 to J.B.). D.C. is supported by the Institute Pasteur, Fondazione Cenci Bolognetti. C.M. is supported by the British Hearth Foundation Fellowship (FS/12/3829640)

Biodeterioration of wood in estuarine ecosystem of Goa

An assessment of macrofouling and wood boring community at different localities of Zuari and Mandovi estuaries of Goa carried out. Wood panels of Mangifera indica of 10 x 15 x 2.5 cm size were exposed in this investigation. The panels were retrieved at an interval of 1 and 4 month. The macrofouling community mainly comprised sessile barnacles, bryzoans, mussels. oysters and tunicates and the wood boring community comprised of Martesia striata, Nausitora hedleyi and Lyrodus pedicellatus. The wood boring community was dominated by Martesia striata in pre-monsoon and post-monsoon seasons and by L. pedicellatus in monsoon. The macrofouling and wood boring communities which mainly contributes in biodeterioration of wood is discussed in this paper

Spatial and temporal distribution of fungi and wood-borers in the coastal tropical waters of Goa, India

Marine wood-degrading fungi are believed to contribute to the settlement and growth of wood-borers in the sea. However, little information is available on the association between species of these two groups of organisms. In view of this, we studied the occurrence of marine lignicolous fungi and wood-borers in mango (Mangifera indica Linn.) panels submerged at three test sites along the Mandovi and Zuari estuarine systems in the coastal waters of Goa, India, during different seasons. A total of 33 fungi (20 Ascomycota, 1 Basidiomycota, 12 Mitosporic fungi) and 8 wood-borers (7 Teredinids and 1 Pholad) were recorded. A wide gamut of distribution patterns of fungi and wood-borers was found. A high frequency of occurrence (> 20 %) and a broad spatial distribution was noticed in the case of four fungi. Two woodborers, likewise, were prevalent at all three sites. Several other fungi were also very frequent, but were restricted in their site distribution. Twenty-three fungi were rare or found infrequently (< 8%). Four of the eight wood-borers recorded were also of sporadic occurrence. The fungi Periconia prolifica and Antennospora quadricornuta and the wood-borers Martesia striata and Lyrodus pedicellatus were present on the wood throughout the year. On the contrary, growth of most fungi and five species of woodborers was adversely affected during the low salinity monsoons. Two fungi and one wood-borer colonized wood preferentially during the monsoon season. Contrary to earlier observations, more fungi appeared as early colonizers on wood during the first month of submergence than later. Our study indicates that in Goa waters, Periconia prolifica and Antennospora quadricornuta and the wood-borers Martesia striata and Lyrodus pedicellatus are highly versatile in their occurrence and were present throughout the year, at all sites. The numerous variations in distributional patterns observed in this study highlight the need to examine the response of marine fungi to physico-chemical parameters at the individual species level

The structure of human mitochondrial branched-chain aminotransferase

X-ray crystal structures of three forms of human mitochondrial branched-chain aminotransferase were solved by molecular-replacement methods. In two of the forms the enzyme is in its active form, with the pyridoxal 5′-phosphate (PLP) cofactor covalently linked to the ε-amino group of the active-site lysine. In the third form, a molecule of the Tris buffer is covalently bound to the PLP on one end and the active-site lysine on the other, inhibiting the enzyme irreversibly

Ecology of the wood-boring Bivalve Martesia striata (Pholadidae) in Indian waters

Martesia striata (Linnaeus) is one of the dominant wood-boring organisms found in Indian waters. Incidence of this organism in the Zuari estuary (Goa) was evaluated by exposing wooden panels (Mangifera indica) to the marine environment between January 1996 and January 1997. Effects of salinity variation on embryonic and larval development were evaluated (salinity 0, 10, 20, 30, 35, 40 and 50, temperature 25 °C) and maximum metamorphic success was observed at 30 salinity. Results of the rearing experiments, destruction pattern of wood in the environment and reproductive biology indicate that although recruitment is halted during the monsoon, adults survive and become reproductively mature in the following post-monsoon, leading to increased recruitment during pre-monsoon months

Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase

Abstract To biosynthesize ribosomally synthesized and post-translationally modified peptides (RiPPs), enzymes recognize and bind to the N-terminal leader region of substrate peptides which enables catalytic modification of the C-terminal core. Our current understanding of RiPP leaders is that they are short and largely unstructured. Proteusins are RiPP precursor peptides that defy this characterization as they possess unusually long leaders. Proteusin peptides have not been structurally characterized, and we possess scant understanding of how these atypical leaders engage with modifying enzymes. Here, we determine the structure of a proteusin peptide which shows that unlike other RiPP leaders, proteusin leaders are preorganized into a rigidly structured region and a smaller intrinsically disordered region. With residue level resolution gained from NMR titration experiments, the intermolecular peptide-protein interactions between proteusin leaders and a flavin-dependent brominase are mapped onto the disordered region, leaving the rigidly structured region of the proteusin leader to be functionally dispensable. Spectroscopic observations are biochemically validated to identify a binding motif in proteusin peptides that is conserved among other RiPP leaders as well. This study provides a structural characterization of the proteusin peptides and extends the paradigm of RiPP modification enzymes using not only unstructured peptides, but also structured proteins as substrates

Computer-aided design, syntheses, and ITC binding data of novel flavanone derivatives for use as potential inhibitors of the papain-like protease of COVID-19

The papain-like protease (PLpro) of SARS-CoV-2 (COVID-19) is a high-profile drug target for treating COVID-19 due to its critical role in making essential proteins crucial in viral replication and host immune sensing. The development of small molecule inhibitors of PLpro is an area of ongoing research and interest. To investigate the development of PLpro inhibitors, a series of novel flavanone derivatives were designed using in silico docking against the papain-like protease of COVID-19. The most promising targets were synthesized and structurally characterized by NMR and mass spectrometry. Using isothermal calorimetry studies, two synthesized derivatives were found to bind PLpro in the low micromolar to nanomolar range