Solution structures and biophysical analysis of full-length group A PAKs reveal they are monomeric and auto-inhibited in cis
The group A p21-activated kinases (PAKs) exist in an auto-inhibited form until activated by GTPase binding and auto-phosphorylation. In the auto-inhibited form, a regulatory domain binds to the kinase domain (KD) blocking the binding of substrates, and CDC42 or Rac binding to the regulatory domain relieves this auto-inhibition allowing auto-phosphorylation on the KD activation loop. We have determined the crystal structure of the PAK3 catalytic domain and by small angle X-ray scattering, the solution-phase structures of full-length inactive PAK1 and PAK3. The structures reveal a compact but elongated molecular shape that d...
Source: Biochemical Journal - April 3, 2019 Category: Biochemistry Authors: Sorrell, F. J., Kilian, L. M., Elkins, J. M. Tags: Research Articles Source Type: research
ADS-J1 disaggregates semen-derived amyloid fibrils
Semen-derived amyloid fibrils, comprising SEVI (semen-derived enhancer of viral infection) fibrils and SEM1 fibrils, could remarkably enhance HIV-1 sexual transmission and thus are potential targets for the development of an effective microbicide. Previously, we found that ADS-J1, apart from being an HIV-1 entry inhibitor, could also potently inhibit seminal amyloid fibrillization and block fibril-mediated enhancement of viral infection. However, the remodeling effects of ADS-J1 on mature seminal fibrils were unexplored. Herein, we investigated the capacity of ADS-J1 to disassemble seminal fibrils and the potential mode of...
Source: Biochemical Journal - March 28, 2019 Category: Biochemistry Authors: Li, J., Yang, Z., Liu, H., Qiu, M., Zhang, T., Li, W., Li, Z., Qi, T., Qiu, Y., Li, L., Zhou, X., Liu, S., Tan, S. Tags: Research Articles Source Type: research
Crystal structure of dimeric Synechococcus spermidine synthase with bound polyamine substrate and product
Spermidine is a ubiquitous polyamine synthesized by spermidine synthase (SPDS) from the substrates, putrescine and decarboxylated S-adenosylmethionine (dcAdoMet). SPDS is generally active as homodimer, but higher oligomerization states have been reported in SPDS from thermophiles, which are less specific to putrescine as the aminoacceptor substrate. Several crystal structures of SPDS have been solved with and without bound substrates and/or products as well as inhibitors. Here, we determined the crystal structure of SPDS from the cyanobacterium Synechococcus (SySPDS) that is a homodimer, which we also observed in solution....
Source: Biochemical Journal - March 28, 2019 Category: Biochemistry Authors: Guedez, G., Pothipongsa, A., Siren, S., Liljeblad, A., Jantaro, S., Incharoensakdi, A., Salminen, T. A. Tags: Research Articles Source Type: research
Unraveling the role of the MOV10 RNA helicase during influenza A virus infection
Moloney leukemia virus 10 (MOV10) is an interferon-inducible RNA helicase that has been implicated in a broad range of cellular functions, including modulating the replication of a diverse range of viruses. However, the mechanisms by which MOV10 promotes or inhibits the replication of particular viruses have not been well defined. A recent paper published in the Biochemical Journal by Li et al. [Biochem. J. (2019) 476, 467–481] provides insight regarding the mechanisms by which MOV10 restricts influenza A virus (IAV) infection in host cells. First, the authors confirm that MOV10 binds to the viral nucleoprotein (NP) ...
Source: Biochemical Journal - March 26, 2019 Category: Biochemistry Authors: Villalon-Letelier, F., Reading, P. C. Tags: Commentaries Source Type: research
Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis
In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulation...
Source: Biochemical Journal - March 21, 2019 Category: Biochemistry Authors: Pillalamarri, V., Arya, T., Haque, N., Bala, S. C., Marapaka, A. K., Addlagatta, A. Tags: Research Articles Source Type: research
Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea
Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to...
Source: Biochemical Journal - March 21, 2019 Category: Biochemistry Authors: He, D., Piergentili, C., Ross, J., Tarrant, E., Tuck, L. R., Mackay, C. L., McIver, Z., Waldron, K. J., Clarke, D. J., Marles-Wright, J. Tags: Research Articles Source Type: research
Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing
In conclusion, both ABA signalling and seed ageing impact seed vigour but not necessarily through the same biochemical mechanisms. (Source: Biochemical Journal)
Source: Biochemical Journal - March 21, 2019 Category: Biochemistry Authors: Schausberger, C., Roach, T., Stöggl, W., Arc, E., Finch-Savage, W. E., Kranner, I. Tags: Research Articles Source Type: research
Proline residues in scavenger receptor-BI's C-terminal region support efficient cholesterol transport
High-density lipoproteins (HDLs) facilitate reverse cholesterol transport, a process in which HDL removes cholesterol from circulation and carries it to the liver for biliary excretion. Reverse cholesterol transport is also facilitated by HDL's high-affinity receptor, scavenger receptor-BI (SR-BI), by mechanisms that are not fully understood. To improve our understanding of SR-BI function, we previously solved the NMR (nuclear magnetic resonance) structure of a peptide encompassing amino acids 405–475 of SR-BI. This segment of SR-BI, that includes the functionally critical C-terminal transmembrane domain and part of ...
Source: Biochemical Journal - March 21, 2019 Category: Biochemistry Authors: Proudfoot, S. C., Sahoo, D. Tags: Research Articles Source Type: research
The DCBLD receptor family: emerging signaling roles in development, homeostasis and disease
The discoidin, CUB, and LCCL domain-containing (DCBLD) receptor family are composed of the type-I transmembrane proteins DCBLD1 and DCBLD2 (also ESDN and CLCP1). These proteins are highly conserved across vertebrates and possess similar domain structure to that of neuropilins, which act as critical co-receptors in developmental processes. Although DCBLD1 remains largely uncharacterized, the functional and mechanistic roles of DCBLD2 are emerging. This review provides a comprehensive discussion of this presumed receptor family, ranging from structural and signaling aspects to their associations with cancer, physiology, and ...
Source: Biochemical Journal - March 21, 2019 Category: Biochemistry Authors: Schmoker, A. M., Ebert, A. M., Ballif, B. A. Tags: Review Articles Source Type: research
ParA proteins of secondary genome elements cross-talk and regulate radioresistance through genome copy number reduction in Deinococcus radiodurans
Deinococcus radiodurans, an extremely radioresistant bacterium has a multipartite genome system and ploidy. Mechanisms underlying such types of bacterial genome maintenance and its role in extraordinary radioresistance are not known in this bacterium. Chromosome I (Chr I), chromosome II (Chr II) and megaplasmid (Mp) encode its own set of genome partitioning proteins. Here, we have characterized P-loop ATPases of Chr II (ParA2) and Mp (ParA3) and their roles in the maintenance of genome copies and extraordinary radioresistance. Purified ParA2 and ParA3 showed nearly similar polymerization kinetics and interaction patterns w...
Source: Biochemical Journal - March 14, 2019 Category: Biochemistry Authors: Kumar Maurya, G., Kota, S., Kumar, N. N., Tewari, R., Misra, H. S. Tags: Research Articles Source Type: research
Azadirachtin inhibits amyloid formation, disaggregates pre-formed fibrils and protects pancreatic {beta}-cells from human islet amyloid polypeptide/amylin-induced cytotoxicity
The human islet amyloid polypeptide (hIAPP) or amylin is the major constituent of amyloidogenic aggregates found in pancreatic islets of type 2 diabetic patients that have been associated with β-cell dysfunction and/or death associated with type 2 diabetes mellitus (T2DM). Therefore, developing and/or identifying inhibitors of hIAPP aggregation pathway and/or compound that can mediate disaggregation of preformed aggregates holds promise as a medical intervention for T2DM management. In the current study, the anti-amyloidogenic potential of Azadirachtin (AZD)—a secondary metabolite isolated from traditional medic...
Source: Biochemical Journal - March 14, 2019 Category: Biochemistry Authors: Dubey, R., Patil, K., Dantu, S. C., Sardesai, D. M., Bhatia, P., Malik, N., Acharya, J. D., Sarkar, S., Ghosh, S., Chakrabarti, R., Sharma, S., Kumar, A. Tags: Research Articles Source Type: research
Conservation of structure, function and inhibitor binding in UNC-51-like kinase 1 and 2 (ULK1/2)
Autophagy is essential for cellular homeostasis and when deregulated this survival mechanism has been associated with disease development. Inhibition of autophagy initiation by inhibiting the kinase ULK1 (Unc-51-like autophagy activating kinase 1) has been proposed as a potential cancer therapy. While inhibitors and crystal structures of ULK1 have been reported, little is known about the other closely related kinase ULK2 (Unc-51-like autophagy activating kinase 2). Here, we present the crystal structure of ULK2 in complex with ATP competitive inhibitors. Surprisingly, the ULK2 structure revealed a dimeric assembly reminisc...
Source: Biochemical Journal - March 11, 2019 Category: Biochemistry Authors: Chaikuad, A., Koschade, S. E., Stolz, A., Zivkovic, K., Pohl, C., Shaid, S., Ren, H., Lambert, L. J., Cosford, N. D. P., Brandts, C. H., Knapp, S. Tags: Research Articles Source Type: research
Cysteine-rich granulin-3 rapidly promotes amyloid-{beta} fibrils in both redox states
Granulins (GRNs 1–7) are cysteine-rich proteolytic products of progranulin (PGRN) that have recently been implicated in neurodegenerative diseases including frontotemporal dementia (FTD) and Alzheimer's disease (AD). Their precise mechanism in these pathologies remains uncertain, but both inflammatory and lysosomal roles have been observed for GRNs. Among the seven GRNs, GRN-3 is well characterized and is implicated within the context of FTD. However, the relationship between GRN-3 and amyloid-β (Aβ), a protein relevant in AD pathology, has not yet been explored. To gain insight into this mechanism, we inve...
Source: Biochemical Journal - March 11, 2019 Category: Biochemistry Authors: Bhopatkar, A. A., Ghag, G., Wolf, L. M., Dean, D. N., Moss, M. A., Rangachari, V. Tags: Research Articles Source Type: research
Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds
We present a list of candidate hydrolases active during seed germination and propose that these protease activities can be used in combination with VPEs to develop novel markers of seed quality. (Source: Biochemical Journal)
Source: Biochemical Journal - March 11, 2019 Category: Biochemistry Authors: Vinegra de la Torre, N., Kaschani, F., Kaiser, M., van der Hoorn, R. A. L., Soppe, W. J. J., Misas Villamil, J. C. Tags: Research Articles Source Type: research
Culture in 10% O2 enhances the production of active hormones in neuro-endocrine cells by up-regulating the expression of processing enzymes
To closely mimic physiological conditions, low oxygen cultures have been employed in stem cell and cancer research. Although in vivo oxygen concentrations in tissues are often much lower than ambient 21% O2 (ranging from 3.6 to 12.8% O2), most cell cultures are maintained at 21% O2. To clarify the effects of the O2 culture concentration on the regulated secretion of peptide hormones in neuro-endocrine cells, we examined the changes in the storage and release of peptide hormones in neuro-endocrine cell lines and endocrine tissues cultured in a relatively lower O2 concentration. In both AtT-20 cells derived from the mouse an...
Source: Biochemical Journal - March 11, 2019 Category: Biochemistry Authors: Sato, E., Maeda, Y., Sato, Y., Hinata, A., Gomi, H., Koga, D., Torii, S., Watanabe, T., Hosaka, M. Tags: Research Articles Source Type: research
