Multiphasic effect of vinyl pyrrolidone polymers on amyloidogenesis, from macromolecular crowding to inhibition
Deposition of misfolded amyloid polypeptides, associated with cell death, is the hallmark of many degenerative diseases (e.g. type II diabetes mellitus and Alzheimer's disease). In vivo, cellular and extracellular spaces are occupied by a high volume fraction of macromolecules. The resulting macromolecular crowding energetically affects reactions. Amyloidogenesis can either be promoted by macromolecular crowding through the excluded volume effect or inhibited due to a viscosity increase reducing kinetics. Macromolecular crowding can be mimicked in vitro by the addition of non-specific polymers, e.g. Ficoll, dextran and pol...
Source: Biochemical Journal - November 9, 2018 Category: Biochemistry Authors: Berwick, R., Vaux, D. J., Jean, L. Tags: Research Articles Source Type: research
Structural and functional characterization of the transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv
Rv3488 of Mycobacterium tuberculosis H37Rv has been assigned to the phenolic acid decarboxylase repressor (PadR) family of transcriptional regulators that play key roles in multidrug resistance and virulence of prokaryotes. The binding of cadmium, zinc, and several other metals to Rv3488 was discovered and characterized by isothermal titration calorimetery to be an exothermic process. Crystal structures of apo-Rv3488 and Rv3488 in complex with cadmium or zinc ions were determined by X-ray crystallography. The structure of Rv3488 revealed a dimeric protein with N-terminal winged-helix-turn-helix DNA-binding domains composed...
Source: Biochemical Journal - November 9, 2018 Category: Biochemistry Authors: Kumari, M., Pal, R. K., Mishra, A. K., Tripathi, S., Biswal, B. K., Srivastava, K. K., Arora, A. Tags: Research Articles Source Type: research
Structure-function studies of the asparaginyl-tRNA synthetase from Fasciola gigantica: understanding the role of catalytic and non-catalytic domains
The asparaginyl-tRNA synthetase (NRS) catalyzes the attachment of asparagine to its cognate tRNA during translation. NRS first catalyzes the binding of Asn and ATP to form the NRS-asparaginyl adenylate complex, followed by the esterification of Asn to its tRNA. We investigated the role of constituent domains in regulating the structure and activity of Fasciola gigantica NRS (FgNRS). We cloned the full-length FgNRS, along with its various truncated forms, expressed, and purified the corresponding proteins. Size exclusion chromatography indicated a role of the anticodon-binding domain (ABD) of FgNRS in protein dimerization. ...
Source: Biochemical Journal - November 9, 2018 Category: Biochemistry Authors: Rajendran, V., Shukla, R., Shukla, H., Tripathi, T. Tags: Research Articles Source Type: research
A structural perspective of plant antimicrobial peptides
Among the numerous strategies plants have developed to fend off enemy attack, antimicrobial peptides (AMPs) stand out as one of the most prominent defensive barriers that grant direct and durable resistance against a wide range of pests and pathogens. These small proteins are characterized by a compact structure and an overall positive charge. AMPs have an ancient origin and widespread occurrence in the plant kingdom but show an unusually high degree of variation in their amino acid sequences. Interestingly, there is a strikingly conserved topology among the plant AMP families, suggesting that the defensive properties of t...
Source: Biochemical Journal - November 9, 2018 Category: Biochemistry Authors: Campos, M. L., Liao, L. M., Alves, E. S. F., Migliolo, L., Dias, S. C., Franco, O. L. Tags: Review Articles Source Type: research
G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants
We describe early and modern observations on G protein subunit phosphorylation and its functional consequences in these three classes of organisms, and suggest future research directions. (Source: Biochemical Journal)
Source: Biochemical Journal - November 9, 2018 Category: Biochemistry Authors: Chakravorty, D., Assmann, S. M. Tags: Review Articles Source Type: research
Variants with increased negative electrostatic potential in the Cx50 gap junction pore increased unitary channel conductance and magnesium modulation
Gap junction (GJ) channels are oligomers of connexins forming channels linking neighboring cells. GJs formed by different connexins show distinct unitary channel conductance (j), transjunctional voltage-dependent gating (Vj-gating) properties, and modulation by intracellular magnesium ([Mg2+]i). The underlying molecular determinants are not fully clear. Previous experimental evidence indicates that residues in the amino terminal (NT) and initial segment of the first extracellular (E1) domain influence the j, Vj-gating, and/or [Mg2+]i modulation in several GJs. Increasing negatively charged residues in Cx50 (connexin50) E1 ...
Source: Biochemical Journal - November 6, 2018 Category: Biochemistry Authors: Tejada, M. G., Sudhakar, S., Kim, N. K., Aoyama, H., Shilton, B. H., Bai, D. Tags: Research Articles Source Type: research
Interaction with complement proteins and dendritic cells implicates LCCL domain-containing proteins (CCps) of malaria parasites in immunomodulation
The evasion of host immune defense is critical for pathogens to invade, establish infection and perpetuate in the host. The complement system is one of the first lines of innate immune defense in humans that destroys pathogens in the blood circulation. Activation of the complement system through direct encounter with pathogens or some other agents leads to osmolysis of pathogens, clearance of soluble immune complexes and recruitment of lymphocytes at the site of activation. Although malaria parasites are not exposed to the complement system owing to their intracellular development for most part of their life cycle in the h...
Source: Biochemical Journal - November 6, 2018 Category: Biochemistry Authors: Sijwali, P. S. Tags: Commentaries Source Type: research
Role of cysteine 416 in N-ethylmaleimide sensitivity of human equilibrative nucleoside transporter 1 (hENT1)
Human equilibrative nucleoside transporter 1 (hENT1), the first identified member of the ENT family of integral membrane proteins, is the primary mechanism for cellular uptake of physiologic nucleosides and many antineoplastic and antiviral nucleoside drugs. hENT1, which is potently inhibited by nitrobenzylthioinosine (NBMPR), possesses 11 transmembrane helical domains with an intracellular N-terminus and an extracellular C-terminus. As a protein with 10 endogenous cysteine residues, it is sensitive to inhibition by the membrane permeable sulfhydryl-reactive reagent N-ethylmaleimide (NEM) but is unaffected by the membrane ...
Source: Biochemical Journal - October 31, 2018 Category: Biochemistry Authors: Yao, S. Y. M., Ng, A. M. L., Cass, C. E., Young, J. D. Tags: Research Articles Source Type: research
Redox regulation of pyruvate kinase M2 by cysteine oxidation and S-nitrosation
We show here that the M2 isoform of human pyruvate kinase (M2PYK) is susceptible to nitrosation and oxidation, and that these modifications regulate enzyme activity by preventing the formation of the active tetrameric form. The biotin-switch assay carried out on M1 and M2 isoforms showed that M2PYK is sensitive to nitrosation and that Cys326 is highly susceptible to redox modification. Structural and enzymatic studies have been carried out on point mutants for three cysteine residues (Cys424, Cys358, and Cys326) to characterise their potential roles in redox regulation. Nine cysteines are conserved between M2PYK and M1PYK....
Source: Biochemical Journal - October 31, 2018 Category: Biochemistry Authors: Mitchell, A. R., Yuan, M., Morgan, H. P., McNae, I. W., Blackburn, E. A., Le Bihan, T., Homem, R. A., Yu, M., Loake, G. J., Michels, P. A., Wear, M. A., Walkinshaw, M. D. Tags: Research Articles Source Type: research
Role of ATP during the initiation of microvascularization: acceleration of an autocrine sensing mechanism facilitating chemotaxis by inorganic polyphosphate
The in vitro tube formation assay with human umbilical vein endothelial cells (HUVEC) was applied to identify the extra- and intracellular sources of metabolic energy/ATP required for cell migration during the initial stage of microvascularization. Extracellularly, the physiological energy-rich polymer, inorganic polyphosphate (polyP), applied as biomimetic amorphous calcium polyP microparticles (Ca-polyP-MP), is functioning as a substrate for ATP generation most likely via the combined action of the alkaline phosphatase (ALP) and the adenylate kinase (AK). The linear Ca-polyP-MP with a size of 40 phosphate units, close to...
Source: Biochemical Journal - October 31, 2018 Category: Biochemistry Authors: Müller, W. E. G., Ackermann, M., Tolba, E., Neufurth, M., Ivetac, I., Kokkinopoulou, M., Schröder, H. C., Wang, X. Tags: Research Articles Source Type: research
Interaction of mammalian and plant H+/sucrose transporters with 14-3-3 proteins
The solute carrier 45 family (SLC45) was defined in the course of the Human Genome Project and consists of four members, A1–A4, which show only 20–30% identity of amino acid sequences among each other. All these members exhibit an identity of ~20% to plant H+/sucrose cotransporters. Recently, we expressed members of the murine SLC45 family in yeast cells and demonstrated that they are, like their plant counterparts, H+/sucrose cotransporters. In contrast with the plant proteins, SLC45 transporters recognise also the monosaccharides glucose and fructose as physiological substrates and seem to be involved in alte...
Source: Biochemical Journal - October 22, 2018 Category: Biochemistry Authors: Vitavska, O., Bartölke, R., Tabke, K., Heinisch, J. J., Wieczorek, H. Tags: Research Articles Source Type: research
Inhibitor potency varies widely among tumor-relevant human isocitrate dehydrogenase 1 mutants
Mutations in isocitrate dehydrogenase 1 (IDH1) drive most low-grade gliomas and secondary glioblastomas and many chondrosarcomas and acute myeloid leukemia cases. Most tumor-relevant IDH1 mutations are deficient in the normal oxidization of isocitrate to α-ketoglutarate (αKG), but gain the neomorphic activity of reducing αKG to D-2-hydroxyglutarate (D2HG), which drives tumorigenesis. We found previously that IDH1 mutants exhibit one of two reactivities: deficient αKG and moderate D2HG production (including commonly observed R132H and R132C) or moderate αKG and high D2HG production (R132Q). Her...
Source: Biochemical Journal - October 22, 2018 Category: Biochemistry Authors: Avellaneda Matteo, D., Wells, G. A., Luna, L. A., Grunseth, A. J., Zagnitko, O., Scott, D. A., Hoang, A., Luthra, A., Swairjo, M. A., Schiffer, J. M., Sohl, C. D. Tags: Research Articles Source Type: research
N-terminal acetylation and methylation differentially affect the function of MYL9
Deciphering the histone code has illustrated that acetylation or methylation on the same residue can have analogous or opposing roles. However, little is known about the interplay between these post-translational modifications (PTMs) on the same nonhistone residues. We have recently discovered that N-terminal acetyltransferases (NATs) and N-terminal methyltransferases (NRMTs) can have overlapping substrates and identified myosin regulatory light chain 9 (MYL9) as the first confirmed protein to occur in either α-amino-methylated (Nα-methyl) or α-amino-acetylated (Nα-acetyl) states in vivo. Here we ai...
Source: Biochemical Journal - October 22, 2018 Category: Biochemistry Authors: Nevitt, C., Tooley, J. G., Schaner Tooley, C. E. Tags: Research Articles Source Type: research
Spontaneous cross-linking of proteins at aspartate and asparagine residues is mediated via a succinimide intermediate
The breakdown of long-lived proteins (LLPs) is associated with aging, as well as disease; however, our understanding of the molecular processes involved is still limited. Of particular relevance, cross-linked proteins are often reported in aged tissues but the mechanisms for their formation are poorly understood. In the present study, sites of protein cross-linking in human ocular lenses were characterized using proteomic techniques. In long-lived lens proteins, several sites of cross-linking were found to involve the addition of Lys to Asp or Asn residues. Using model peptides containing Asp or Asn, a mechanism was elucid...
Source: Biochemical Journal - October 22, 2018 Category: Biochemistry Authors: Friedrich, M. G., Wang, Z., Schey, K. L., Truscott, R. J. W. Tags: Research Articles Source Type: research
Structural biology of 11-cis-retinaldehyde production in the classical visual cycle
The vitamin A derivative 11-cis-retinaldehyde plays a pivotal role in vertebrate vision by serving as the chromophore of rod and cone visual pigments. In the initial step of vision, a photon is absorbed by this chromophore resulting in its isomerization to an all-trans state and consequent activation of the visual pigment and phototransduction cascade. Spent chromophore is released from the pigments through hydrolysis. Subsequent photon detection requires the delivery of regenerated 11-cis-retinaldehyde to the visual pigment. This trans–cis conversion is achieved through a process known as the visual cycle. In this r...
Source: Biochemical Journal - October 22, 2018 Category: Biochemistry Authors: Daruwalla, A., Choi, E. H., Palczewski, K., Kiser, P. D. Tags: Review Articles Source Type: research
