Human mitochondrial branched chain aminotransferase: structural basis for substrate specificity and role of redox active cysteines

Crystal structures of the fold type IV pyridoxal phosphate (PLP)-dependent human mitochondrial branched chain aminotransferase (hBCATm) reaction intermediates have provided a structural explanation for the kinetically determined substrate specificity of hBCATm. The isoleucine side chain in the ketimine intermediate occupies a hydrophobic binding pocket that can be defined by three surfaces. Modeling of amino acids on the ketimine structure shows that the side chains of nonsubstrate amino acids such as the aromatic amino acids, alanine, or aspartate either are unable to interact through van der Waals' interactions or have steric clashes. The structural and biochemical basis for the sensitivity of the mammalian BCAT to reducing agents has also been elucidated. Two cysteine residues in hBCATm, Cys315 and Cys318 (CXXC), are part of a redox-controlled mechanism that can regulate hBCATm activity. The residues surrounding Cys315 and Cys318 show considerable sequence conservation in the prokaryotic and eukaryotic BCAT sequences, however, the CXXC motif is found only in the mammalian proteins. The results suggest that the BCAT enzymes may join the list of enzymes that can be regulated by redox status.     

A Bacteriophage Capsid Protein Provides a General Amyloid Interaction Motif (GAIM) That Binds and Remodels Misfolded Protein Assemblies

Misfolded protein aggregates, characterized by a canonical amyloid fold, play a central role in the pathobiology of neurodegenerative diseases. Agents that bind and sequester neurotoxic intermediates of amyloid assembly, inhibit the assembly or promote the destabilization of such protein aggregates are in clinical testing. Here, we show that the gene 3 protein (g3p) of filamentous bacteriophage mediates potent generic binding to the amyloid fold. We have characterized the amyloid binding and conformational remodeling activities using an array of techniques, including X-ray fiber diffraction and NMR. The mechanism for g3p binding with amyloid appears to reflect its physiological role during infection of Escherichia coli, which is dependent on temperature-sensitive interdomain unfolding and cis–trans prolyl isomerization of g3p. In addition, a natural receptor for g3p, TolA-C, competitively interferes with Aβ binding to g3p. NMR studies show that g3p binding to Aβ fibers is predominantly through middle and C-terminal residues of the Aβ subunit, indicating β strand–g3p interactions. A recombinant bivalent g3p molecule, an immunoglobulin Fc (Ig) fusion of the two N-terminal g3p domains, (1) potently binds Aβ fibers (fAβ) (K_D = 9.4 nM); (2); blocks fAβ assembly (IC₅₀ ~ 50 nM) and (3) dissociates fAβ (EC₅₀ = 40–100 nM). The binding of g3p to misfolded protein assemblies is generic, and amyloid-targeted activities can be demonstrated using other misfolded protein systems. Taken together, our studies show that g3p(N1N2) acts as a general amyloid interaction motif.     

Human mitochondrial branched chain aminotransferase isozyme: structural role of the CXXC center in catalysis

Mammalian branched chain aminotransferases (BCATs) have a unique CXXC center. Kinetic and structural studies of three CXXC center mutants (C315A, C318A, and C315A/C318A) of human mitochondrial (hBCATm) isozyme and the oxidized hBCATm enzyme (hBCATm-Ox) have been used to elucidate the role of this center in hBCATm catalysis. X-ray crystallography revealed that the CXXC motif, through its network of hydrogen bonds, plays a crucial role in orienting the substrate optimally for catalysis. In all structures, there were changes in the structure of the beta-turn preceding the CXXC motif when compared with wild type protein. The N-terminal loop between residues 15 and 32 is flexible in the oxidized and mutant enzymes, the disorder greater in the oxidized protein. Disordering of the N-terminal loop disrupts the integrity of the side chain binding pocket, particularly for the branched chain side chain, less so for the dicarboxylate substrate side chain. The kinetic studies of the mutant and oxidized enzymes support the structural analysis. The kinetic results showed that the predominant effect of oxidation was on the second half-reaction rather than the first half-reaction. The oxidized enzyme was completely inactive, whereas the mutants showed limited activity. Model building of the second half-reaction substrate alpha-ketoisocaproate in the pyridoxamine 5'-phosphate-hBCATm structure suggests that disruption of the CXXC center results in altered substrate orientation and deprotonation of the amino group of pyridoxamine 5'-phosphate, which inhibits catalysis.     

Resource limitation and recruitment patterns in a coral reef fish assemblage

The potential effects of food and shelter availability on the recruitment and early survivorship of coral reef fishes were studied on St. Croix, U.S. Virgin Islands. The faunal assemblage studied included diurnally active fishes found in the “rubble/sand” habitat. The most abundant members were: beaugregory, Stegastes leucostictus (Muller & Troschel), goldspotted goby, Gnatholepis thompsoni Jordan, bridled goby, Coryphopterus glaucofraenum Gill, surgeonfishes, Acanthurus bahianus Castelnau and A. chirurgus (Bloch), and French grunt, Haemulon flavolineatum (Desmarest). Comparisons of recruitment to reefs constructed from substrata that varied in morphological characteristics showed that there were differences in the relative abundances of recruits attracted to and/or surviving on the different reef types. Juveniles of most species appeared to prefer the branching coral Porites porites (Pallas), which provided a large number of small crevices between the branches.Manipulations of the availability of shelter sites for fishes demonstrated that recruitment and/or early survivorship were strongly limited by the number of refuges. This result was found in six separate carried out during different years and in different seasons. Shelter site availability presumably limits fish populations through its effects on prédation rates.Experimental manipulations of food availability indicated that food does not directly influence settlement or early survivorship of coral reef fishes. However, it is probable that correlations between habitat characteristics and food availability have influenced the evolution of settling preferences.     

Both α2,3- and α2,6-Linked Sialic Acids on O-Linked Glycoproteins Act as Functional Receptors for Porcine Sapovirus

Sapovirus, a member of the Caliciviridae family, is an important cause of acute gastroenteritis in humans and pigs. Currently, the porcine sapovirus (PSaV) Cowden strain remains the only cultivable member of the Sapovirus genus. While some caliciviruses are known to utilize carbohydrate receptors for entry and infection, a functional receptor for sapovirus is unknown. To characterize the functional receptor of the Cowden strain of PSaV, we undertook a comprehensive series of protein-ligand biochemical assays in mock and PSaV-infected cell culture and/or piglet intestinal tissue sections. PSaV revealed neither hemagglutination activity with red blood cells from any species nor binding activity to synthetic histo-blood group antigens, indicating that PSaV does not use histo-blood group antigens as receptors. Attachment and infection of PSaV were markedly blocked by sialic acid and Vibrio cholerae neuraminidase (NA), suggesting a role for α2,3-linked, α2,6-linked or α2,8-linked sialic acid in virus attachment. However, viral attachment and infection were only partially inhibited by treatment of cells with sialidase S (SS) or Maackia amurensis lectin (MAL), both specific for α2,3-linked sialic acid, or Sambucus nigra lectin (SNL), specific for α2,6-linked sialic acid. These results indicated that PSaV recognizes both α2,3- and α2,6-linked sialic acids for viral attachment and infection. Treatment of cells with proteases or with benzyl 4-O-β-D-galactopyranosyl-β-D-glucopyranoside (benzylGalNAc), which inhibits O-linked glycosylation, also reduced virus binding and infection, whereas inhibition of glycolipd synthesis or N-linked glycosylation had no such effect on virus binding or infection. These data suggest PSaV binds to cellular receptors that consist of α2,3- and α2,6-linked sialic acids on glycoproteins attached via O-linked glycosylation.     

Epsins and Vps27p/Hrs contain ubiquitin-binding domains that function in receptor endocytosis

Ubiquitin functions as a signal for sorting cargo at multiple steps of the endocytic pathway and controls the activity of trans-acting components of the endocytic machinery (reviewed in refs 1, and 2). By contrast to proteasome degradation, which generally requires a polyubiquitin chain that is at least four subunits long, internalization and sorting of endocytic cargo at the late endosome are mediated by mono-ubiquitination. Here, we demonstrate that ubiquitin-interacting motifs (UIMs) found in epsins and Vps27p (ref. 9) from Saccharomyces cerevisiae are required for ubiquitin binding and protein transport. Epsin UIMs are important for the internalization of receptors into vesicles at the plasma membrane. Vps27p UIMs are necessary to sort biosynthetic and endocytic cargo into vesicles that bud into the lumen of a late endosomal compartment, the multivesicular body. We propose that mono-ubiquitin regulates internalization and endosomal sorting by interacting with modular ubiquitin-binding domains in core components of the protein transport machinery. UIM domains are found in a broad spectrum of proteins, consistent with the idea that mono-ubiquitin can function as a regulatory signal to control diverse biological activities.     

Repair of bleomycin-damaged DNA by human fibroblasts

The ability of human fibroblasts to repair bleomycin-damaged DNA was examined in vivo. Repair of the specific lesions caused by bleomycin (BLM) was investigated in normal cell strains as well as those isolated from patients with apparent DNA repair defects. The diseases ataxia telangiectasia (AT), Bloom syndrome (BS), Cockayne syndrome (CS), Fanconi anemia (FA), and xeroderma pigmentosum (XP) were those selected for study. The method used for studying the repair of DNA after BLM exposure was alkaline sucrose gradient centrifugation. After exposure to BLM, a fall in the molecular weight of DNA was observed, and after drug removal the DNA reformed rapidly to high molecular weight. The fall in molecular weight upon exposure to BLM was observed in all cells examined with the exception of some XP strains. Prelabeled cells from some XP complementation groups were found to have a higher percentage of low molecular weight DNA on alkaline gradients than did normal cells. This prelabeled low molecular weight DNA disappeared upon exposure to BLM.     

Automatic real-time calibration,assessment, and maintenance of generic Raman models for online monitoring of cell culture processes

Raman spectroscopy is a multipurpose analytical technology that has found great utility in real-time monitoring and control of critical performance parameters of cell culture processes. As a process analytical technology (PAT) tool, the performance of Raman spectroscopy relies on chemometric models that correlate Raman signals to the parameters of interest. The current calibration techniques yield highly specific models that are reliable only on the operating conditions they are calibrated in. Furthermore, once models are calibrated, it is typical for the model performance to degrade over time due to various recipe changes, raw material variability, and process drifts. Maintaining the performance of industrial Raman models is further complicated due to the lack of a systematic approach to assessing the performance of Raman models. In this article, we propose a real-time just-in-time learning (RT-JITL) framework for automatic calibration, assessment, and maintenance of industrial Raman models. Unlike traditional models, RT-JITL calibrates generic models that can be reliably deployed in cell culture experiments involving different modalities, cell lines, media compositions, and operating conditions. RT-JITL is a first fully integrated and fully autonomous platform offering a self-learning approach for calibrating and maintaining industrial Raman models. The efficacy of RT-JITL is demonstrated on experimental studies involving real-time predictions of various cell culture performance parameters, such as metabolite concentrations, viability, and viable cell density. RT-JITL framework introduces a paradigm shift in the way industrial Raman models are calibrated, assessed, and maintained, which to the best of authors' knowledge, have not been done before.     

Promoter-Like Mutant with Increased Expression of the Glycerol Kinase Operon of Escherichia coli

A glycerol-specific phenotypic revertant isolated from a mutant of Escherichia coli missing enzyme I of the phosphoenolpyruvate phosphotransferase system was studied. This revertant is capable of producing higher levels of glycerol kinase and the protein mediating the facilitated diffusion of glycerol (facilitator) than wild-type cells. The kinase of the revertant is indistinguishable from the wild-type enzyme with respect to its sensitivity to feedback inhibition by fructose-1,6-diphosphate, its pH optimum, and its turnover number. The synthesis of glycerol kinase in strains bearing the suppressor locus is resistant to catabolite repression. The suppressor mutation mapped at the known glpK locus. Thus, it is suggested that the mutation occurred in the promoter of the operon specifying the kinase and the facilitator.