Optical activity of polypeptides in the infrared. Predicted CD of the amide I and amide II bands.

The Miyazawa-Blout-Krimm (M-B-K) treatment of polypeptide absorption in the infrared is extended to the calculation of circular dichroism (CD), linear dichroism, and oriented CD for the amide I and amide II transitions. Matrix methods are applied to the α helix and β structures using measured values for the strengths and directions of the transition dipole moments and empirical values from M-B-K for the coupling constants. Relatively small aggregates, a 36-residue helix, and 8-chain × 4-residue β sheets, are large enough to show calculated absorption agreeing with M-B-K results, which are based on infinite lattices. In all cases the predicted CD is an approximately conservative couple. The strongest CD should appear in the α helix, Δε/ε ?± 10^?3 for both transitions. The amide II transition should show moderate CD couples in both β structures, Δε/ε ? (+2 to ?1) × 10^?4. The amide I transitions in β structures should show weak CD couples, Δε/ε = (+3 to ?2) × 10^?5, except that the negative branch in the antiparallel structure may be detectable (Δε/ε ? ?2 × 10^?4) because absorption is very low at its wavelength peak. CD on oriented samples should be enhanced over the unoriented cases, giving values as large as Δε/ε = 3 × 10^?3 because particular directions of observation allow the light to avoid much of the absorption in the sample. If all three structures are considered as helices, then the larger distance of the transition dipoles from the axis in the α helix, and the orientations of the transitions in the different structures, are the factors that, in terms of our previous theoretical work [Snir and Schellman (1973) J. Phys. Chem. 77 , 1653] satisfactorily explain the calculated results. Simple dipole–dipole interaction is calculated to make a substantial contribution to the coupling between groups.     

Aspirin prevention of NMDA-induced neuronal death by direct protein kinase Czeta inhibition

Abstract Aspirin has been shown to protect against glutamate neurotoxicity via the nuclear factor kappaB pathway. Some studies have implicated the atypical protein kinase C (PKC) zeta (zeta) isoform in cell protection, but the mechanism involved remains unclear. We show here that aspirin exerts at least some of its effects through PKCzeta, decreasing the NMDA-induced activation, cleavage and nuclear translocation of this molecule. Aspirin (acetylsalicylic acid) directly inhibited the protein kinase activity of PKCzeta, whereas salicylic acid did not. This direct effect of aspirin on purified human PKCzeta is consistent with PKCzeta inhibition preventing the NMDA-induced death of cortical neurones. Caspase-3 inhibition blocked the cleavage and nuclear translocation of PKCzeta, whereas caspase-1-inhibition did not. Thus, PKCzeta (protein kinase Mzeta) regulates nuclear events essential for the initiation of the apoptotic pathway. Aspirin protects cells against NMDA-induced apoptosis by means of a novel mechanism targeting PKCzeta, a key molecule in inflammatory responses and neurodegeneration.     

Modifications of protein kinase C activity and phosphorylation of lipocortin I in cultures of pig thyroid cells

When cultured in the absence of thyreostimulin (TSH), thyroid cells lose some of their differentiated functions such as iodide transport and its incorporation into thyroglobulin. In the presence of TSH (0.1 mU/ml), these differentiated functions are preserved ("TSH cells"). The addition of tetradecanoyl phorbol 13 acetate (TPA) inhibits some differentiated functions of the cells and provokes important modifications of bio-signalling pathways. The protein kinase C (pKC) activity, unchanged in "control" and "TSH cells", was dramatically modified in TPA treated cells. After translocation, the pKC activity was down-regulated and the phosphorylation of its endogenous substrates (35-38 kDa) disappeared. Among these substrates, we identified the lipocortin I (LC I) (35 kDa), a phospholipase A2 inhibitory protein related to the Ca2+ binding protein family. By monodimensional electrophoresis (PAGE-SDS) and western-blot, we evidenced the presence of LCI in cytosols and particulate extracts. By 2 dimensional electrophoresis (PAGE-SDS and IEF) and western-blot we identified a phosphorylated and unphosphorylated LCI protein. The phosphorylation of LCI by pKC decreased its isoelectric point from 6.9-6.6. The modifications of pKC activity and LCI phosphorylation and the changes in the bio-signalling pathways can partly account for the loss of differentiation observed in control or TPA treated cells.     

Ubiquitylation-dependent downregulation of Nck regulates its functional activity

The Nck adapter protein is involved in key cellular functions, such as actin polymerization and reorganization, serving as a molecular bridge between the surface complex essential for foreign antigen recognition, the T-cell antigen receptor (TCR), and the actin machinery. However, the mechanisms regulating Nck expression and functions are unknown. In this study, we revealed Nck negative regulation and demonstrated that Nck is ubiquitylated following cellular activation. We identified the molecular determinants and mediators involved in this process. Our data suggest that Nck ubiquitylation might serve as a mechanism controlling Nck-mediated effector functions during cellular activation.     

Structural relatedness via flow networks in protein sequence space

A novel approach for evaluation of sequence relatedness via a network over the sequence space is presented. This relatedness is quantified by graph theoretical techniques. The graph is perceived as a flow network, and flow algorithms are applied. The number of independent pathways between nodes in the network is shown to reflect structural similarity of corresponding protein fragments. These results provide an appropriate parameter for quantitative estimation of such relatedness, as well as reliability of the prediction. They also demonstrate a new potential for sequence analysis and comparison by means of the flow network in the sequence space.     

Structural and functional features of yeast V-ATPase subunit C

V-ATPase is a multi-subunit membrane protein complex, it translocates protons across biological membranes, generating electrical and pH gradients which are used for varieties of cellular processes. V-ATPase is composed of two distinct sub-complexes: a membrane bound V0 sub-complex, composed of 6 different subunits, which is responsible for proton transport and a soluble cytosolic facing V1 sub-complex, composed of 8 different subunits which hydrolyse ATP. The two sub-complexes are held together via a flexible stator. One of the main features of eukaryotic V-ATPase is its ability to reversibly dissociate to its sub-complexes in response to changing cellular conditions, which arrest both proton translocation and ATP hydrolysis, suggesting a regulation function. Subunit C (vma5p in yeast) was shown by several biochemical, genetic and recent structural data to function as a flexible stator holding the two sectors of the complex together and regulating the reversible association/dissociation of the complex, partly via association with F-actin filaments. Structural features of subunit C that allow smooth energy conversion and interaction with actin and nucleotides are discussed.     

Abnormal vasculature interferes with optic fissure closure in lmo2 mutant zebrafish embryos

Ocular coloboma is a potentially blinding congenital eye malformation caused by failure of optic fissure closure during early embryogenesis. The optic fissure is a ventral groove that forms during optic cup morphogenesis, and through which hyaloid artery and vein enter and leave the developing eye, respectively. After hyaloid artery and vein formation, the optic fissure closes around them. The mechanisms underlying optic fissure closure are poorly understood, and whether and how this process is influenced by hyaloid vessel development is unknown. Here we show that a loss-of-function mutation in lmo2, a gene specifically required for hematopoiesis and vascular development, results in failure of optic fissure closure in zebrafish. Analysis of ocular blood vessels in lmo2 mutants reveals that some vessels are severely dilated, including the hyaloid vein. Remarkably, reducing vessel size leads to rescue of optic fissure phenotype. Our results reveal a new mechanism leading to coloboma, whereby malformed blood vessels interfere with eye morphogenesis.