Identification of the rapamycin-sensitive phosphorylation sites within the Ser/Thr-rich domain of the yeast Npr1 protein kinase

The Saccharomyces cerevisae nitrogen permease reactivator Npr1 is a hyperphosphorylated protein that belongs to a fungus-specific family of Ser/Thr protein kinases dedicated to the regulation of plasma membrane transporters. Its activity is regulated by the TOR (target of rapamycin) signalling pathway. Inhibition of the TOR proteins by treating yeast cells with the immunosuppressant drug rapamycin promotes rapid dephosphorylation of Npr1. To identify the rapamycin-sensitive phosphorylation sites in yeast Npr1, glutathione-S-transferase (GST)-tagged Npr1 was isolated from untreated or rapamycin-treated cells, and analyzed by mass spectrometry. Here, we report for the first time 22 phosphorylation sites that are clustered in two regions of the N-terminal serine-rich domain. All phosphorylation sites, except two, were found to be rapamycin-sensitive. Some phosphorylation sites are contained in motifs that closely resemble those in mammalian S6K (serines followed by a tyrosine or a phenylalanine) and 4E-BP1 (serines followed by a proline). Other sites, such as serines followed by Ala, Asn, Gln, His, Ile, Leu, or Val, appear to define new motifs. Thus, TOR controls an unusually broad array of phosphorylation sites in Npr1. In addition to phosphorylation by upstream kinases, Npr1 undergoes autophosphorylation that was mapped to three distinct serines in the N-terminal domain of which Ser257 appears to be the main autophosphorylation site. Site-directed mutagenesis confirmed the mass spectral assignments of the autophosphorylation sites and shows that Ser257 is specifically involved in forming an in vitro substrate-binding site.     

The octarepeat domain of the prion protein binds Cu(II) with three distinct coordination modes at pH 7.4

The prion protein (PrP) binds Cu2+ in its N-terminal octarepeat domain. This unusual domain is comprised of four or more tandem repeats of the fundamental sequence PHGGGWGQ. Previous work from our laboratories demonstrates that at full copper occupancy, each HGGGW segment binds a single Cu2+. However, several recent studies suggest that low copper occupancy favors different coordination modes, possibly involving imidazoles from histidines in adjacent octapeptide segments. This is investigated here using a combination of X-band EPR, S-band EPR, and ESEEM, along with a library of modified peptides designed to favor different coordination interactions. At pH 7.4, three distinct coordination modes are identified. Each mode is fully characterized to reveal a series of copper-dependent octarepeat domain structures. Multiple His coordination is clearly identified at low copper stoichiometry. In addition, EPR detected copper-copper interactions at full occupancy suggest that the octarepeat domain partially collapses, perhaps stabilizing this specific binding mode and facilitating cooperative copper uptake. This work provides the first complete characterization of all dominant copper coordination modes at pH 7.4.     

Ground- and excited-state properties of Zn(II) tetrakis(4-tetramethylpyridyl) pophyrin specifically encapsulated within a Zn(II) HKUST metal-organic framework

We have examined the photophysical properties of Zn(II) tetramethylpyridyl porphyrin (ZnT4MPyP) specifically encapsulated within the cubioctahedral cavities of a ZnHKUST metal- organic framework. The encapsulated ZnT4MPyP exhibits a Soret maxima at ～458 nm that is bathochromically shifted relative to ZnT4PyP in ethanol solution (Soret maxima centered at 440 nm). The corresponding emission spectra of the encapsulated porphyrin exhibit resolvable bands centered at 636 and 677 nm relative to a single broad emission band of the ZnT4MPyP in ethanol solution centered at 636 nm with a shoulder situated near ～660 nm. The fluorescence lifetime of the encapsulated porphyrin is also perturbed relative to that of the free porphyrin in solution (1.88 ns for the encapsulated porphyrin relative to 1.2 ns in solution). These results are consistent with the ZnT4MPyP being in a more constrained environment in which the peripheral pyridyl groups have restricted rotational motion. The ZnT4MPyP triplet lifetime is also affected by encapsulation, giving rise to a longer lifetime (τ ≈ 3.3 ms) relative to that for the free porphyrin in solution (τ ≈ 1 ms). The triplet-state results indicate that nonplanar vibrational modes of the porphyrin leading to intersystem crossing are retained by encapsulation of the porphyrin but that either the density of vibrational states or the specific nonplanar modes coupling the singlet and triplet states may be perturbed, resulting in the longer observed lifetime.     

C-reactive protein (CRP) aptamer binds to monomeric but not pentameric form of CRP

Native C-reactive protein (CRP) is composed of five identical subunits arranged in a pentameric structure (pCRP). Binding of pCRP to damaged cell membranes produces a second isoform, modified CRP, which has similar antigenicity to isolated monomeric subunits of CRP (mCRP). Emerging evidence indicates that modified CRP plays a role in inflammation and atherosclerosis, however, there are very few techniques that can distinguish the different isoforms of CRP. Here we show that an RNA aptamer binds specifically to mCRP and not to pCRP. Using this aptamer, we describe a simple, fast, and sensitive assay to detect nanomolar concentrations of mCRP using fluorescence anisotropy. In addition, we show that this aptamer can be used to detect mCRP in polyacrylamide gels and bound to a surface using total internal reflection fluorescence microscopy. The biological activity of the mCRP we prepared by heating pCRP with 0.1% sodium dodecyl sulfate was confirmed by observing binding to the complement protein, C1q. This probe provides an important tool for CRP research and has the potential to improve clinical diagnostics that predict risk for cardiovascular disease.     

Protein phosphatase 2a (PP2A) binds within the oligomerization domain of striatin and regulates the phosphorylation and activation of the mammalian Ste20-Like kinase Mst3

Background

The repertoire of the antigen-binding receptors originates from the rearrangement of immunoglobulin and T-cell receptor genetic loci in a process known as V(D)J recombination. The initial site-specific DNA cleavage steps of this process are catalyzed by the lymphoid specific proteins RAG1 and RAG2. The majority of studies on RAG1 and RAG2 have focused on the minimal, core regions required for catalytic activity. Though not absolutely required, non-core regions of RAG1 and RAG2 have been shown to influence the efficiency and fidelity of the recombination reaction.

Results

Using a partial proteolysis approach in combination with bioinformatics analyses, we identified the domain boundaries of a structural domain that is present in the 380-residue N-terminal non-core region of RAG1. We term this domain the Central Non-core Domain (CND; residues 87-217).

Conclusions

We show how the CND alone, and in combination with other regions of non-core RAG1, functions in nuclear localization, zinc coordination, and interactions with nucleic acid. Together, these results demonstrate the multiple roles that the non-core region can play in the function of the full length protein.     

Interface-specific chi(4) coherent Raman spectroscopy in the frequency domain

We demonstrate interface-specific fourth-order (chi(4)) coherent Raman spectroscopy in the frequency domain for the first time. Because the chi(4) Raman spectroscopy uses only visible (vis) or near-IR light, it is expected to be a potential alternative to the widely utilized IR-vis sum frequency generation spectroscopy that cannot be applied to interfaces buried in thick IR absorbers such as water. We present the vibrational absolute value(chi(4))2 spectrum of rhodamine 800 at the air/water interface in a wide spectral range 100-3600 cm(-1). Comparison of the absolute value(chi(4))2 spectrum with the absolute value(chi(3))2 spectrum leads us to conclude that the present chi(4) spectroscopy successfully probes the interface distinguished clearly from the bulk.     

Competition between the albumin and three histidine fragment of amyloid precursor protein sites to bind Cu(II)

The aim of this work was to check experimentally the relationship between the five-nitrogen donor system {3 × N_imid, 2 × N⁻} seen e.g. in the peptide fragments of the cysteine-rich amyloid precursor protein (APP) region and the albumin-like {NH₂, 2 × N⁻, N_imid} coordination site. The protected and unprotected octadecapeptides DAHQERMDVSETHLHWHT and Ac-DAHQERMDVSETHLHWHT-NH₂ were synthesized and potentiometric and spectroscopic studies were performed. A comparison of both metal-binding sites that occur in both peptides clearly shows that in the unprotected ligand albumin-like binding is much more efficient than the three His site, although around pH 5 both sites have a comparable ability to bind the Cu(II) ion. However, a comparison of the protected and unprotected peptides with their metal binding sites clearly shows that the three His site is very efficient in binding Cu(II) although less effective than the albumin-like motif.     

Data self-recalibration and mixture mass fingerprint searching (DASER-MMF) to enhance protein identification within complex mixtures

A novel algorithm based on Data Self-Recalibration and a subsequent Mixture Mass Fingerprint search (DASER-MMF) has been developed to improve the performance of protein identification from online 1D and 2D-LC-MS/MS experiments conducted on high-resolution mass spectrometers. Recalibration of 40% to 75% of the MS spectra in a human serum dataset is demonstrated with average errors of 0.3±0.3 ppm, regardless of the original calibration quality. With simple protein mixtures, the MMF search identifies new proteins not found in the MS/MS based search and increases the sequence coverage for identified proteins by six times. The high mass accuracy allows proteins to be identified with as little as three peptide mass hits. When applied to very complex samples, the MMF search shows less dramatic performance improvements. However, refinements such as additional discriminating factors utilized within the search space provide significant gains in protein identification ability and indicate that further enhancements are possible in this realm.     

Adsorption energies, inter-adsorbate interactions, and the two binding sites within monolayer benzene on Ag(111)

The adsorption of monolayer and multilayer benzene on the Ag(111) surface was characterized using temperature programmed desorption (TPD). TPD spectra revealed two broad peaks at approximately 205 and approximately 150 K at submonolayer coverage and a sharper, multilayer peak at 140 K. Analysis of the coverage-dependent shape and shift of the two submonolayer peaks has resulted in their assignment to desorption from two different binding geometries on threefold-hollow sites with symmetries C(3v)(sigma d) and C(3v)(sigma v). The TPD peak analysis incorporated inter-adsorbate repulsive interaction that resulted from the local dipole moment at the adsorption site induced by the adsorbate-surface charge transfer bonding. The analysis has yielded desorption energies of 54.9 +/- 0.8 and 50.4 +/- 0.4 kJ/mol for the C(3v)(sigma d) and C(3v)(sigma v) configurations, respectively. The interface dipole and polarizability of the benzene-silver complex have been determined to be 5.4 +/- 1.8 D and 14 +/- 10 A3, respectively. Repulsive interactions in the monolayer were found to lower the desorption energy from the zero-coverage value by 14.8 kJ/mol. Leading edge analysis of the multilayer peak yielded a desorption energy of 40.9 +/- 0.7 kJ/mol.     

Kinesin superfamily protein member 4 (KIF4) is localized to midzone and midbody in dividing cells

In association with microtubules, a variety of kinesins play important roles in cellular functions such as intracellular transport of organelles or vesicles, signal transduction, and cell division. In a previous study we revealed that human kinesin superfamily protein member 4 (KIF4) is a chromokinesin that binds to chromosomes. Since localization of several kinds of kinesin at midzone called central spindle, or midbody that connects two daughter cells, or both, suggests their implication in cell division, we investigated KIF4 localization of during mitosis and cytokinesis in Hela cells. In addition to association with segregating chromosomes through entire mitosis, it also localized to the midzone and to midbody at ana/telophase through cytokinesis. Especially in cells at cytokinesis, KIF4 appeared as a doublet facing each other at the apical ends of two daughter cells. Three- dimensional analysis of architectural relationship between microtubule bundles and KIF4 indicated that KIF4 forms a ring structure wrapping around the microtubule bundles. These results suggest that KIF4 is involved in cytokinesis, although direct evidence was not provided in this study.     

One octarepeate expansion to the human prion protein alters both the Zn2+ and Cu2+ coordination environments within the octarepeate domain

The influence of a single octarepeat expansion on the Cu(II) and Zn(II) coordination environments within the octarepeat domain of the human prion protein is examined. Using X-ray absorption spectroscopy and diethyl pyrocarbonate labeling studies, we find that at low copper concentrations the "normal" octarepeat domain (four PHGGGWGQ repeats) coordinates Zn(II) in an (N/O)(6) coordination environment with two histidine residues and Cu(II) in a redox-inactive (N/O)(4) coordination environment using one imidazole residue. Expansion of the octarepeat region by one repeat (five PHGGGWGQ repeats) yields a three-histidine (N/O)(6) coordination environment for Zn(II) and a two-histidine (N/O)(4) coordination environment for Cu(II) at low copper concentrations. This Cu(II)[(N/O)(2)-histidine(2)] coordination motif is redox-active and capable of generating H(2)O(2) under reducing aerobic conditions.     

Molecular and vibrational structure of the extracellular bacterial signal compound N-butyryl-homoserine lactone (C4-HSL)

The molecular and vibrational structure of the title compound (C4-HSL) was studied by experimental and theoretical methods. The infrared (IR) absorption spectrum was measured in the solid state and in CCl₄ suspension. The observed absorption bands were compared with transitions obtained with B3LYP/cc-pVTZ density functional theory (DFT) calculations. Two stable molecular conformations were predicted, corresponding to an endo- and an exo-conformer with similar energies. Intermolecular amide–amide hydrogen bonding in the crystal state was approximated by a simple cluster model, leading to excellent agreement with the observed solid state IR spectrum. Due to the low solubility of C4-HSL in common solvents for IR spectroscopy, such as CS₂ and CCl₄, a liquid solution spectrum of pure, monomeric C4-HSL was not obtained. However, absorbance peaks observed in oversaturated CCl₄ solution could be assigned to distinct contributions from suspended micro-crystalline aggregates and dissolved monomeric species. The key vibrational bands of the monomeric form of C4-HSL are reported here for the first time: 3425 cm^?1 [ν(N–H)], 1784 cm^?1 [ν(CO), lactone], 1688 cm^?1 [amide I], and 1494 cm^?1 [amide II] (CCl₄).