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Huntingtin interacting protein 14 (HIP14), a membrane-bound palmitoyl transferase, palmitoylates a number of neuronal proteins (including Huntingtin) and affects the trafficking, stability, aggregation, and/or functional activity of substrate proteins. HIP14 contains an N-terminal ankyrin repeat domain that may function in its substrate recognition. Sequence analysis suggests that the HIP14 ankyrin repeats share approximately 50% identity with the ankyrin repeats of G9a and G9a-like protein (GLP) histone lysine methyltransferases. The crystal structure of the HIP14 ankyrin repeats reveals a surface aromatic cage, formed by two tryptophans, one tyrosine, and one methionine. The all-hydrophobic cage resembles the tri-methylated lysine binding pocket of the plant homeodomain (PHD) of human BPTF (bromodomain and PHD domain transcription factor) 1. HIP14, a Huntingtin interacting protein 2, is a 633-residue protein, including 7-8 ankyrin repeats in the N-terminal region followed by five predicted transmembrane helices. The protein contains a signature DHHC palmitoyl transferases motif located close to the predicted fourth transmembrane helix 3. Importantly, the ankyrin repeats (a protein-protein interaction domain that may function in substrate recognition) and the DHHC sequence (the hypothetical active site) are both predicted to reside on the cytoplasmic face of the lipid bilayer 4, presumably allowing the substrate recognition and the active site to interact with the same substrate. Posttranslational palmitoylation involves the attachment of the saturated C16 fatty acid palmitate to specific cysteines via a thioester linkage 5-7. HIP14 palmitoylates Huntingtin at cysteine 214 8. Other substrates of HIP14-mediated palmitoylation include SNAP-25 (synaptosome associated protein 25 kDa), PSD-95 (postsynaptic density 95 kDa), GAD-65 (glutamate decarboxylase 65 kDa), and Synaptotagmin I 9. Ankyrin repeats are known to mediate protein-protein interactions 10. Recently we showed that the ankyrin repeat domains of G9a and GLP, two euchromatin associated histone lysine methyltranferases, bind N-terminal histone H3 peptides containing mono- or di-methylated lysine 9 (H3K9me1, me2) via a partial aromatic cage with three tryptophans and one acidic residue 11. Besides the ankyrin repeats of G9a and GLP, other protein domains including the Chromodomain 12, plant homeodomain 1,13-15, and Tudor domain 16, also recognize methylated lysines (Review 17). The common mode of methyl-lysine interactions is via a surface aromatic cage consisting of 2-4 aromatic residues. These aromatic cages are highly selective for methyllysine. In a study of Chromodomain-methyllysine interaction, binding was driven primarily by cation-π interactions (i.e, a methyllysine carries a positive charge), and secondarily by the packing of methyl group(s) against the aromatic ring(s) of the cage, with the hydrophobic effect contributing the least to binding 18. This eliminates the possibility of such cages generically binding hydrophobic residues, and suggests that other methyllysine binding ankyrin repeats could be identified by the presence of a surface aromatic cage.

Huntington and related neurological diseases result from expansion of a polyglutamine (polyQ) tract. The linear lattice model for the structure and binding properties of polyQ proposes that both expanded and normal polyQ tracts in the preaggregation state are random-coil structures but that an expanded polyQ repeat contains a larger number of epitopes recognized by antibodies or other proteins. The crystal structure of polyQ bound to MW1, an antibody against polyQ, reveals that polyQ adopts an extended, coil-like structure. Consistent with the linear lattice model, multimeric MW1 Fvs bind more tightly to longer than to shorter polyQ tracts and, compared with monomeric Fv, bind expanded polyQ repeats with higher apparent affinities. These results suggest a mechanism for the toxicity of expanded polyQ and a strategy to link anti-polyQ compounds to create high-avidity therapeutics.

The circadian input kinase (CikA) is a major element of the pathway that provides environmental information to the circadian clock of the cyanobacterium Synechococcus elongatus. CikA is a polypeptide of 754 residues and has three recognizable domains: GAF, histidine protein kinase, and receiver-like. This latter domain of CikA lacks the conserved phospho-accepting aspartyl residue of bona fide receiver domains and is thus a pseudo-receiver (PsR). Recently, it was shown that the PsR domain (1) attenuates the autokinase activity of CikA, (2) is necessary to localize CikA to the cell pole, and (3) is necessary for the destabilization of CikA in the presence of the quinone analog 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). The solution structure of the PsR domain of CikA, CikAPsR, is presented here. A model of the interaction between the PsR domain and HPK portion of CikA provides a potential explanation for how the PsR domain attenuates the autokinase activity of CikA. Finally, a likely quinone-binding surface on CikAPsR is shown here.

The screening results were reported based on the Fourier transform infrared spectroscopy (FTIR) analysis of the samples of exfoliated cervical cells from 354 women. Their spectra can be sorted into two types based on the emerging or not of the absorption bands near 970 cm−1 and 1 170 cm−1: T1 (83.1%) type without emerging, and T2 (16.9%) type with obviously emerging. All of the samples assigned to T1 were cytologically diagnosed as normal or within normal limits (Pap I). 28.9% and 71.1% of samples exhibiting T2 profile, were cytologically evaluated as Pap I and abnormal respectively. 3 women in the abnormal group were diagnosed as to have cervical cells with changes associated with high grade of inflammation, cervical scar and cervical erosion. Furthermore, based on the progressive change of the relative intensities of the absorption bands, both T1 and T2 profiles can be categorized into 6 subtypes. The observed heterogeneous spectra and the progressive changes in the absorption frequencies and the relative intensities exhibit features suggestive of the progressive process of cervical lesion. The FTIR method has the potential to complement the cytological smear for large-volume screening of cervical lesions.

Fourier transform infrared spectra of U937 cells treated with chlorogenic acid (CGA) and caffeic acid (CA) for 1, 6, 12 and 24 h were recorded and analyzed. Some considerable changes in the ratio of the absorbance of the bands at 2960 and 2855 cm −1 ( D 2960 / D 2855 ) and the ratio of the integrated areas of the absorption at 1540 and 1086 cm −1 ( A 1540 / A 1086 ) of the spectra of the tumor cells were observed for different times of incubation and drug concentrations. The cells treated for 6 h have the highest D 2960 / D 2855 and lowest A 1540 / A 1086 ratios. CGA has stronger interaction with U937 than that with CA. These two phenolic acids could interact with both proteins and nucleic acids of tumor cells. And these changes in the spectra of cells could be explained as the degeneration of the protein and nucleic acids in cells.

The compositions of the secondary structures of protein in the human breast normal, hyperplasia, fibroadenoma and invasive ductal carcinoma tissues have been estimated from the Fourier self deconvolved spectra, the second derivative spectra and the curve-fitting analysis of the amide I bands in their spectra. Some parameters of the secondary structures of proteins in these 4 types of tissues are significantly different and located in separate ranges. Fibroadenoma tissue demonstrates the most remarkable difference in the compositions of α-helical and atypical helical structures. The carcinoma tissue has the highest ratio of the intermolecular β-sheet content and the intramolecular β-sheet content. This noticeable difference in the secondary structure may have important implications for analyzing the properties and types of human breast disease.

Some remarkable FTIR spectral differences are observed and the differences at the molecular level are extracted between benign and malignant breast tissue samples. For the malignant tissue, the relative content of nucleic acids is increased whereas the collagen is decreased . The proteins are phosphorylated and become more flexible and disordered. And these significant differences have important implications not only for probing the process of the breast lesion at the molecular level, but also for evaluating the histological types and grades of breast diseases.

The circadian rhythms exhibited in the cyanobacterium Synechococcus elongatus are generated by an oscillator comprised of the proteins KaiA, KaiB, and KaiC. An external signal that commonly affects the circadian clock is light. Previously, we reported that the bacteriophytochrome-like protein CikA passes environmental signals to the oscillator by directly binding a quinone and using cellular redox state as a measure of light in this photosynthetic organism. Here, we report that KaiA also binds the quinone analog 2,5-dibromo-3-methyl-6-isopropyl- p -benzoquinone (DBMIB), and the oxidized form of DBMIB, but not its reduced form, decreases the stability of KaiA in vivo, causes multimerization in vitro, and blocks KaiA stimulation of KaiC phosphorylation, which is central to circadian oscillation. Our data suggest that KaiA directly senses environmental signals as changes in redox state and modulates the circadian clock.

Circadian rhythms are endogenous cellular programs that time metabolic and behavioral events to occur at optimal times in the daily cycle. Light and dark cycles synchronize the endogenous clock with the external environment through a process called entrainment. Previously, we identified the bacteriophytochrome-like circadian input kinase CikA as a key factor for entraining the clock in the cyanobacterium Synechococcus elongatus PCC 7942. Here, we present evidence that CikA senses not light but rather the redox state of the plastoquinone pool, which, in photosynthetic organisms, varies as a function of the light environment. Furthermore, CikA associates with the Kai proteins of the circadian oscillator, and it influences the phosphorylation state of KaiC during resetting of circadian phase by a dark pulse. The abundance of CikA varies inversely with light intensity, and its stability decreases in the presence of the quinone analog 2,5-dibromo-3-methyl-6-isopropyl- p -benzoquinone (DBMIB). The pseudo-receiver domain of CikA is crucial for sensitivity to DBMIB, and it binds the quinone directly, a demonstration of a previously unrecognized ligand-binding role for the receiver fold. Our results suggest that resetting the clock in S. elongatus is metabolism-dependent and that it is accomplished through the interaction of the circadian oscillator with CikA.

Considerable compositional differences of water, nucleic acids and proteins were observed between benign and malignant breast tissues based on the curve-fitting analysis of the infrared absorption band in the frequency region 3100–3600 cm–1. Compared to normal tissue, the tendency of an increase in the proportions of strongly H-bonded water (ASBW) with biomolecules and a decrease in that of weakly H-bonded water (AWBW) was observed in abnormal tissues. Subsequently, ASBW/AWBW ratios dramatically increased. The proportions of nucleic acid–NH2 groups (ANA) and the proportions of protein N–H groups (APR) in abnormal tissues increased from those of normal tissue. The ratios ANA/APR in fibroadenoma and carcinoma tissues are higher than those in normal and hyperplasia tissues whose ANA/APR ratios are located in the same region. The ANA and ANA/APR in carcinoma tissue are the highest. These differences may be related to the cell proliferation in abnormal tissues and the unregulated growth and dedifferentiation of carcinoma cells.