Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors

Metabotropic glutamate receptors (mGluRs) are G protein coupled receptors that play important roles in synaptic plasticity and other neuro-physiological and pathological processes. Allosteric mGluR ligands are particularly promising drug targets because of their modulatory effects--enhancing or suppressing the response of mGluRs to glutamate. The mechanism by which this modulation occurs is not known. Here, we propose the hypothesis that positive and negative modulators will differentially stabilize the active and inactive conformations of the receptors, respectively. To test this hypothesis, we have generated computational models of the transmembrane regions of different mGluR subtypes in two different conformations. The inactive conformation was modeled using the crystal structure of the inactive, dark state of rhodopsin as template and the active conformation was created based on a recent model of the light-activated state of rhodopsin. Ligands for which the nature of their allosteric effects on mGluRs is experimentally known were docked to the modeled mGluR structures using ArgusLab and Autodock softwares. We find that the allosteric ligand binding pockets of mGluRs are overlapping with the retinal binding pocket of rhodopsin, and that ligands have strong preferences for the active and inactive states depending on their modulatory nature. In 8 out of 14 cases (57%), the negative modulators bound the inactive conformations with significant preference using both docking programs, and 6 out of 9 cases (67%), the positive modulators bound the active conformations. Considering results by the individual programs only, even higher correlations were observed: 12/14 (86%) and 8/9 (89%) for ArgusLab and 10/14 (71%) and 7/9 (78%) for AutoDock. These findings strongly support the hypothesis that mGluR allosteric modulation occurs via stabilization of different conformations analogous to those identified in rhodopsin where they are induced by photochemical isomerization of the retinal ligand--despite the extensive differences in sequences between mGluRs and rhodopsin.     

Exploring the potential of 3'-O-carboxy esters of thymidine as inhibitors of ribonuclease A and angiogenin

In this study, compounds with a carboxy ester in lieu of the phosphate ester at the 3'-position have been employed to inhibit the ribonucleolytic activity of ribonuclease A (RNase A). Phosphates at the 3'-position of pyrimidine bases are well-known inhibitors of the protein. We have investigated the inhibition of RNase A by 3'-O-carboxy esters of thymidine. The compounds behave as competitive inhibitors with inhibition constants ranging from 42 to 95 microM. The mode of inhibition has also been confirmed by (1)H NMR studies of the active site histidines of RNase A. Docking studies have further substantiated the experimental results. The compounds are also found to inhibit the ribonucleolytic activity of angiogenin, a homologous protein and potent inducer of blood vessel formation.     

Huntingtin interacting protein HYPK is intrinsically unstructured

To characterize HYPK, originally identified as a novel huntingtin (Htt) interacting partner by yeast two hybrid assay, we used various biophysical and biochemical techniques. The molecular weight of the protein, determined by gel electrophoresis, was found to be about 1.3-folds ( approximately 22 kDa) higher than that obtained from mass spectrometric analysis (16.9 kDa). In size exclusion chromatography experiment, HYPK was eluted in three fractions, the hydrodynamic radii for which were calculated to be approximately 1.5-folds (23.06 A) higher than that expected for globular proteins of equivalent mass (17.3 A). The protein exhibited predominantly (63%) random coil characteristics in circular dichroism spectroscopy and was highly sensitive to limited proteolysis by trypsin and papain, indicating absence of any specific domain. Experimental evidences with theoretical analyses of amino acids composition of HYPK and comparison with available published data predicts that HYPK is an intrinsically unstructured protein (IUP) with premolten globule like conformation. In presence of increasing concentration of Ca(2+), HYPK showed conformational alterations as well as concomitant reduction of hydrodynamic radius. Even though any link between the natively unfolded nature of HYPK, its conformational sensitivity towards Ca(2+) and interaction with Htt is yet to be established, its possible involvement in Huntington's disease pathogenesis is discussed.     

The Transition of Closely Opposed Lesions to Double-Strand Breaks during Long-Patch Base Excision Repair Is Prevented by the Coordinated Action of DNA Polymerase δ and Rad27/Fen1

DNA double-strand breaks can result from closely opposed breaks induced directly in complementary strands. Alternatively, double-strand breaks could be generated during repair of clustered damage, where the repair of closely opposed lesions has to be well coordinated. Using single and multiple mutants of Saccharomyces cerevisiae (budding yeast) that impede the interaction of DNA polymerase δ and the 5′-flap endonuclease Rad27/Fen1 with the PCNA sliding clamp, we show that the lack of coordination between these components during long-patch base excision repair of alkylation damage can result in many double-strand breaks within the chromosomes of nondividing haploid cells. This contrasts with the efficient repair of nonclustered methyl methanesulfonate-induced lesions, as measured by quantitative PCR and S1 nuclease cleavage of single-strand break sites. We conclude that closely opposed single-strand lesions are a unique threat to the genome and that repair of closely opposed strand damage requires greater spatial and temporal coordination between the participating proteins than does widely spaced damage in order to prevent the development of double-strand breaks.Endogenous metabolism or environmental factors such as oxidizing and alkylating agents can produce a wide variety of lesions in DNA. The genomes of mammalian cells experience from 10,000 to as many as 200,000 modifications per day (37, 44). Most lesions are repaired by a complex network of proteins that are part of an elaborate, multistep base excision repair (BER) system that generates single-strand break (SSB) intermediates. Importantly, defects in BER can lead to malignancies and can be associated with age-associated disease, especially neurodegeneration (60).BER is initiated by specific DNA N-glycosylases that remove damaged bases, yielding apurinic/apyrimidinic (AP) sites. Subsequent incision by AP endonucleases results in SSBs, and excision results in a single base gap as a repair intermediate (33, 53). SSBs are expected to be frequent in the genome due to the abundance of base damage as well as intermediates of repair, recombination, replication, and other DNA transactions (15, 16). Because they are generally repaired efficiently by BER and SSB repair enzymes (16, 57), SSBs per se may not be a major source of genome instability. However, if lesions are clustered, the formation of two closely spaced SSBs on opposing strands (or a single SSB and a modified nucleotide or AP site) might pose a special risk in terms of the potential to generate mutations or the possibility of conversion to double-strand breaks (DSBs), which are potent genotoxic lesions. Clustered lesions can arise within cells by chance association of random DNA lesions in a small region or the induction of multiple events in a narrow region, as found for ionizing radiation and various chemicals, such as those used in cancer treatments (47, 58, 59). While efficient BER is important for genome integrity, the repair must be well coordinated to avoid the generation of closely opposed SSB intermediates at closely spaced lesions that could result in the secondary generation of DSBs, especially since cells have limited DSB repair capacity (<50 DSBs/cell in the case of Saccharomyces cerevisiae) (48). While the impact of clustered lesions on repair of DNA has been examined in vitro by use of purified enzymes or cell extracts (13, 14, 27, 39, 56), there has been little opportunity to address specifically the repair of clustered lesions, except for those arising from UV damage (49).Whether formed directly from sugar damage or as BER intermediates, SSBs formed during the repair of base damage often possess 5′-deoxyribose phosphate (5′-dRP) ends that are not suitable for rejoining by DNA ligases (9, 15). In humans, removal and repair of 5′-dRP are accomplished by different combinations of proteins (3, 15) that result in short-patch repair, involving replacement of a single nucleotide (nt), or long-patch repair, involving 2 to 10 nt. The budding yeast Saccharomyces cerevisiae lacks a DNA polymerase β that provides AP lyase activity required for short-patch repair in mammalian cells. Instead, removal and repair of a 5′-dRP rely on the long-patch pathway, involving the successive actions of DNA polymerase δ (Pol δ) for strand displacement, the Rad27/Fen1 endonuclease to remove 5′ flaps, and DNA ligase (Cdc9) to rejoin the resulting nicks (9). The sliding clamp protein PCNA, which interacts with all three players, has been proposed to play a central role in coordinating these processes (18, 19, 34). The coupling between the strand displacement reaction by Pol δ and the flap cutting reaction by Fen1 is highly efficient, with over 90% of the products released by Fen1 being mononucleotides (17).Although the coordination of Pol δ, PCNA, and Rad27/Fen1 provides efficient processing of individual lesions in DNA, closely opposed SSBs that arise during repair of base damage could manifest as DSBs, either directly or as a result of SSB processing. A DNA damaging agent that has been used frequently to characterize long- and short-patch BER is methyl methanesulfonate (MMS). Recently, we described the detection of closely opposed MMS-induced lesions in yeast (42). Since the closely opposed lesions might represent a special challenge to BER, we considered the possibility that they might specifically impact long-patch repair through Pol δ and/or coordination of events with Rad27/Fen1. Pol δ of S. cerevisiae is a heterotrimeric enzyme consisting of Pol3, Pol31, and Pol32 (23). The nonessential Pol32 subunit is involved in translesion DNA synthesis (TLS) (24, 30) and also break-induced replication (41). However, its role in other types of DNA repair remains unclear. Using our in vivo assay for specifically detecting closely spaced methylated DNA lesions (42) and SSBs, we examined the role of Pol32 as well as the cooperation between Pol δ, Rad27/Fen1, and PCNA in the repair of clustered DNA lesions induced by MMS in G₁ stationary-phase haploid yeast. We found that Pol32 plays an important role in ensuring that clustered lesions are efficiently repaired and do not transition to DSBs.     

Malarial infection develops mitochondrial pathology and mitochondrial oxidative stress to promote hepatocyte apoptosis

Activation of the mitochondrial apoptosis pathway by oxidative stress has been implicated in hepatocyte apoptosis during malaria. Because mitochondria are the source and target of reactive oxygen species (ROS), we have investigated whether hepatocyte apoptosis is linked to mitochondrial pathology and mitochondrial ROS generation during malaria. Malarial infection induces mitochondrial pathology by inhibiting mitochondrial respiration, dehydrogenases, and transmembrane potential and damaging the ultrastructure as evident from transmission electron microscopic studies. Mitochondrial GSH depletion and formation of protein carbonyl indicate that mitochondrial pathology is associated with mitochondrial oxidative stress. Fluorescence imaging of hepatocytes documents intramitochondrial superoxide anion (O₂^?) generation during malaria. O₂^? inactivates mitochondrial aconitase to release iron from iron–sulfur clusters, which forms the hydroxyl radical (OH) interacting with H₂O₂ produced concurrently. Malarial infection inactivates mitochondrial aconitase, and carbonylation of aconitase is evident from Western immunoblotting. The release of iron has been documented by fluorescence imaging of hepatocytes using Phen Green SK, and mitochondrial OH generation has been confirmed. During malaria, the depletion of cardiolipin and formation of the mitochondrial permeability transition pore favor cytochrome c release to activate caspase-9. Interestingly, mitochondrial OH generation correlates with the activation of both caspase-9 and caspase-3 with the progress of malarial infection, indicating the critical role of OH.     

Cell Proliferation and Epidermal Growth Factor Signaling in Non-small Cell Lung Adenocarcinoma Cell Lines Are Dependent on Rin1

Rin1 is a Rab5 guanine nucleotide exchange factor that plays an important role in Ras-activated endocytosis and growth factor receptor trafficking in fibroblasts. In this study, we show that Rin1 is expressed at high levels in a large number of non-small cell lung adenocarcinoma cell lines, including Hop62, H650, HCC4006, HCC827, EKVX, HCC2935, and A549. Rin1 depletion from A549 cells resulted in a decrease in cell proliferation that was correlated to a decrease in epidermal growth factor receptor (EGFR) signaling. Expression of wild type Rin1 but not the Rab5 guanine nucleotide exchange factor-deficient Rin1 (Rin1Δ) complemented the Rin1 depletion effects, and overexpression of Rin1Δ had a dominant negative effect on cell proliferation. Rin1 depletion stabilized the cell surface levels of EGFR, suggesting that internalization was necessary for robust signaling in A549 cells. In support of this conclusion, introduction of either dominant negative Rab5 or dominant negative dynamin decreased A549 proliferation and EGFR signaling. These data demonstrate that proper internalization and endocytic trafficking are critical for EGFR-mediated signaling in A549 cells and suggest that up-regulation of Rin1 in A549 cell lines may contribute to their proliferative nature.Internalization of epidermal growth factor receptors (EGFR)² and their subsequent delivery to lysosomes play key roles in attenuating EGF-mediated signaling cascades (1, 2). The proper delivery of EGFR into lysosomes for degradation requires a series of highly regulated targeting and delivery events. Following ligand binding, EGFR is internalized via endocytic vesicles that are subsequently targeted to early endosomes. This targeting event is mediated by the small GTPase, Rab5 (3, 4). Once delivered to the early endosome, receptors that are destined for degradation are incorporated into vesicles that bud into the lumen of the endosome, forming the multivesicular body (reviewed in Refs. 5, 6). Sequestration of the activated cytoplasmic domain of EGFR into the intralumenal vesicles of the multivesicular body effectively terminates receptor signaling (7). Subsequent fusion of the multivesicular body with lysosomes delivers the intralumenal vesicles and their contents into the lumen of the lysosome where they are degraded (reviewed in Refs. 8–10). Inactivating mutations in Rab5 disrupt the delivery of cell surface receptors, such as EGFR, to early endosomes, thereby inhibiting receptor trafficking to the lysosome and receptor degradation (11, 12). Therefore, activation of Rab5 is a key point of regulation for EGFR signaling.Rab5 cycles between an inactive GDP-bound state and an active GTP-bound state, and Rab5 activation requires the exchange of GDP to GTP. This exchange is catalyzed by guanine nucleotide exchange factors (GEFs) that are specific to the Rab5 family of proteins (reviewed in Ref. 13). Rab5 family GEFs all contain a catalytic vacuolar protein sorting 9 (Vps9) domain that facilitates the GDP to GTP exchange (14–17). Many Rab5 GEFs contain other functional domains that are involved in cell signaling events (13). Rin1 is a good example of a multidomain Rab5 GEF. In addition to the Vps9 domain, Rin1 also contains an Src homology 2 domain, a proline-rich domain, and a Ras association domain. Rin1 was originally identified through its ability to interact with active Ras (18), and a role for Rin1 in a number of cell signaling systems has been established, including EGF-mediated signaling (19–21). Rin1 directly interacts with the activated EGFR through its Src homology 2 domain (22). Furthermore, Ras occupation of the Rin1 Ras association domain positively impacts the Rab5 GEF activity of Rin1, which promotes EGFR internalization and attenuation in fibroblasts (23). However, Rin1 expression is up-regulated in several types of cancers, including squamous cell carcinoma (24), colorectal cancer (25), and cervical cancer (26), through duplications or rearrangements of the RIN1 locus. These studies suggest that Rin1 may also play a role in enhancing cell proliferation.It is well established that a large percentage of non-small cell lung adenocarcinomas exhibit up-regulation of EGFR and aberrant signaling through the Ras/MAPK pathway (reviewed in Ref. 27). In addition, a recent study examining 188 human lung adenocarcinomas identified that 132 of 188 tumor samples exhibited mutations relating to the Ras/MAPK signaling pathway (28). Accordingly, the role of Rin1 in non-small cell lung adenocarcinoma was addressed. Examination of a panel of non-small cell lung adenocarcinoma lines (including A549) revealed enhanced Rin1 expression relative to a nontransformed lung epithelial cell line (BEAS-2B). Depletion of Rin1 from A549 cells resulted in decreased proliferation. This decrease correlated with a reduction in EGF-activated ERK phosphorylation and the stabilization of cell surface EGFR. These defects were complemented by wild type Rin1 expression but not by mutant Rin1 lacking a functional Vps9 domain, suggesting that the GEF activity of Rin1 is necessary for proper EGFR signaling in A549 cells. In addition, overexpression of Rin1Δ, dominant negative Rab5, and dynamin resulted in similar defects in cell proliferation and EGFR signaling as Rin1 depletion. These data indicate that proper EGFR internalization and trafficking are critical for robust EGFR-mediated signaling and cell proliferation in A549 cells and offer evidence that Rin1 positively regulates cell proliferation in non-small cell lung adenocarcinoma.