Molecular inscription of environmental information into protein suprastructures: temperature effects on unit assembly of α-synuclein oligomers into polymorphic amyloid fibrils.

Bhak, Ghibom,Lee, Junghee,Kim, Tae-Hwan,Lee, Soonkoo,Lee, Daekyun,Paik, Seung R Biochemical Society 2014 Biochemical journal Vol.464 No.2

<P>Molecular-level storage of environmental information in biological structures in tangible forms, and their subsequent transfer to the next generation, has been studied using the phenomenon of amyloidogenesis, which defines a biochemical condition generating highly ordered protein aggregates known as amyloid fibrils. α-Synuclein oligomers shown to experience unit assembly as the formation of amyloid fibrils were used in the present study as an environment-sensing agent. With temperature varying in 2 C intervals between 37 C and 43 C, the oligomeric unit assembly led to fibrillar polymorphism from a straight to a curly appearance, as assessed using TEM and small-angle neutron scattering; the different effects on the secondary structures were evaluated using attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy. The resulting diversified amyloid fibrils, which have distinctive molecular characteristics, were shown to be inherited by the next generation through the self-propagating property of amyloidogenesis. Storage of intangible temperature information in the diversified protein suprastructures and perpetuation of the stored information in the form of polymorphic amyloid fibrils could represent molecular inscription of environmental information into biological systems; this could further extend our understanding of any physiological/pathological significance of amyloidogenic polymorphism and be utilized in the area of nanobiotechnology to process various external signals.</P>

Mimicry and functions of photosynthetic reaction centers

Fukuzumi, Shunichi,Lee, Yong-Min,Nam, Wonwoo Biochemical Society 2018 Biochemical Society transactions Vol.46 No.5

<P>The structure and function of photosynthetic reaction centers (PRCs) have been modeled by designing and synthesizing electron donor-acceptor ensembles including electron mediators, which can mimic multi-step photoinduced charge separation occurring in PRCs to obtain long-lived charge-separated states. PRCs in photosystem I (PSI) or/and photosystem II (PSII) have been utilized as components of solar cells to convert solar energy to electric energy. Biohybrid photoelectrochemical cells composed of PSII have also been developed for solar-driven water splitting into H-2 and O-2. Such a strategy to bridge natural photosynthesis with artificial photosynthesis is discussed in this minireview.</P>

Computational characterization of moonlighting proteins.

Khan, Ishita K,Kihara, Daisuke Biochemical Society 2014 Biochemical Society transactions Vol.42 No.6

<P>Moonlighting proteins perform multiple independent cellular functions within one polypeptide chain. Moonlighting proteins switch functions depending on various factors including the cell-type in which they are expressed, cellular location, oligomerization status and the binding of different ligands at different sites. Although an increasing number of moonlighting proteins have been experimentally identified in recent years, the quantity of known moonlighting proteins is insufficient to elucidate their overall landscape. Moreover, most moonlighting proteins have been identified as a serendipitous discovery. Hence, characterization of moonlighting proteins using bioinformatics approaches can have a significant impact on the overall understanding of protein function. In this work, we provide a short review of existing computational approaches for illuminating the functional diversity of moonlighting proteins.</P>

Chemical genetics and its application to moonlighting in glycolytic enzymes.

Jung, Da-Woon,Kim, Woong-Hee,Williams, Darren R Biochemical Society 2014 Biochemical Society transactions Vol.42 No.6

<P>Glycolysis is an ancient biochemical pathway that breaks down glucose into pyruvate to produce ATP. The structural and catalytic properties of glycolytic enzymes are well-characterized. However, there is growing appreciation that these enzymes participate in numerous moonlighting functions that are unrelated to glycolysis. Recently, chemical genetics has been used to discover novel moonlighting functions in glycolytic enzymes. In the present mini-review, we introduce chemical genetics and discuss how it can be applied to the discovery of protein moonlighting. Specifically, we describe the application of chemical genetics to uncover moonlighting in two glycolytic enzymes, enolase and glyceraldehyde dehydrogenase. This led to the discovery of moonlighting roles in glucose homoeostasis, cancer progression and diabetes-related complications. Finally, we also provide a brief overview of the latest progress in unravelling the myriad moonlighting roles for these enzymes.</P>

Dynamical simulations of DNA supercoiling and compression.

Swigon, David,Lim, Sookkyung,Kim, Yongsam Biochemical Society 2013 Biochemical Society transactions Vol.41 No.2

<P>In the present article, we summarize our recent studies of DNA dynamics using the generalized immersed boundary method. Our analysis of the effects of electrostatic repulsion on the dynamics of DNA supercoiling revealed that, after perturbation, a pre-twisted DNA collapses into a compact supercoiled configuration that is sensitive to the initial excess link and ionic strength of the solvent. A stochastic extension of the generalized immersed boundary method shows that DNA in solution subjected to a constant electric field is compressed into a configuration with smaller radius of gyration and smaller ellipticity ratio than those expected for such a molecule in a thermodynamic equilibrium.</P>

Fasting induces ketoacidosis and hypothermia in PDHK2/PDHK4-double-knockout mice.

Jeoung, Nam Ho,Rahimi, Yasmeen,Wu, Pengfei,Lee, W N Paul,Harris, Robert A Biochemical Society 2012 The Biochemical journal Vol.443 No.3

<P>The importance of PDHK (pyruvate dehydrogenase kinase) 2 and 4 in regulation of the PDH complex (pyruvate dehydrogenase complex) was assessed in single- and double-knockout mice. PDHK2 deficiency caused higher PDH complex activity and lower blood glucose levels in the fed, but not the fasted, state. PDHK4 deficiency caused similar effects, but only after fasting. Double deficiency intensified these effects in both the fed and fasted states. PDHK2 deficiency had no effect on glucose tolerance, PDHK4 deficiency produced only a modest effect, but double deficiency caused a marked improvement and also induced lower insulin levels and increased insulin sensitivity. In spite of these beneficial effects, the double-knockout mice were more sensitive than wild-type and single-knockout mice to long-term fasting, succumbing to hypoglycaemia, ketoacidosis and hypothermia. Stable isotope flux analysis indicated that hypoglycaemia was due to a reduced rate of gluconeogenesis and that slightly more glucose was converted into ketone bodies in the double-knockout mice. The findings establish that PDHK2 is more important in the fed state, PDHK4 is more important in the fasted state, and survival during long-term fasting depends upon regulation of the PDH complex by both PDHK2 and PDHK4.</P>

PKCδ as a regulator for TGF-β-stimulated connective tissue growth factor production in human hepatocarcinoma (HepG2) cells.

Lee, Su Jin,Kang, Jeong Han,Choi, Soo Young,Kwon, Oh-Shin Biochemical Society 2013 The Biochemical journal Vol.456 No.1

<P>CTGF (connective tissue growth factor) is widely regarded as an important amplifier of the profibrogenic action of TGF-β (transforming growth factor β) in a variety of tissues, although the precise mechanism of how the TGF-β signalling pathways modulate CTGF expression remains unclear. In the present study, the role of PKCδ (protein kinase Cδ) in TGF-β1-mediated CTGF expression was investigated using HepG2 cells. TGF-β1 treatment specifically elevated PKCδ activation and CTGF expression. In contrast, blockade of PKCδ by the selective inhibitor Rottlerin or by siRNA knockdown significantly reduced TGF-β1-induced CTGF production. The regulatory mechanism was further demonstrated in HepG2 cells whereby TGF-β1-induced PKCδ activation negatively regulated the nuclear levels of PPM1A (protein phosphatase, Mg2+/Mn2+ dependent, 1A) through the RhoA/ROCK (Rho-associated kinase) pathway. Moreover, we showed that both Smad signalling and the PKCδ pathway appeared to be stimulated by TGF-β1?in parallel. Time course assessments indicated that PKCδ signalling may have a function in maintaining nuclear phospho-Smads at a maximal level. The collective results of the present study demonstrated that PKCδ-stimulated RhoA/ROCK activation resulted in a reduction in PPM1A, thereby up-regulating Smad-dependent gene induction for extended periods. These findings indicated that PKCδ plays a critical role in TGF-β1-induced CTGF production in HepG2 cells.</P>

Ganglioside GM3 participates in the TGF-β1-induced epithelial-mesenchymal transition of human lens epithelial cells.

Kim, Seok-Jo,Chung, Tae-Wook,Choi, Hee-Jung,Kwak, Choong-Hwan,Song, Kwon-Ho,Suh, Seok-Jong,Kwon, Kyung-Min,Chang, Young-Chae,Park, Young-Guk,Chang, Hyeun Wook,Kim, Kyoung-Sook,Kim, Cheorl-Ho,Lee, Youn Biochemical Society 2013 The Biochemical journal Vol.449 No.1

<P>TGF-β (transforming growth factor-β)-induced EMT (epithelial-mesenchymal transition) induces the proliferation and migration of the HLE (human lens epithelial) cells. Ganglioside GM3, simple sialic-acid-containing glycosphingolipids on mammalian cell membranes, regulates various pathological phenomena such as insulin resistance and tumour progression. However, the relationship between ganglioside GM3 and TGF-β-induced EMT in the HLE B-3 cells is poorly understood. In the present study we demonstrated that ganglioside GM3 was involved in TGF-β1-induced EMT in HLE B-3 cells. Our results indicated that the expression of ganglioside GM3 and GM3 synthase mRNA were significantly increased in TGF-β1-induced HLE B-3 cells. Reporter gene analysis also demonstrated that transcriptional activation of the GM3 synthase gene was regulated by Sp1 (specificity protein 1) in HLE B-3 cells upon TGF-β1 stimulation. Interestingly, the inhibition of ganglioside GM3 expression by d-PDMP [d-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol] and GM3 synthase shRNA (short hairpin RNA) resulted significantly in the suppression of cell migration and EMT-related signalling in HLE B-3 cells stimulated by TGF-β. Furthermore, exogenous treatment of ganglioside GM3 rescued the expression of EMT molecules and cell migration suppressed by the depletion of ganglioside GM3?in TGF-β1-induced HLE B-3 cells. We also found that ganglioside GM3 interacted with TGFβRs (TGF-β receptors) in TGF-β1-induced HLE B-3 cells. Taken together, these results suggest that ganglioside GM3 induced by TGF-β1 regulates EMT by potential interaction with TGFβRs.</P>

Lys1110 of TRPM2 is critical for channel activation.

Kim, Taek-Keun,Nam, Joo Hyun,Ahn, Won-Gyun,Kim, Nam-Ho,Ham, Hwa-Yong,Hong, Chang-Won,Nam, Ju-Suk,Lee, Jongho,Huh, Sung-Oh,So, Insuk,Kim, Sung Joon,Song, Dong-Keun Biochemical Society 2013 The Biochemical journal Vol.455 No.3

<P>TRPM2 (transient receptor potential melastatin 2) is a non-selective Ca2+-permeable cation channel activated by ADPR (adenosine diphosphoribose) and H2O2. It is widely expressed in mammalian cells and plays an important role in the regulation of various cell functions. However, the mechanisms of TRPM2 channel activation are not fully understood. Previously, we reported that TRPM2 channel activation is induced by high intracellular Cl- concentration. In the present study, we investigated the functional role of Lys1110 in the membrane-proximal C-terminal region by site-directed mutagenesis. Replacement of the positively charged amino acid lysine (Lys1110) with the neutrally charged amino acid asparagine (K1110N) or the negatively charged amino acid glutamic acid (K1110E) generated mutants that failed to induce an increase in free cytosolic calcium concentration ([Ca2+]i) not only by intracellular injection of Cl-, but also by H2O2 or ADPR. However, a mutant generated by replacing the lysine residue with a positively charged amino acid arginine (K1110R) displayed channel activity similar to wild-type TRPM2. Interestingly, in the K1107N/K1110N double-point mutant, the impaired function of the K1110N mutant in response to ADPR and H2O2, but not to Cl-, was recovered. There were no changes in protein expression, membrane trafficking and oligomerization of the mutant channels. The extent of [Ca2+]i increase by H2O2 in HEK (human embryonic kidney)-293 cells expressing TRPM2 mutants was well correlated with the degree of susceptibility to H2O2-induced cell death. These results display the crucial role of a positively charged amino acid residue at position 1110 for TRPM2 channel activity.</P>

STIM1 negatively regulates Ca2? release from the sarcoplasmic reticulum in skeletal myotubes.

Lee, Keon Jin,Woo, Jin Seok,Hwang, Ji-Hye,Hyun, Changdo,Cho, Chung-Hyun,Kim, Do Han,Lee, Eun Hui Biochemical Society 2013 The Biochemical journal Vol.453 No.2

<P>STIM1 (stromal interaction molecule 1) mediates SOCE (store-operated Ca2? entry) in skeletal muscle. However, the direct role(s) of STIM1 in skeletal muscle, such as Ca2? release from the SR (sarcoplasmic reticulum) for muscle contraction, have not been identified. The times required for the maximal expression of endogenous STIM1 or Orai1, or for the appearance of puncta during the differentiation of mouse primary skeletal myoblasts to myotubes, were all different, and the formation of puncta was detected with no stimulus during differentiation, suggesting that, in skeletal muscle, the formation of puncta is a part of the differentiation. Wild-type STIM1 and two STIM1 mutants (Triple mutant, missing Ca2?-sensing residues but possessing the intact C-terminus; and E136X, missing the C-terminus) were overexpressed in the myotubes. The wild-type STIM1 increased SOCE, whereas neither mutant had an effect on SOCE. It was interesting that increases in the formation of puncta were observed in the Triple mutant as well as in wild-type STIM1, suggesting that SOCE-irrelevant puncta could exist in skeletal muscle. On the other hand, overexpression of wild-type or Triple mutant, but not E136X, attenuated Ca2? releases from the SR in response to KCl [evoking ECC (excitation-contraction coupling) via activating DHPR (dihydropyridine receptor)] in a dominant-negative manner. The attenuation was removed by STIM1 knockdown, and STIM1 was co-immunoprecipitated with DHRP in a Ca2?-independent manner. These results suggest that STIM1 negatively regulates Ca2? release from the SR through the direct interaction of the STIM1 C-terminus with DHPR, and that STIM1 is involved in both ECC and SOCE in skeletal muscle.</P>