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  • 1
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    Effects of site-directed mutagenesis of Asn116 in the {beta}-hairpin of the N-terminal domain of thermolysin on its activity and stability (2012)
    Oxford University Press
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    Publication Date: 2012-08-29
    Description: In the N-terminal domain of thermolysin, two anti-parallel β-strands, Asn112–Ala113–Phe114–Trp115 and Ser118–Gln119–Met120–Val121–Tyr122 are connected by an Asn116–Gly117 turn to form a β-hairpin structure. In this study, we examined the role of Asn116 in the activity and stability of thermolysin by site-directed mutagenesis. Of the 19 Asn116 variants, four (N116A, N116D, N116T and N116Q) were produced in Escherichia coli , by co-expressing the mature and pro domains separately, while the other 15 were not. In the hydrolysis of N -[3-(2-furyl)acryloyl]-glycyl- l -leucine amide (FAGLA) at 25°C, the intrinsic k cat / K m value of N116D was 320% of that of the wild-type thermolysin (WT), and in the hydrolysis of N -carbobenzoxy- l -aspartyl- l -phenylalanine methyl ester (ZDFM) at pH 7.5 at 25°C, the k cat / K m value of N116D was 140% of that of WT, indicating that N116D exhibited higher activity than WT. N116Q exhibited similar activity as WT, and N116A and N116T exhibited reduced activities. The first-order rate constants, k obs , of the thermal inactivation at 80°C were in the order N116A, N116D, N116T 〉 N116Q 〉 WT at all CaCl 2 concentrations examined (1–100 mM), indicating that all variants exhibited reduced stabilities. These results suggest that Asn116 plays an important role in the activity and stability of thermolysin presumably by stabilizing this β-hairpin structure.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 2
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    Interaction of 8-anilinonaphthalene 1-sulphonate (ANS) and human matrix metalloproteinase 7 (MMP-7) as examined by MMP-7 activity and ANS fluorescence (2012)
    Oxford University Press
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    Publication Date: 2012-04-27
    Description: Human matrix metalloproteinase 7 (MMP-7) is the smallest matrix metalloproteinase. It plays important roles in tumour invasion and metastasis. 8-Anilinonaphthalene 1-sulphonate (ANS) is a fluorescent probe widely used for the analysis of proteins. It emits large fluorescence energy when its anilinonaphthalene group binds with hydrophobic regions of protein. In this study, we analysed the interaction of ANS and MMP-7. At pH 4.5–9.5, ANS inhibited MMP-7 activity in the hydrolysis of (7-methoxycoumarin-4-yl)acetyl– L -Pro– L -Leu–Gly– L -Leu-[ N 3 -(2,4-dinitrophenyl)- L -2,3-diaminopropionyl]– L -Ala– L -Arg–NH 2 . The inhibition was a non-competitive manner and depended on the time for pre-incubation of ANS and MMP-7. At pH 4.5–9.5, the fluorescence of ANS was not changed by the addition of MMP-7. At pH 3.5, MMP-7 lacked activity, and the fluorescence of ANS was increased by the addition of MMP-7. These results suggest that at pH 4.5–9.5, the sulphonic group of ANS binds with MMP-7 through electrostatic interaction, whereas at pH 3.5, the anilinonaphthalene group of ANS binds with MMP-7 through hydrophobic interaction.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 3
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    A possibility of a protein-bound water molecule as the ionizable group responsible for pKe at the alkaline side in human matrix metalloproteinase 7 activity (2012)
    Oxford University Press
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    Publication Date: 2012-04-27
    Description: Human matrix metalloproteinase 7 (MMP-7) activity exhibits broad bell-shaped pH profile with the acidic and alkaline p K a (p K e1 and p K e2 ) values of about 4 and 10. The ionizable group for p K e2 was assigned to Lys or Arg by thermodynamic analysis; however, no such residues are present in the active site. Hence, based on the crystal structure, we hypothesized that a water molecule bound to the main-chain nitrogen of Ala162 (W1) or the main-chain carbonyl oxygen of Pro217 (W2) is a candidate for the ionizable group for p K e2 [Takeharu, H. et al. (2011) Biochim. Biophys. Acta 1814, 1940–1946]. In this study, we inspected this hypothesis. In the hydrolysis of (7-methoxycoumarin-4-yl)acetyl- L -Pro- L -Leu–Gly- L -Leu-[ N 3 -(2,4-dinitrophenyl)- L -2,3-diaminopropionyl]- L -Ala- L -Arg-NH 2 , all 19 variants, in which one of all Lys and Arg residues was replaced by Ala, retained activity, indicating that neither Lys nor Arg is the ionizable group. p K e2 values of A162S, A162V and A162G were 9.6 ± 0.1, 9.5 ± 0.1 and 10.4 ± 0.2, respectively, different from that of wild-type MMP-7 (WT) (9.9 ± 0.1) by 0.3–0.5 pH unit, and those of P217S, P217V and P217G were 10.1 ± 0.1, 9.8 ± 0.1 and 9.7 ± 0.1, respectively, different from that of WT by 0.1–0.2 pH unit. These results suggest a possibility of W1 or W2 as the ionizable group for p K e2 .
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 4
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    Effects of site-directed mutagenesis in the N-terminal domain of thermolysin on its stabilization (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-22
    Description: The thermolysin variant G8C/N60C/S65P in which the triple mutation in the N-terminal domain, Gly8-〉Cys/Asn60-〉Cys/Ser65-〉Pro, is undertaken increases stability [Yasukawa, K. and Inouye, K. (2007) Improving the activity and stability of thermolysin by site-directed mutagenesis. Biochim. Biophys. Acta 1774, 1281–1288] and its mechanism is examined in this study. The apparent denaturing temperatures based on ellipticity at 222 nm of the wild-type thermolysin (WT), G8C/N60C, S65P and G8C/N60C/S65P were 85, 〉95, 88 and 〉95°C, respectively. The first-order rate constants, k obs , of the thermal inactivation of WT and variants at 10 mM CaCl 2 increased with increasing thermal treatment temperatures (70–95°C), and those at 80°C decreased with increasing CaCl 2 concentrations (1–100 mM). The k obs values were in the order of WT 〉 S65P 〉 G8C/N60CG8C/N60C/S65P at all temperatures and CaCl 2 concentrations. These results indicate that the mutational combination, Gly8-〉Cys/Asn60-〉Cys and Ser65-〉Pro, increases stability only as high as Gly8-〉Cys/Asn60-〉Cys does. Assuming that irreversible inactivation of thermolysin occurs only in the absence of calcium ions, the dissociation constants, K d , to the calcium ions of WT, G8C/N60C, S65P and G8C/N60C/S65P were 47, 8.9, 17 and 7.2 mM, respectively, suggesting that Gly8-〉Cys/Asn60-〉Cys and Ser65-〉Pro stabilize thermolysin by improving its affinity to calcium ions, most probably the one at the Ca 2+ -binding site III in the N-terminal domain.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 5
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    Interaction of wheat {beta}-amylase with maltose and glucose as examined by fluorescence (2013)
    Oxford University Press
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    Publication Date: 2013-06-27
    Description: Fluorescence of wheat β-amylase (WBA) was quenched by the interaction with maltose or glucose, which are competitive inhibitors of WBA, suggesting that the states of tryptophan and tyrosine residues could be changed by the interaction. The fluorescence emitted by excitation at 280 and 295 nm was titrated by changing the concentrations of maltose and glucose. The dissociation constant ( K d ) values of the WBA–maltose and WBA–glucose complexes were determined to be 0.20 ± 0.12 M for maltose and 0.36 ± 0.11 M for glucose at 25°C, pH 5.4. Maltose exhibited additional binding mode at higher concentration with a distinct K d value (1.5 ± 0.4 M). The K d values at various temperatures and pHs are in agreement with the inhibitor constant ( K i ) values previously reported. The negative standard enthalpy changes ( H °) of the WBA association with glucose and maltose indicate that the associations are exothermic. The association constant ( K a ) and G ° values of the maltose and glucose binding to WBA decreased slightly with increasing temperature from 25°C to 45°C but not dependent on pH change (pH 3.0, 5.4 and 9.0). Fluorescence of WBA could be used as a structural probe to examine the inhibitory interaction with the products of starch hydrolysis.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 6
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    Novel role of PKR in inflammasome activation and HMGB1 release (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-07-18
    Description: The inflammasome regulates the release of caspase activation-dependent cytokines, including interleukin (IL)-1beta, IL-18 and high-mobility group box 1 (HMGB1). By studying HMGB1 release mechanisms, here we identify a role for double-stranded RNA-dependent protein kinase (PKR, also known as EIF2AK2) in inflammasome activation. Exposure of macrophages to inflammasome agonists induced PKR autophosphorylation. PKR inactivation by genetic deletion or pharmacological inhibition severely impaired inflammasome activation in response to double-stranded RNA, ATP, monosodium urate, adjuvant aluminium, rotenone, live Escherichia coli, anthrax lethal toxin, DNA transfection and Salmonella typhimurium infection. PKR deficiency significantly inhibited the secretion of IL-1beta, IL-18 and HMGB1 in E. coli-induced peritonitis. PKR physically interacts with several inflammasome components, including NOD-like receptor (NLR) family pyrin domain-containing 3 (NLRP3), NLRP1, NLR family CARD domain-containing protein 4 (NLRC4), absent in melanoma 2 (AIM2), and broadly regulates inflammasome activation. PKR autophosphorylation in a cell-free system with recombinant NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC, also known as PYCARD) and pro-caspase-1 reconstitutes inflammasome activity. These results show a crucial role for PKR in inflammasome activation, and indicate that it should be possible to pharmacologically target this molecule to treat inflammation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163918/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163918/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Ben -- Nakamura, Takahisa -- Inouye, Karen -- Li, Jianhua -- Tang, Yiting -- Lundback, Peter -- Valdes-Ferrer, Sergio I -- Olofsson, Peder S -- Kalb, Thomas -- Roth, Jesse -- Zou, Yongrui -- Erlandsson-Harris, Helena -- Yang, Huan -- Ting, Jenny P-Y -- Wang, Haichao -- Andersson, Ulf -- Antoine, Daniel J -- Chavan, Sangeeta S -- Hotamisligil, Gokhan S -- Tracey, Kevin J -- DK052539/DK/NIDDK NIH HHS/ -- G0700654/Medical Research Council/United Kingdom -- R01 DK052539/DK/NIDDK NIH HHS/ -- R01 GM057226/GM/NIGMS NIH HHS/ -- R01 GM062508/GM/NIGMS NIH HHS/ -- R01 GM62508/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Aug 30;488(7413):670-4. doi: 10.1038/nature11290.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biomedical Science, The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York 11030, USA. blu@nshs.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22801494" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Adenosine Triphosphate/pharmacology ; Animals ; Antigens, Bacterial/pharmacology ; Apoptosis Regulatory Proteins/metabolism ; Bacterial Toxins/pharmacology ; CARD Signaling Adaptor Proteins/metabolism ; Calcium-Binding Proteins/metabolism ; Carrier Proteins/metabolism ; Cell Line ; Cells, Cultured ; Crystallins/metabolism ; Escherichia coli/immunology/physiology ; Escherichia coli Infections/immunology/metabolism ; Female ; HMGB1 Protein/blood/*secretion ; Humans ; Inflammasomes/agonists/*metabolism ; Interleukin-18/blood ; Interleukin-1beta/blood ; Interleukin-6/analysis/blood ; Macrophages, Peritoneal/drug effects/metabolism ; Male ; Membrane Proteins/metabolism ; Mice ; Mice, Inbred C57BL ; Peritonitis/metabolism ; Phosphorylation ; RNA, Double-Stranded/immunology/pharmacology ; Rotenone/pharmacology ; Salmonella Infections/immunology/metabolism ; Salmonella typhimurium/immunology/physiology ; Transfection ; Uric Acid/pharmacology ; eIF-2 Kinase/antagonists & inhibitors/deficiency/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    A diurnal serum lipid integrates hepatic lipogenesis and peripheral fatty acid use (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-10-25
    Description: Food intake increases the activity of hepatic de novo lipogenesis, which mediates the conversion of glucose to fats for storage or use. In mice, this program follows a circadian rhythm that peaks with nocturnal feeding and is repressed by Rev-erbalpha/beta and an HDAC3-containing complex during the day. The transcriptional activators controlling rhythmic lipid synthesis in the dark cycle remain poorly defined. Disturbances in hepatic lipogenesis are also associated with systemic metabolic phenotypes, suggesting that lipogenesis in the liver communicates with peripheral tissues to control energy substrate homeostasis. Here we identify a PPARdelta-dependent de novo lipogenic pathway in the liver that modulates fat use by muscle via a circulating lipid. The nuclear receptor PPARdelta controls diurnal expression of lipogenic genes in the dark/feeding cycle. Liver-specific PPARdelta activation increases, whereas hepatocyte-Ppard deletion reduces, muscle fatty acid uptake. Unbiased metabolite profiling identifies phosphatidylcholine 18:0/18:1 (PC(18:0/18:1) as a serum lipid regulated by diurnal hepatic PPARdelta activity. PC(18:0/18:1) reduces postprandial lipid levels and increases fatty acid use through muscle PPARalpha. High-fat feeding diminishes rhythmic production of PC(18:0/18:1), whereas PC(18:0/18:1) administration in db/db mice (also known as Lepr(-/-)) improves metabolic homeostasis. These findings reveal an integrated regulatory circuit coupling lipid synthesis in the liver to energy use in muscle by coordinating the activity of two closely related nuclear receptors. These data implicate alterations in diurnal hepatic PPARdelta-PC(18:0/18:1) signalling in metabolic disorders, including obesity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141623/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141623/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Sihao -- Brown, Jonathan D -- Stanya, Kristopher J -- Homan, Edwin -- Leidl, Mathias -- Inouye, Karen -- Bhargava, Prerna -- Gangl, Matthew R -- Dai, Lingling -- Hatano, Ben -- Hotamisligil, Gokhan S -- Saghatelian, Alan -- Plutzky, Jorge -- Lee, Chih-Hao -- K08 HL105678/HL/NHLBI NIH HHS/ -- K08HL105678/HL/NHLBI NIH HHS/ -- P01 HL048743/HL/NHLBI NIH HHS/ -- R01 DK075046/DK/NIDDK NIH HHS/ -- R01DK075046/DK/NIDDK NIH HHS/ -- R01HL048743/HL/NHLBI NIH HHS/ -- T32 ES016645/ES/NIEHS NIH HHS/ -- England -- Nature. 2013 Oct 24;502(7472):550-4. doi: 10.1038/nature12710.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Genetics and Complex Diseases, Division of Biological Sciences, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24153306" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl-CoA Carboxylase/metabolism ; Animals ; *Circadian Rhythm ; Diabetes Mellitus/metabolism ; Fatty Acids/*metabolism ; Gene Expression Regulation ; Homeostasis ; Lipids/*blood ; *Lipogenesis/genetics ; Liver/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Muscles/metabolism ; Obesity/metabolism ; PPAR delta/metabolism ; Phosphatidylcholines/blood ; Principal Component Analysis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna (2013)
    National Academy of Sciences
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    Publication Date: 2013-06-18
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    Regulation of movement speed by intracellular pH during Dictyostelium discoideum chemotaxis. (1991)
    National Academy of Sciences
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    Publication Date: 1991-06-01
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Talin couples the actomyosin cortex to the plasma membrane during rear retraction and cytokinesis (2012)
    National Academy of Sciences
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    Publication Date: 2012-07-23
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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