The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

The DNA-binding mode of archaeal feast/famine-regulatory proteins (FFRPs), i.e. paralogs of the Esherichia coli leucine-responsive regulatory protein (Lrp), was studied. Using the method of systematic evolution of ligands by exponential enrichment (SELEX), optimal DNA duplexes for interacting with TvFL3, FL10, FL11 and Ss-LrpB were identified as TACGA[AAT/ATT]TCGTA, GTTCGA[AAT/ATT]TCGAAC, CCGAAA[AAT/ATT]TTTCGG and TTGCAA[AAT/ATT]TTGCAA, respectively, all fitting into the form abcdeWWWedcba. Here W is A or T, and e.g. a and a are bases complementary to each other. Apparent equilibrium binding constants of the FFRPs and various DNA duplexes were determined, thereby confirming the DNA-binding specificities of the FFRPs. It is likely that these FFRPs recognize DNA in essentially the same way, since their DNA-binding specificities were all explained by the same pattern of relationship between amino-acid positions and base positions to form chemical interactions. As predicted from this relationship, when Gly36 of TvFL3 was replaced by Thr, the b base in the optimal DNA duplex changed from A to T, and, when Thr36 of FL10 was replaced by Ser, the b base changed from T to G/A. DNA-binding characteristics of other archaeal FFRPs, Ptr1, Ptr2, Ss-Lrp and LysM, are also consistent with the relationship.     

Changes in reactivities of scallop adductor myosin with 5,5'-dithiobis-(2-nitrobenzoate) and with 2,4,6-trinitrobenzene sulfonate accompanying dissociation and association of regulatory light chain

1. The reactivities of scallop myosin with 5,5'-dithiobis-(2-nitrobenzoate) (DTNB) and with 2,4,6-trinitrobenzene sulfonate (TNBS) were found to be affected by dissociation and association of regulatory light chains (RLC) of myosin. 2. Approximately 4 mol of sulfhydryl groups of "desensitized" myosin (DM) were masked on association of DM with RLC. When these sulfhydryl groups were reacted with DTNB, the modified DM became incapable of associating with RLC, but when the modified DM was treated with 2-mercaptoethanol, the ability to associate with RLC was fully recovered. 3. The DTNB-reactivity of scallop myosin and its RLC content were measured as a function of calcium and magnesium concentrations. The results thus obtained could be explained in terms of our previous suggestion (J. Biochem. 94, 1061 (1983] that there are two different attachments between DM and RLC. 4. The relation between the TNBS-reactivity and the RLC content was not simple but complex. Not the extent, but the rate of trinitrophenylation of scallop myosin was affected by dissociation and association of DM with RLC; thus, the involved TNBS-reactive lysine residues did not seem to be in the regions on DM and RLC that would be physically covered upon DM-RLC association. 5. The amount of the involved lysine residues was estimated to be only 1 mol per mol of myosin. Modification of the specific lysine residues resulted in a partial decrease in the DM-RLC association.     

Methylation of translation-associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases

This study aimed to identify sites of lysine methylation in Saccharomyces cerevisiae and the associated methyltransferases. Hexapeptide ligand affinity chromatography was used to normalize the abundance levels of proteins in whole cell lysate. MS/MS, in association with antibody-based detection, was then used to identify lysine methylated proteins and the precise sites of modification. Lysine methylation was found on the proteins elongation factor (EF) 1-α, 2, and 3A, as well as ribosomal proteins 40S S18-A/B, 60S L11-A/B, L18-A/B, and L42-A/B. Precise sites were mapped in all cases. Single-gene knockouts of known and putative methyltransferase(s), in association with MS/MS, showed that EF1-α is monomethylated by Efm1 at lysin 30 and dimethylated by See1 at lysine 316. Methyltransferase Rkm1 was found to monomethylate 40S ribosomal protein S18-A/B at lysine 48. Knockout analysis also revealed that putative methyltransferase YBR271W affects the methylation of proteins EF2 and 3A; this was detected by Western blotting and immunodetection. This methyltransferase shows strong interspecies conservation and a tryptophan-containing motif associated with its active site. We suggest that enzyme YBR271W is named EF methyltransferase 2 (Efm2), in line with the recent naming of YHL039W as Efm1.     

Crystal structure of the kringle 2 domain of tissue plasminogen activator at 2.4-A resolution.

The crystal structure of the kringle 2 domain of tissue plasminogen activator was determined and refined at a resolution of 2.43 A. The overall fold of the molecule is similar to that of prothrombin kringle 1 and plasminogen kringle 4; however, there are differences in the lysine binding pocket, and two looping regions, which include insertions in kringle 2, take on very different conformations. Based on a comparison of the overall structural homology between kringle 2 and kringle 4, a new sequence alignment for kringle domains is proposed that results in a division of kringle domains into two groups, consistent with their proposed evolutionary relation. The crystal structure shows a strong interaction between a lysine residue of one molecule and the lysine/fibrin binding pocket of a noncrystallographically related neighbor. This interaction represents a good model of a bound protein ligand and is the first such ligand that has been observed in a kringle binding pocket. The structure shows an intricate network of interactions both among the binding pocket residues and between binding pocket residues and the lysine ligand. A lysine side chain is identified as the positively charged group positioned to interact with the carboxylate of lysine and lysine analogue ligands. In addition, a chloride ion is located in the kringle-kringle interface and contributes to the observed interaction between kringle molecules.     

Structural characterization of the maytansinoid-monoclonal antibody immunoconjugate, huN901-DM1, by mass spectrometry

Immunoconjugates are being explored as novel cancer therapies with the promise of target-specific drug delivery. The immunoconjugate, huN901-DM1, composed of the humanized monoclonal IgG1 antibody, huN901, and the maytansinoid drug, DM1, is being tested in clinical trials to treat small cell lung carcinoma (SCLC). huN901-DM1 contains an average of three to four DM1 drug molecules per huN901 antibody molecule. The drug molecules are linked to huN901 through random modification of huN901 at epsilon-amino groups of lysine residues, thus yielding a heterogeneous population of conjugate species. We studied the drug distribution profile of huN901-DM1 by electrospray time-of-flight mass spectrometry(ESI-TOFMS), which showed that one to six DM1 drug molecules were attached to an antibody molecule. Both light and heavy chains contained linked drugs. The conjugation sites in both chains were determined by peptide mapping using trypsin and Asp-N protease digestion. Trypsin digestion identified modified lysine residues, since these residues were no longer susceptible to enzymatic cleavage after conjugation with the drug. With respect to Asp-N digestion, modified peptides were identified by observing a mass increase corresponding to the modification. The two digestion methods provided consistent results, leading to the identification of 20 modified lysine residues in both light and heavy chains. Each lysine residue was only partially modified. No conjugation sites were found in complementarity determining regions (CDRs). Using structural models of human IgG1, it was found that modified lysine residues were on the surface in areas of structural flexibility and had large solvent accessibility.     

Common and distinct features of cytokine effects on hematopoietic stem and progenitor cells revealed by dose-response surface analysis

Recent studies have identified thrombopoietin (TPO), flt-3 ligand (FL), Steel factor (SF), and interleukin-11 (IL-11) as cytokines able to stimulate amplification of the most primitive murine hematopoietic cells in vitro. However, dose-response and interaction parameters that predict how to optimize mixtures of these cytokines have not been previously defined. To obtain this information, Sca-1(+)lin(-) and c-kit(+)Sca-1(+)lin(-) adult mouse bone marrow cells were cultured for 10 and 14 days, respectively, in serum-free medium with varying concentrations of these cytokines. Quantitative assays were performed to determine the influences of the cytokine combinations tested on changes in long-term repopulating hematopoietic stem cells (HSCs), in vitro colony-forming cells (CFCs), and total cell numbers. A two-level factorial design was first used to screen the effects of TPO, SF, FL, and IL-11 as well as two different incubation temperatures. IL-11 and SF were found to be the most significant stimulators of murine HSC expansion. More detailed analyses of the effects on c-kit(+)Sca-1(+)lin(-) cells of IL-11, SF, and FL concentrations and their interactions using response surface methodology showed IL-11 to have a maximal stimulatory effect on HSC expansion at 20 ng/mL with higher concentrations being inhibitory. In contrast, not even high concentration saturation of the effects of either SF or FL was observed as the stimulatory effect of both SF and FL increased beyond 300 ng/mL. A negative interaction between SF and FL on HSCs was discovered. Interestingly, a generally similar pattern of cytokine effects was found to influence the 14-day output of CFCs and total cells from the same c-kit(+)Sca-1(+)lin(-) starting cell population. However, compared with HSCs, the cytokine requirements for maximizing the generation of CFCs and total cells were at much lower cytokine doses. From the information provided by the factorial analysis, mathematical models based on Monod kinetics for inhibitory substrates were developed that allow total cell, CFC, and HSC expansion to be predicted as a function of the IL-11, SF, and FL concentrations in terms of more widely recognized parameters. Overall, these methods should also serve as a guide for the future design and testing of other ex vivo stem cell expansion systems.     

Oxidation of glycated proteins: age-dependent accumulation of N epsilon-(carboxymethyl)lysine in lens proteins

N epsilon-(Carboxymethyl)lysine (CML) has been identified as a product of oxidation of fructoselysine (FL) in glycated (nonenzymatically glycosylated) proteins in vitro and has also been detected in human tissues and urine [Ahmed et al. (1986) J. Biol. Chem. 261, 4889-4894]. In this study, we compare the amounts of CML and FL in normal human lens proteins, aged 0-79 years, using specific and sensitive assays based on selected ion monitoring gas chromatography-mass spectrometry. Our results indicate that the lens content of FL increases significantly between infancy and about age 5 but that there is only a slight, statistically insignificant increase in FL between age 5 and 80 (mean +/- SD = 1.4 +/- 0.4 mmol of FL/mol of Lys). In contrast, the lens content of the oxidation product, CML, increased linearly with age, ranging from trace levels at infancy up to 8 mmol of CML/mol of lysine at age 79. The ratio of CML to FL also increased linearly from 0.5 to 5 mol of CML/mol of FL between age 1 and 79, respectively. These results indicate that CML, rather than FL, is the major product of glycation detectable in adult human lens protein. The age-dependent accumulation of CML in lens protein indicates that products of both glycation and oxidation accumulate in the lens with age, while the constant rate of accumulation of CML in lens with age argues against an age-dependent decline in free radical defense mechanisms in this tissue.     

亚麻木酚素对2型糖尿病小鼠学习记忆的影响及其机制初探

目的:研究亚麻木酚素(Flax ligands,FL)对2型糖尿病模型小鼠空间学习记忆的影响及其初步机制。方法:雄性C57小鼠随机分为对照组(Con)、糖尿病模型组(DM)及亚麻木酚素治疗组(DM+FL),DM与DM+FL组给予高脂饮食加小剂量链脲佐菌素(Streptozotocin,STZ)诱导2型糖尿病模型,之后DM+FL组灌胃给予FL 10 mg/kg,每日一次,连续14天,Con与DM组给予等量生理盐水。通过新物体识别试验、Morris水迷宫试验检测小鼠的学习记忆能力,利用Western blot技术测定小鼠海马脑源性神经营养因子(BDNF)及谷酰胺AMPA受体845位磷酸化(pGluA1-Ser845)蛋白表达水平。结果:与Con组比较,DM组小鼠新物体识别指数显著下降(P<0.01),在Morris水迷宫中逃避潜伏期延长(P<0.05),在目的象限内徘徊时间减少(P<0.01);小鼠海马区BDNF和pGluA1-Ser845的蛋白表达水平均显著低于对照组(P<0.01)。与DM组相比,DM+FL组小鼠新物体识别指数显著提高(P<0.01),在Morris水迷宫中逃避潜伏期明显缩短(P<0.05),目的象限徘徊时间显著增多(P<0.05);小鼠海马区BDNF和pGluA1-Ser845的蛋白表达水平均显著升高(P<0.01)。结论:亚麻木酚素对2型糖尿病小鼠学习记忆有明确改善作用,增加海马BDNF和pGlu-A1-Ser845的表达可能是其潜在作用机制。