Mutational analysis of Lys65 of HIV-1 reverse transcriptase

Amino acid Lys(65) is part of the highly flexible beta3-beta4 loop in the fingers domain of the 66 kDa subunit of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). Recent crystal data show that the epsilon-amino group of Lys(65) interacts with the gamma-phosphate of the bound deoxynucleoside triphosphate ('dNTP') substrate [Huang, Chopra, Verdine and Harrison (1998) Science 282, 1669-1675]. In order to biochemically define the function of RT Lys(65), we have used site-specific mutagenesis to generate RT with a variety of substitutions at this position, including K65E, K65Q, K65A and K65R. Kinetic analyses demonstrate that if Lys(65) in RT is substituted with an amino acid other than arginine the enzyme exhibits dramatic decreases in the binding affinity (K(m)) for all dNTP substrates, in RT catalytic efficiency (k(cat)/K(m)) and in the mutant enzyme's ability to carry out pyrophosphorolysis, the reverse reaction of DNA synthesis. The pH optimum for the DNA polymerase activity of K65E RT was 6.5, compared to 7.5 for the wild-type enzyme, and 8.0 for the K65R, K65A and K65Q mutants. Molecular modelling studies show that mutations of Lys(65) do not affect the geometry of the loop's alpha-carbon backbone, but rather lead to changes in positioning of the side chains of residues Lys(70) and Arg(72). In particular, Glu in K65E can form a salt bridge with Arg(72), leading to the diminution of the latter residue's interaction with the alpha-phosphate of the dNTP residue. This alteration in dNTP-binding may explain the large pH-dependent changes in both dNTP-binding and catalytic efficiency noted with the enzyme. Furthermore, the K65A, K65Q and K65E mutant enzymes are 100-fold less sensitive to all dideoxynucleoside triphosphate ('ddNTP') inhibitors, whereas the K65R mutation results in a selective 10-fold decrease in binding of ddCTP and ddATP only. This implies that mutations at position 65 in HIV-1 RT influence the nucleotide-binding specificity of the enzyme.

Role of Lys335 in the metastability and function of inhibitory serpins

The native form of inhibitory serpins (serine protease inhibitors) is not in the thermodynamically most stable state but in a metastable state, which is critical to inhibitory functions. To understand structural basis and functional roles of the native metastability of inhibitory serpins, we have been characterizing stabilizing mutations of human alpha1-antitrypsin, a prototype inhibitory serpin. One of the sites that has been shown to be critical in stability and inhibitory activity of alpha1-antitrypsin is Lys335. In the present study, detailed roles of this lysine were analyzed by assessing the effects of 13 different amino acid substitutions. Results suggest that size and architect of the side chains at the 335 site determine the metastability of alpha1-antitrypsin. Moreover, factors such as polarity and flexibility of the side chain at this site, in addition to the metastability, seem to be critical for the inhibitory activity. Substitutions of the lysine at equivalent positions in two other inhibitory serpins, human alpha1-antichymotrypsin and human antithrombin III, also increased stability and decreased inhibitory activity toward alpha-chymotrypsin and thrombin, respectively. These results and characteristics of lysine side chain, such as flexibility, polarity, and the energetic cost upon burial, suggest that this lysine is one of the structural designs in regulating metastability and function of inhibitory serpins in general.

Further assessment of the dietary lysine requirement of finishing gilts

A cooperative research study involving 635 gilts was conducted at eight research stations to further estimate the lysine requirement of finishing gilts. Dietary crude protein levels of the five dietary treatments ranged from 16.0 to 24.4% with calculated lysine levels of .80, .95, 1.10, 1.25, or 1.40%. Each station contributed a minimum of two replicate pens of pigs per treatment. Average initial and final weights were 53.6 and 116.4 kg, respectively. At the end of the experimental period, pigs were killed and hot carcass weight, 10th-rib fat depth, and longissimus muscle area were measured. Carcass fat-free lean percentage and fat-free lean gain were estimated from these data. Daily lysine intakes averaged 21.8, 25.9, 30.5, 34.3, and 37.8 g/d for the five treatment groups, respectively. Increasing the dietary lysine from .80 to .95% numerically increased weight gain and gain:feed, but these increases were not maintained at higher levels of dietary lysine. Overall, rate and efficiency of gain decreased (cubic, P < .01) with increasing dietary lysine. Carcasses were leaner at the two higher levels of dietary lysine as evidenced by reduced 10th rib backfat (linear, P < .01), increased longissimus area (quadratic, P < .04), and increased percentage of estimated fat-free lean (linear, P < .01). Carcass fat-free lean gain was not influenced by dietary lysine except for a small numerical improvement (P < .11) at the .95% level of dietary lysine that paralleled the improvement in body weight gain. The results indicate that the dietary lysine requirement of finishing gilts with a mean carcass fat-free lean growth rate of 306 g/d from 54 to 116 kg body weight is probably no higher than .80% of the diet to achieve maximum rate and efficiency of body weight gain and carcass lean growth rate. The results also indicate that higher dietary lysine levels may increase carcass leanness in finishing gilts, possibly due to reduced intake of NE. Whether this response is due to the effects of lysine alone, protein (i.e., other amino acids), or soybean meal is unknown.

Effects of dietary lysine intake during lactation on blood metabolites, hormones, and reproductive performance in primiparous sows

Effects of three dietary lysine (protein) concentrations during lactation on metabolic state, protein metabolism, reproductive hormones, and performance were investigated in 36 primiparous sows. Sows were assigned randomly to one of three diets containing .4% (low lysine, LL), 1.0% (medium lysine, ML), or 1.6% (high lysine, HL) total lysine from intact protein sources. All diets contained 2.1 Mcal NE/kg and exceeded the recommended requirements for all other nutrients. Actual lysine intakes over an 18-d lactation were 16, 36, and 56 g/d for sows fed LL, ML, and HL, respectively. Fractional breakdown rate of muscle was determined on d 4 and 15 of lactation by using a three-compartment kinetic model of 3-methylhistidine metabolism. Increasing lysine intake during lactation did not affect fractional breakdown rate of muscle on d 4 of lactation but decreased it on d 15 (P < .05). Sows fed LL had a reduced number of LH pulses on d 12 and 18 (P < .05) and reduced serum estradiol (E2) concentration on d 18 of lactation compared with sows fed ML and HL treatments. However, LH pulses and E2 concentrations were similar between ML and HL treatments (P > .35). Increasing lysine intake increased serum urea nitrogen (SUN) and postprandial insulin concentrations (P < .05) during lactation but had no effect on plasma glucose concentrations (P > .20). Sows fed HL had greater serum IGF-I on d 6 and 18 than sows fed ML (P < .05). Number of LH peaks was correlated with serum insulin concentration 25 min after feeding on d 6 and 18 (r = .31 to .41; P < .1) and pre- (r = .33 to .46) and postprandial (r = .30 to .58) SUN concentrations (P < .05) during different stages of lactation. Results indicate that, compared with medium lysine intake, low lysine intake increased muscle protein degradation and decreased concentrations of insulin, SUN, and estradiol and LH pulsatility. In contrast, high lysine (protein) intake increased SUN, insulin, and IGF-I, but did not increase secretion of estradiol and LH compared with medium lysine intake. Furthermore, nutritional impacts on reproduction may be mediated in part through associated effects on circulating insulin concentration.

The 4'lysine in the putative channel lining domain affects desensitization but not the single-channel conductance of recombinant homomeric 5-HT3A receptors

The 5-HT3 receptor is a transmitter-gated ion channel of the Cys-loop superfamily. Uniquely, 5-HT3 receptor subunits (5-HT3A and 5-HT3B) possess a positively charged lysine residue within the putative channel lining M2 domain (4' position). Using whole cell recording techniques, we examined the role of this residue in receptor function using wild-type (WT) and mutant 5-HT3A receptor subunits of murine origin transiently expressed in human embryonic kidney (HEK 293) cells. WT 5-HT3A receptors mediated rapidly activating currents in response to 5-HT (10-90 % rise time, 103 ms; EC50, 2.34 microM; Hill coefficient, nH, 2.87). The currents rectified inwardly, reversed in sign at a potential of -9 mV and desensitized in the continuous presence of agonist (half-time of desensitization, t(1/2), 2.13 s). 5-HT3A receptor subunits in which the 4'lysine was mutated to arginine, glutamine, serine or glycine formed functional receptors. 5-HT EC50 values were approximately 2-fold lower than for WT 5-HT3A receptors, but Hill coefficients, kinetics of current activation, rectification, and reversal potentials were unaltered. Each of the mutants desensitized more slowly than the WT 5-HT3A receptor, with the arginine and glycine mutations exhibiting the greatest effect (5-fold reduction). The rank order of effect was arginine > glycine > serine > glutamine. The single-channel conductance of the WT 5-HT3A receptor, as assessed by fluctuation analysis of macroscopic currents, was 390 fS. A similar value was obtained for the 4'lysine mutant receptors. Thus it appears unlikely that 4'lysine is exposed to the channel lumen. Mutation of residues immediately adjacent to 4'lysine to glutamate or lysine resulted in lack of receptor expression or function. We conclude that 4'lysine does not form part of the channel lining, but may play an important role in 5-HT3 receptor desensitization.

The language of covalent histone modifications

Histone proteins and the nucleosomes they form with DNA are the fundamental building blocks of eukaryotic chromatin. A diverse array of post-translational modifications that often occur on tail domains of these proteins has been well documented. Although the function of these highly conserved modifications has remained elusive, converging biochemical and genetic evidence suggests functions in several chromatin-based processes. We propose that distinct histone modifications, on one or more tails, act sequentially or in combination to form a 'histone code' that is, read by other proteins to bring about distinct downstream events.

Metabolize methionine and lysine requirements of growing cattle

Two growth studies were conducted to determine the Met and Lys requirements of growing cattle. In each 84-d trial, steer calves were fed individually diets containing 44% sorghum silage, 44% corn cobs, and 12% supplement (DM basis) at an equal percentage of BW. In Trial 1, 95 crossbred steers (251 kg) were supplemented with urea or meat and bone meal (MBM). Incremental amounts of rumen-protected Met were added to MBM to provide 0, .45, .9, 1.35, 3, and 6 g/d metabolizable Met. In Trial 2, 60 steers (210 kg) were supplemented with urea or corn gluten meal (CGM). Incremental amounts of rumen-protected Lys were added to CGM to provide 0, 1, 2, 3, 4, 5, 6, 8, and 10 g/d metabolizable Lys. Supplementation with MBM and CGM increased the supply of metabolizable protein to the animal. Steers fed MBM plus 0 Met gained 49 g/d more than steers fed urea, whereas steers fed CGM plus 0 Lys gained 150 g/d more than steers fed urea. Supplementation of rumen-protected Met and Lys improved ADG in steers fed MBM and CGM, respectively (P < .10). Nonlinear analysis, comparing gain vs supplemental Met and Lys intake, predicted supplemental Met and Lys requirements of 2.9 and .9 g/d, respectively. This amount of additional Met promoted .13 kg/ d gain greater than MBM alone, and this amount of additional Lys promoted .10 kg/d gain greater than the CGM alone. Metabolizable Met and Lys requirements were predicted from Level 1 of NRC (1996) calculated metabolizable protein supply, amino acid analysis of abomasal contents, and the maximum response to supplemental AA. Steers gaining .39 kg/d required 11.6 g/ d Met or 3. 1% of the metabolizable protein requirement, whereas steers gaining .56 kg/d required 22.5 g/d Lys or 5.7% of the metabolizable protein requirement.

Mammary gland growth as influenced by litter size in lactating sows: impact on lysine requirement

Twenty-eight primiparous sows were used to determine the effect of litter size on the growth of mammary glands and nursing pigs during lactation. Litter size was set to 6, 7, 8, 9, 10, 11, or 12 pigs by cross-fostering immediately after birth. Four sows were allotted to each litter-size group. Sows were allowed to consume a daily maximum of 13.6 Mcal ME and 46.3 g of lysine during lactation. Sows were slaughtered on d 21 (20.6+/-1.1) of lactation. Mammary glands were collected at slaughter and trimmed of skin and the extraneous fat pad. Each gland was separated, weighed, and ground for chemical analysis. Dry matter, dry fat-free tissue (DFFT), crude protein, ash, and DNA contents were measured. Only glands known to have been nursed were included in the data set. Wet and dry weights and the amounts of DFFT, protein, DNA, ash, and fat in individual nursed mammary glands linearly decreased (P<.05) as litter size increased. Percentages of DFFT, protein, and DNA were quadratically affected (P<.05) by litter size on d 21 of lactation. Total mammary wet and dry weights and total DFFT, protein, DNA, fat, and ash amount of all nursed mammary glands of each sow were increased as litter size increased (P<.05). Changing litter size from 6 to 12 pigs resulted in 2,098, 432, 253, 227, 4.4, 178, and 20 g increases in the amounts of total mammary wet weight, dry weight, DFFT, protein, DNA, fat, and ash, respectively, on d 21 of lactation. Litter weight gain was 18.1 kg greater in sows with 12 pigs than in sows with 6 pigs. Sows with a larger litter size had a greater increase in total mass of mammary gland tissue and litter weight but had lower growth of individual nursed mammary glands and individual pigs than sows with the smaller litter size. The need for nutrients to support additional mammary gland and litter growth as litter size increases should be considered when estimating nutrient requirements for lactating sows. Sows need an additional .96 g lysine per day to account for mammary gland growth for each pig added to a litter.

Estimates of essential amino acid requirements from dose-response studies with rainbow trout and broiler chicken: effect of mathematical model

A total of 37 dose-response experiments with essential amino acids performed with rainbow trout and broiler chicken were re-evaluated with different mathematical approaches: an exponential model, a four-parameter logistic function, the saturation kinetics model and the broken line approach. The different approaches were compared both with regard to the goodness of fit (r2 and sy.x) and with regard to the allowances which were derived regarding the optimal amino acid level in the diet. The experimental design, particularly the chosen range in dietary amino acid concentration was found to be important for the comparison of models. Amongst the non-linear models, the four-parameter logistic function and the saturation kinetics model appeared superior to the exponential approach, when the range in dietary amino acid concentration was very wide and included both a severely deficient basal level and a level that exceeded the needs of the animal by approximately the factor 2. In these cases, allowances derived from individual experiments were considerably different depending on the model. The allowances based on the exponential and the saturation kinetics approach were 27.7 and 20.7 g lysine/kg DM and 8.0 and 6.3 g methionine/kg DM, respectively, for rainbow trout. For other amino acids studied in rainbow trout the difference due to model was less. Consequently, the predicted 'ideal protein' for rainbow trout was considerably different depending on the model used. The maximum deviation found in different experiments with broiler chicken for the exponential vs. the saturation kinetics approach was 13.0 and 9.7 g lysine/kg and 11.4 and 8.2 g sulfur-containing amino acids/kg, respectively. However, the more restricted the range in dietary concentration was, the lesser became the differences between the different non-linear models. No definite recommendation can therefore be extracted regarding the most suitable, generally applicable mathematical model.

The role of lysine 185 in the kir6.2 subunit of the ATP-sensitive channel in channel inhibition by ATP

1. ATP-sensitive potassium (KATP) channels are composed of pore-forming Kir6.2 and regulatory SUR subunits. A truncated isoform of Kir6.2, Kir6.2DeltaC26, forms ATP-sensitive channels in the absence of SUR1, suggesting the ATP-inhibitory site lies on Kir6.2. 2. Previous studies have shown that mutation of the lysine residue at position 185 (K185) in the C-terminus of Kir6.2 to glutamine, decreased the channel sensitivity to ATP without affecting the single-channel conductance or the intrinsic channel kinetics. This mutation also impaired 8-azido[32P]-ATP binding to Kir6.2. 3. To determine if K185 interacts directly with ATP, we made a range of mutations at this position, and examined the effect on the channel ATP sensitivity by recording macroscopic currents in membrane patches excised from Xenopus oocytes expressing wild-type or mutant Kir6.2DeltaC26. 4. Substitution of K185 by a positively charged amino acid (arginine) had no substantial effect on the sensitivity of the channel to ATP. Mutation to a negatively charged residue markedly decreased the channel ATP sensitivity: the Ki for ATP inhibition increased from 85 microM to >30 mM when arginine was replaced with aspartic acid. Substitution of neutral residues had intermediate effects. 5. The inhibitory effects of ADP, ITP and GTP were also reduced when K185 was mutated to glutamine or glutamate. 6. The results indicate that a positively charged amino acid at position 185 is required for high-affinity ATP binding to Kir6.2. Our results demonstrate that ATP does not interact with the side-chain of K185. It remains unclear whether ATP interacts with the backbone of this residue, or whether its mutation influences ATP binding allosterically.

Effects of lysine:calorie ratio on growth performance of 10- to 25-kilogram pigs

Crossbred barrows (n = 336 Newsham Hybrids) initially 9.9 kg and 31+/-2 d of age were used to evaluate the effects of energy density and lysine:calorie ratio on growth performance. Pigs were allotted by initial weight in a 3 x 4 factorial arrangement of treatments in a randomized complete block design with six replicate pens per treatment. Each pen had four or five pigs with an equal number of pigs per pen within replicate. Pigs were fed increasing dietary energy densities (3.25, 3.38, and 3.51 Mcal ME/kg) and lysine:calorie ratios (3.00, 3.45, 3.90, and 4.35 g lysine/Mcal ME). Energy density was changed by levels of choice white grease (0, 3, and 6%), and lysine:calorie ratio was changed by altering the corn:soybean meal ratio. Over the 21-d trial, an energy density x lysine:calorie ratio interaction was observed for ADG (P < .05). Pigs fed diets containing 3.25 or 3.51 Mcal ME/kg had increasing ADG with increasing lysine:calorie ratio, whereas ADG of pigs fed 3.38 Mcal ME/kg was not affected by lysine:calorie ratio. Feed efficiency (gain:feed ratio) increased and ADFI decreased as lysine:calorie ratio increased (linear, P < .01) and as energy density increased (quadratic, P < .01 and .10, respectively). On d 21, two pigs per pen were scanned ultrasonically for backfat depth. An energy density x lysine:calorie ratio interaction (P < .06) was observed. Pigs fed diets containing 3.25 and 3.38 Mcal ME/kg had decreasing fat depth as lysine:calorie ratio increased; however, backfat depth was not affected by lysine:calorie ratio and was greatest for pigs fed 3.51 Mcal ME/kg. These results suggest that 10- to 25-kg pigs fed diets containing 3.38 Mcal ME/kg had maximum feed efficiency and that they required at least 4.35 g lysine/Mcal ME. However, pigs fed 3.51 Mcal ME/kg had increased fat depth regardless of calorie:lysine ratio.

Effects of dietary energy density and lysine:calorie ratio on growth performance and carcass characteristics of growing-finishing pigs

We conducted two experiments to evaluate the effects of dietary energy density and lysine:calorie ratio on the growth performance and carcass characteristics of growing and finishing pigs. In Exp. 1, 80 crossbred barrows (initially 44.5 kg) were fed a control diet or diets containing 1.5, 3.0, 4.5, or 6.0% choice white grease (CWG). All diets contained 3.2 and 2.47 g of lysine/Mcal ME during growing (44.5 to 73 kg) and finishing (73 to 104 kg), respectively. Increasing energy density did not affect overall ADG; however, ADFI decreased and feed efficiency (Gain:feed ratio; G:F) increased (linear, P < .01). Increasing energy density decreased and then increased (quadratic, P < .06) skinned fat depth and lean percentage. In Exp. 2, 120 crossbred gilts (initially 29.2 kg) were used to determine the effects of increasing levels of CWG and lysine:calorie ratio fed during the growing phase on growth performance and subsequent finishing growth. Pigs were fed increasing energy density (3.31, 3.44, or 3.57 Mcal ME/kg) and lysine:calorie ratio (2.75, 3.10, 3.45, or 3.80 g lysine/Mcal ME). No energy density x lysine:calorie ratio interactions were observed (P > .10). Increasing energy density increased ADG and G:F and decreased ADFI of pigs from 29.5 to 72.6 kg (linear, P < .05). Increasing lysine:calorie ratio increased ADG and ADFI (linear, P < .01 and .07, respectively) but had no effect on G:F. From 72.6 to 90.7 kg, all pigs were fed the same diet containing .90% lysine and 2.72 g lysine/Mcal ME. Pigs previously fed with increasing lysine:calorie ratio had decreased (linear, P < .02) ADG and G:F. Also, pigs previously fed increasing CWG had decreased (linear, P < .03) ADG and ADFI. From 90.7 to 107 kg when all pigs were fed a diet containing .70% lysine and 2.1 g lysine/Mcal ME, growth performance was not affected by previous dietary treatment. Carcass characteristics were not affected by CWG or lysine:calorie ratio fed from 29.5 to 72.6 kg. Increasing the dietary energy density and lysine:calorie ratio improved ADG and G:F of growing pigs; however, pigs fed a low-energy diet or a low lysine:calorie ratio from 29 to 72 kg had compensatory growth from 72 to 90 kg.

Hepatitis B virus maturation is affected by the incorporation of core proteins having a C-terminal substitution of arginine or lysine stretches

Assembly of replication-competent hepadnavirus nucleocapsids requires interaction of core protein, polymerase and encapsidation signal (epsilon) with viral pregenomic RNA. The N-terminal portion (aa 1-149) of the core protein is able to self-assemble into nucleocapsids, whereas the C-terminal portion (aa 150-183) is known to interact with pregenomic RNA. In this study, two hepatitis B virus (HBV) core mutants (C144Arg and C144Lys) in which the C-terminal SPRRR (Ser-Pro-Arg-Arg-Arg) motif was replaced by a stretch of arginine or lysine residues were generated to test their role in pregenome encapsidation and virus maturation. Mutant or wild-type core-expression plasmids were co-transfected with a core-negative plasmid into human hepatoma HuH-7 cells to compare trans-complementation efficiency for virus replication. Both low- and high-density capsids were present in -the cytoplasm and culture medium of HuH-7 cells in all transfections. Nucleocapsids formed by C144Arg and C144Lys, however, lost the endogenous polymerase activity to repair HBV DNA. Furthermore, in co-transfection of pHBVC144Arg or pHBVC144Lys with a plasmid which produces replication-competent nucleocapsids, the HBV DNA repairing signal was reduced 40- to 80-fold. This is probably due to formation of mosaic particles of wild-type and mutant cores. Results indicated that the SPRRR motif at the core protein C terminus is important for HBV DNA replication and maturation. Additionally, triple-plasmid transfection experiments showed that nucleocapsids containing various amounts of C144Arg and wild-type core proteins exhibited a bias in selecting a shorter pregenome for encapsidation and DNA replication. It is therefore suggested that unknown factors are also involved in HBV pregenome packaging.

Crucial role of Lys(423) in the electron transfer of neuronal nitric-oxide synthase

Nitric-oxide synthase (NOS) is composed of an oxygenase domain having cytochrome P450-type heme active site and a reductase domain having FAD- and FMN-binding sites. To investigate the route of electron transfer from the reductase domain to the heme, we generated mutants at Lys(423) in the heme proximal site of neuronal NOS and examined the catalytic activities, electron transfer rates, and NADPH oxidation rates. A K423E mutant showed no NO formation activity (<0.1 nmol/min/nmol heme), in contrast with that (72 nmol/min/nmol heme) of the wild type enzyme. The electron transfer rate (0.01 min(-1)) of the K423E on addition of excess NADPH was much slower than that (>10 min(-1)) of the wild type enzyme. From the crystal structure of the oxygenase domain of endothelial NOS, Lys(423) of neuronal NOS is likely to interact with Trp(409) which lies in contact with the heme plane and with Cys(415), the axial ligand. It is also exposed to solvent and lies in the region where the heme is closest to the protein surface. Thus, it seems likely that ionic interactions between Lys(423) and the reductase domain may help to form a flavin to heme electron transfer pathway.

A lysine-to-arginine change found in natural alleles of the human T-cell lymphotropic/leukemia virus type 1 p12(I) protein greatly influences its stability

The HTLV-1 singly spliced open reading frame I protein, p12(I), is highly unstable and appears to be necessary for persistent infection in rabbits. Here we demonstrate that p12(I) forms dimers through two putative leucine zipper domains and that its stability is augmented by specific proteasome inhibitors. p12(I) is ubiquitylated, and mutations of its unique carboxy-terminus lysine residue to an arginine greatly enhance its stability. Interestingly, analysis of 53 independent HTLV-1 strains revealed that the natural p12(I) alleles found in ex vivo samples of tropical spastic paraparesis-HTLV-1-associated myelopathy patients contain a Lys at position 88 in some cases, whereas arginine is consistently found at position 88 in HTLV-1 strains from all adult T-cell leukemia-lymphoma (ATLL) cases and healthy carriers studied. This apparent segregation of different alleles in tropical spastic paraparesis-HTLV-associated myelopathy and ATLL or healthy carriers may be relevant in vivo, since p12(I) binds the interleukin-2 receptor beta and gammac chains, raising the possibility that the two natural alleles might affect differently the regulation of these molecules.

Receptor activation by human C5a des Arg74 but not intact C5a is dependent on an interaction between Glu199 of the receptor and Lys68 of the ligand

Despite the expression of only one type of receptor, there is great variation in the ability of different cell types to discriminate between C5a and its more stable metabolite, C5a des Arg74. The mechanism that underlies this phenomenon is not understood but presumably involves differences in the interaction with the C5a receptor. In this paper, we have analyzed the effects of a substitution mutation of the receptor (Glu199 --> Lys199) and the corresponding reciprocal mutants (Lys68 --> Glu68) of C5a, C5a des Arg74 and peptide analogues of the C-terminus of C5a on the ability of the C5a receptor to discriminate between ligands with and without Arg74. The use of these mutants indicates that the Lys68/Glu199 interaction is essential for activation of receptor by C5a des Arg74 but not for activation by intact C5a. The substitution of Asp for Arg74 of C5a [Lys68] produces a ligand with equal potency on both the wild-type and mutant receptors, suggesting that it is the C-terminal carboxyl group rather than the side chain of Arg74 that controls the responsiveness of the receptor to Lys68. In contrast, the mutation of Lys68 to Glu(68) has little effect on the ability of either C5a or C5a des Arg(74) to displace [(125)I]C5a from the receptors, indicating that binding of ligand and receptor activation are distinct but interdependent events. C5a and the truncated ligand, C5a des Arg74, appear to have different modes of interaction with the receptor and the ability of the human C5a receptor to discriminate between these ligands is at least partly dependent on an interaction with the receptor residue, Glu199.

Chemical modification of lysine and arginine residues of bovine heart 2-oxoglutarate dehydrogenase: effect on the enzyme activity and regulation

Chemical modification of arginine and lysine residues of bovine heart 2-oxoglutarate dehydrogenase with phenylglyoxal and pyridoxal 5'-phosphate inactivated the enzyme, indicating the importance of these residues for the catalysis. Inactivation caused by pyridoxal 5'-phosphate was prevented in the presence of thiamine pyrophosphate and Mg2+ allowing the assumption that lysine residues participate in binding of the cofactor.

The activity of mammalian brm/SNF2alpha is dependent on a high-mobility-group protein I/Y-like DNA binding domain

The mammalian SWI-SNF complex is a chromatin-remodelling machinery involved in the modulation of gene expression. Its activity relies on two closely related ATPases known as brm/SNF2alpha and BRG-1/SNF2beta. These two proteins can cooperate with nuclear receptors for transcriptional activation. In addition, they are involved in the control of cell proliferation, most probably by facilitating p105(Rb) repression of E2F transcriptional activity. In the present study, we have examined the ability of various brm/SNF2alpha deletion mutants to reverse the transformed phenotype of ras-transformed fibroblasts. Deletions within the p105(Rb) LXCXE binding motif or the conserved bromodomain had only a moderate effect. On the other hand, a 49-amino-acid segment, rich in lysines and arginines and located immediately downstream of the p105(Rb) interaction domain, appeared to be essential in this assay. This region was also required for cooperation of brm/SNF2alpha with the glucocorticoid receptor in transfection experiments, but only in the context of a reporter construct integrated in the cellular genome. The region has homology to the AT hooks present in high-mobility-group protein I/Y DNA binding domains and is required for the tethering of brm/SNF2alpha to chromatin.

Role of a conserved lysine residue in the peripheral cannabinoid receptor (CB2): evidence for subtype specificity

The human cannabinoid receptors, central cannabinoid receptor (CB1) and peripheral cannabinoid receptor (CB2), share only 44% amino acid identity overall, yet most ligands do not discriminate between receptor subtypes. Site-directed mutagenesis was employed as a means of mapping the ligand recognition site for the human CB2 cannabinoid receptor. A lysine residue in the third transmembrane domain of the CB2 receptor (K109), which is conserved between the CB1 and CB2 receptors, was mutated to alanine or arginine to determine the role of this charged amino acid in receptor function. The analogous mutation in the CB1 receptor (K192A) was found to be crucial for recognition of several cannabinoid compounds excluding (R)-(+)-[2, 3-dihydro-5-methyl-3-[(4-morpholinyl)methyl]pyrrolo[1,2,3-de]-1, 4-benzoxazin-6-yl](1-naphthalenyl)methanone (WIN 55,212-2). In contrast, in human embryonic kidney (HEK)-293 cells expressing the mutant or wild-type CB2 receptors, we found no significant differences in either the binding profile of several cannabinoid ligands nor in inhibition of cAMP accumulation. We identified a high-affinity site for (-)-3-[2-hydroxyl-4-(1, 1-dimethylheptyl)phenyl]-4-[3-hydroxyl propyl] cyclohexan-1-ol (CP-55,940) in the region of helices 3, 6, and 7, with S3.31(112), T3.35(116), and N7.49(295) in the K109A mutant using molecular modeling. The serine residue, unique to the CB2 receptor, was then mutated to glycine in the K109A mutant. This double mutant, K109AS112G, retains the ability to bind aminoalkylindoles but loses affinity for classical cannabinoids, as predicted by the molecular model. Distinct cellular localization of the mutant receptors observed with immunofluorescence also suggests differences in receptor function. In summary, we identified amino acid residues in the CB2 receptor that could lead to subtype specificity.

Identification of positively charged residues of FomA porin of Fusobacterium nucleatum which are important for pore function

FomA porin is the major outer-membrane protein of Fusobacterium nucleatum. It exhibits the functional properties of a general diffusion porin, but has no sequence similarity to other porins. According to the proposed topology model, each monomer of this trimeric protein is a beta-barrel consisting of 16 transmembrane segments with eight surface-exposed loops. Several conserved charged residues are proposed to extend from the beta-barrel wall into the aqueous channel lumen, and may contribute to a transverse electric field similar to that at the pore constriction of porins with known structure. The goal of our study was to identify particular basic residues contributing to such an electric field in FomA. Several arginines and lysines were replaced by negatively charged glutamates or uncharged alanines. The mutated FomA porins were expressed in Escherichia coli, and the effects on pore function were studied in vivo, by assaying the uptake rate of beta-lactam antibiotics, and in vitro after reconstitution of the purified proteins in lipid bilayer membranes. Some of the point mutations had a significant impact on the channel properties. The substitution R92A produced a 130% increased permeability of the zwitterionic beta-lactam cephaloridine, and the cation selectivity of R92E increased by 70%. The effects of the R90E substitution on channel properties were similar. Most of the point mutations had a minor effect on the voltage gating of the FomA channel, resulting in an increased sensitivity, except for K78E, which showed a decreased sensitivity. The latter mutation had no effect on cation selectivity, but the K78A substitution improved the uptake rate of cephaloridine. The results presented here indicate that arginines 90 and 92 are probably part of the constriction zone of the FomA porin, and lysine 78 and arginines 115 and 117 are probably in close proximity to this region as well.

Interaction of the N-terminus of chicken skeletal essential light chain 1 with F-actin

Skeletal myosin has two isoforms of the essential light chain (ELC), called LC1 and LC3, which differ only in their N-terminal amino acid sequence. The LC1 has 41 additional residues containing seven pairs of Ala-Pro, which form an elongated structure, and two pairs of lysines located near the N-terminus. When myosin subfragment-1 (S1) binds to actin, these lysines may interact with the C-terminus of actin and be responsible for the isoform specific properties of myosin. Here we employ cross-linking to identify the LC1 residues that are in contact with actin. S1 was reconstituted with various LC1 mutants and reacted with the zero-length cross-linker 1-ethyl-3-[3-dimethyl-aminopropyl]-carbodiimide (EDC). Cross-linking occurred only when actin was in molar excess over S1. Wild-type LC1 could be cross-linked through the terminal alpha-NH2 group, as well as via the two pairs of lysines. In a mutant ELC, where the lysines were deleted but two arginines were introduced near the N-terminus, the light chain could still be cross-linked via the terminal alpha-NH2 group. When the charge was reduced in the N-terminal region while retaining the Ala-Pro rich region, the mutant could not be cross-linked. These results suggest that as long as the N-terminus contains charged residues and an Ala-Pro rich extension, the binding between LC1 and actin can occur.

Specificity of the tryptophan depletion method

Thirteen healthy subjects were subjected to tryptophan (TRP) depletion, lysine (LYS) depletion, and a placebo condition in a double blind cross-over study. The aim of the study was to test the specificity of psychological effects induced by TRP depletion. Subjects ingested a 100 g amino acid mixture with or without TRP or LYS. Six hours later, plasma TRP levels had decreased by 77% in the TRP depletion test and LYS levels by 51% in the LYS depletion condition. After 6 h of TRP depletion, subjects reported significantly more tiredness and lowering of mood, compared to subjects in the placebo group, and memory performance declined. After 6 h of LYS depletion, no significant differences in mood and memory compared to placebo were found. We conclude that the effects of TRP depletion on mood and memory are specific for the depletion of TRP and are not caused by the depletion of an amino acid per se. This supports the hypothesis that TRP depletion affects brain serotonin metabolism and not only brain protein metabolism in general.

The central lysine in the P-loop motif of the Escherichia coli DnaA protein is essential for initiating DNA replication from the chromosomal origin, oriC, and the F factor origin, oriS, but is dispensable for initiation from the P1 plasmid origin, oriR

The Escherichia coli DnaA protein is essential for initiation of DNA replication from the chromosomal origin, oriC, and from certain plasmid origins such as oriR of P1, oriS of F, and ori of pSCS101. The DnaA protein binds ATP with high affinity and contains a P-loop motif assumed to be the binding site. Three mutations in the E. coli dnaA gene were constructed by oligonucleotide-directed mutagenesis that changed amino acids in the P-loop. A DnaA protein, K178T, in which the central lysine was changed to the smaller amino acid threonine, was able to initiate DNA replication from P1 oriR, but was unable to initiate replication from E. coli oriC or F oriS in vivo. Mutant and wild-type DnaA proteins were overexpressed, partially purified, and tested for replication activity in vitro. The K178T DnaA protein could initiate replication from oriR, although with a decreased activity compared to the wild-type DnaA protein. No replication activity was detected for this mutant protein from oriC. The different responses of the oriR and oriC replicons to the K178T DnaA protein indicate that the role of DnaA is different in the two systems.

[Relationship between vascular endothelial growth factors and advanced glycation end products in the human vitreous]

The relation between vascular endothelial growth factor (VEGF) and advanced glycation end product (AGE) is considered a primary factor in the development of diabetic retinopathy. Regarding the relation between VEGF in the vitreous body and pentosidine, an AGE, we compared a diabetic (DM) group (7 eyes) with a nondiabetic (nonDM) group (7 eyes), and investigated the correlation between VEGF and pentosidine by calculating the correlation coefficient. Levels of both VEGF and pentosidine were significantly higher in the DM group (p < 0.01, p < 0.05), and a positive correlation was observed between the levels of VEGF and pentosidine (r = 0.770, p < 0.001). Since it is clear that there is a relation between VEGF and pentosidine in the vitreous body, we speculated that AGE is related to the secretion of cytokine in patients with diabetic retinopathy, and that it affects the development and progression of the disease.

Step-wise DNA relaxation and decatenation by NaeI-43K

Nae I protein was originally isolated for its restriction endonuclease properties. Nae I was later discovered to either relax or cleave supercoiled DNA, depending upon whether Nae I position 43 contains a lysine (43K) or leucine (43L) respectively. Nae I-43K DNA relaxation activity appears to be the product of coupling separate endonuclease and ligase domains within the same polypeptide. Whereas Nae I relaxes supercoiled DNA like a topoisomerase, even forming a transient covalent intermediate with the substrate DNA, Nae I shows no obvious sequence similarity to the topoisomerases. To further characterize the topoisomerase activity of Nae I, we report here that Nae I-43K changes the linking number of a single negatively supercoiled topoisomer of pBR322 by units of one and therefore is a type I topoisomerase. Positively supercoiled pBR322 was resistant to Nae I-43K. At low salt concentration Nae I-43K was processive; non-saturating amounts of enzyme relaxed a fraction of the DNA. At high salt concentration the same non-saturating amounts of Nae I-43K partially relaxed all the DNA in a step-wise fashion to give a Gaussian distribution of topoisomers, demonstrating a switch from a processive to a distributive mode of action. Nae I-43K decatenated kinetoplast DNA containing nicked circles, implying that Nae I-43K can cleave opposite a nick. The products of the reaction are decatenated nicked circles under both processive and distributive conditions. The behavior of Nae I-43K is consistent with that of a prokaryotic type I topoisomerase.