Influence of the g− conformation of Ser and Thr on the structure of transmembrane helices

In order to study the influence of Ser and Thr on the structure of transmembrane helices we have analyzed a database of helix stretches extracted from crystal structures of membrane proteins and an ensemble of model helices generated by molecular dynamics simulations. Both complementary analyses show that Ser and Thr in the g? conformation induce and/or stabilize a structural distortion in the helix backbone. Using quantum mechanical calculations, we have attributed this effect to the electrostatic repulsion between the side chain Oγ atom of Ser and Thr and the backbone carbonyl oxygen at position i ? 3. In order to minimize the repulsive force between these negatively charged oxygens, there is a modest increase of the helix bend angle as well as a local opening of the helix turn preceding Ser/Thr. This small distortion can be amplified through the helix, resulting in a significant displacement of the residues located at the other side of the helix. The crystal structures of aquaporin Z and the β₂-adrenergic receptor are used to illustrate these effects. Ser/Thr-induced structural distortions can be implicated in processes as diverse as ligand recognition, protein function and protein folding.     

Influence of the protein conformation on the interaction between α-lactalbumin and dimyristoylphosphatidylcholine vesicles

α-Lactalbumin is a globular protein containing helical regions with highly amphiphathic character. In this work, the interaction between bovine α-lactalbumin and sonicated dimyristoylphosphatidylcholine vesicles has been compared in different circumstances which influence the protein conformation i.e., pH, ionic strength, decalcification, guanidine hydrochloride denaturation. Above the isoelectric point the interaction is mainly electrostatic; improved electrostatic interaction results in better contact with the apolar lipid phase. Below the isoelectric point, hydrophobic forces dominate the interaction and the vesicles are solubilized. The mode of interaction is not determined to a great extent by the demetallization of the protein. However, by a more explicit unfolding of the globular structure with guanidine hydrochloride, micellar complexes can be formed with the lipid, even at neutral pH. From this study it is obvious that the presence or capability for formation of helices with high amphipathic character is not a sufficient condition for lipid solubilization by a globular protein. Also, the capability of a globular protein to unfold its tertiary structure seems to be a prerequisite for its capability to lipid solubilization.     

Studies on the chemical constituents of Kalimeris indica(Ⅱ)

采用冷渗漉提取的方法提取马兰的化学成分.经硅胶柱色谱和Sephadex LH-20进行分离纯化,通过理化方法和波谱数据分析进行结构鉴定.从80%乙醇冷渗漉提取物的水不溶物中分离并鉴定了12个化合物,分别为正十六烷酸(1)、6-羟基-桉烷-4(14)-烯(2)、β-谷甾醇(3)、α-菠菜甾醇(4)、香草醛(5)、β-20(21),24-二烯-达玛烷-3-酮(6)、豆甾醇(7)、木栓酮(8)、羽扇豆酮(9)、α-香树脂醇(10)、表木栓醇(11)、神经酰胺(12).化合物2、6、9、12均为首次从该种植物中分得.     

Topography and chemical reactivity of the active–inactive transition-sensitive SH-group in the mitochondrial NADH:ubiquinone oxidoreductase (Complex I)

The spatial arrangement and chemical reactivity of the activation-dependent thiol in the mitochondrial Complex I was studied using the membrane penetrating N-ethylmaleimide (NEM) and non-penetrating anionic 5,5′-dithiobis-(2-nitrobenzoate) (DTNB) as the specific inhibitors of the enzyme in mitochondria and inside-out submitochondrial particles (SMP). Both NEM and DTNB rapidly inhibited the de-activated Complex I in SMP. In mitochondria NEM caused rapid inhibition of Complex I, whereas the enzyme activity was insensitive to DTNB. In the presence of the channel-forming antibiotic alamethicin, mitochondrial Complex I became sensitive to DTNB. Neither active nor de-activated Complex I in SMP was inhibited by oxidized glutathione (10 mM, pH 8.0, 75 min). The data suggest that the active/de-active transition sulfhydryl group of Complex I which is sensitive to inhibition by NEM is located at the inner membrane–matrix interface. These data include the sidedness dependency of inhibition, effect of pH, ionic strength, and membrane bilayer modification on enzyme reactivity towards DTNB and its neutral analogue.     

Influence of nonionic surfactants and hydroxypropyl-β-cyclodextrin on the biodegradation of nitrobenzene

This paper investigates the effect of two nonionic surfactants (Tween 80 and Triton X-100) and hydroxypropyl--cyclodextrin (HP--CD) on the biodegradation of nitrobenzene (NB) by Acinetobacter sp. in liquid cultures at different dosages as well as the fate of both surfactants. When the initial concentration of NB was about 400 mg/l, neither Tween 80 nor HP--CD had any effect on the degradation of NB. However, Triton X-100 retarded the full removal of NB and the bacterial growth entering the stationary phase. While the initial concentration of NB was increased to about 850 mg/l, they all significantly enhanced the extent and rate of biodegradation if they were added at concentrations above 2000 mg/l. HP--CD could not be utilized by Acinetobacter sp. as the sole carbon source whereas both surfactants could, but no surfactant depletion was observed during the biodegradation of NB. So the rapid bacterial growth observed in the presence of each additive should be attributed to the rapid metabolism of NB. Both surfactants would promote the degradation of NB more than HP--CD would do if their dosages were increased properly.     

Influence of Mahanarva fimbriolata (Stål) (Hemiptera: Cercopidae) injury on the quality of cane juice

Mahanarva fimbriolata (St?l) is an important pest in Latin America and causes significant reduction in sugarcane productivity. There is no information regarding the effect of this pest on the quality of cane juice used for sugar and alcohol production. This work aimed at evaluating the quality of sugarcane juice from plants attacked by spittlebugs. The experiment was arranged in a completely randomized design with 15 replications, and comprised two treatments: control and chemical treatment with thiamethoxam. An average of 9.2 +/- 4.44 spittlebug nymphs m-1 were found in the plots prior to insecticide application. Nymphs were counted 18, 35, 55, and 82 days after the initial sampling (december/2003). During the mid growing season (July 2004), the juice was extracted from stalks and analyzed for Brix, Pol, RS, pH, fiber, purity, TRS, dextran, starch, and total phenolic compounds. Stalk yield was also measured. Chemical treatment was efficient in reducing spittlebug population, and elevated both stalk yield and juice pH. The accumulated infestation expressed as insect-days was significantly and negatively correlated to yield, Pol, pH, and purity. The concentration of phenolic compounds increased with pest infestation, while dextran and starch levels were not affected. The infestation of 2.4 and 7.3 nymphs m-1 day-1 caused reductions of 8.3% and 29.8% in yield; 1.9% and 5.8% in Pol; 0.4% and 1.1% in pH and 0.4% and 1.2% in purity, respectively, in comparison to areas where the pest population was extremely low (< 0.1 nymphs m-1).     

Reversible protection of Cys-93(β) by PEG alters the structural and functional properties of the PEGylated hemoglobin

As a potential hemoglobin (Hb)-based oxygen carrier (HBOC), the PEGylated Hb has received much attention for its non-nephrotoxicity. However, PEGylation can adversely alter the structural and functional properties of Hb. The site of PEGylation is an important factor to determine the structure and function of the PEGylated Hb. Thus, protection of some sensitive residues of Hb from PEGylation is of great significance to develop the PEGylated Hb as HBOC. Here, Cys-93(β) of Hb was conjugated with 20 kDa polyethylene glycol (PEG20K) through hydrazone and disulfide bonds. Then, the conjugate was modified with PEG5K succinimidyl carbonate (PEG5K-SC) using acylation chemistry, followed by removal of PEG20K Hb with hydrazone hydrolysis and disulfide reduction. Reversible conjugation of PEG20K at Cys-93(β) can protect Lys-95(β), Val-1(α) and Lys-16(α) of Hb from PEGylation with PEG5K-SC. The autoxidation rate, oxygen affinity, structural perturbation and tetramer instability of the PEGylated Hb were significantly decreased upon protection with PEG20K. The present study is expected to improve the efficacy of the PEGylated Hb as an oxygen therapeutic.     

On the conformation of proteins: The handedness of the β-strand-α-helix-β-strand unit

The β-strand-α-helix-β-strand unit consists of two parallel, but not necessarily adjacent, β-strands which lie in a β-pleated sheet and are connected by one or more α-helices. This unit, which occurs in 17 functionally different globular proteins, may adopt a right- or a left-handed conformation. An analysis of the distribution shows that 57 out of the 58 units are right-handed. If the unit had no right-handed preference, the probability of observing such a distribution by chance is 10^?16. This may be explained in terms of the twist of the β-sheet which is shown to favour a right-handed unit, as otherwise steric hindrance occurs in the loop regions. We show that the right-handed strand-helix-strand unit determines the sense of the super-secondary structure found in the dehydrogenases and of related folds found in other structures. The evolutionary relationships between proteins containing this unit are re-evaluated in terms of this preference. The high probability that the unit will fold with a right-handed conformation has implications for the prediction of tertiary structure.     

Influence of the Recombinant Heat Shock Protein 90β (HSP90β) on the Wound Healing Rate in Mice

Biology Bulletin - It is known that the alpha isoform of heat shock protein 90 (HSP90α) plays an important role in wound healing. HSP90α has a stimulating effect on migration and invasion...     

Influence of the Environment on the Structure of the European Badger (Meles meles) (Mustelidae,Mammalia) Family Groups on the Oka–Don Plain

Biology Bulletin - Abstract—Diverse variants of the social organization of European badger populations (Meles meles L.) are observed in different parts of the living range. This paper...     

Spectrophotometric, electron paramagnetic resonance and oxygen binding studies on the hemoglobin from the marine polychaete Perinereis aibuhitensis (Grübe): comparative physiology of hemoglobin

The physicochemical properties of giant hemoglobin (Hb) of the marine polychaete Perinereis aibuhitensis were extensively studied and the following results were obtained. (1) Light absorption spectra of the oxy, deoxy, CO, met, and cyanomet derivatives were similar to those for human Hb, except for a somewhat peculiar shape and pH-dependence of the met derivative, and high absorbance values around 277 nm for all these derivatives of Perinereis Hb. Abnormal pH dependence for the met derivative was confirmed by powder electron parmagnetic resonance (EPR) spectroscopy, which revealed that a water molecule does not coordinate to the heme iron as a sixth ligand. The high absorption around 277 nm is indicative of the existence of some non-heme polypeptide chains and/or a high content of aromatic residues in the molecule. (2) UV difference and derivative spectra revealed oxygenation-induced conformational changes in the protein moiety that are related to the degree of cooperativity. (3) The EPR spectrum for the nitrosyl derivative showed well-resolved triplet-triplet splittings due to 14N, indicating that the proximal residue is probably a histidine. (4) The oxygen affinity and cooperativity of this Hb were pH-dependent. Mg2+ markedly increased the oxygen affinity, the Bohr effect, and the cooperativity, which was maximal at physiological pH. CO2 and anions such as 2,3-diphosphoglycerate and inositol hexaphosphate had no effect on the oxygenation properties. Thus, different from vertebrate Hb, the oxygen-binding properties of this Hb are regulated by divalent cations which bind preferentially to the oxy form. The low temperature-dependence of oxygen affinity observed for this Hb is a sign of adaptation to the environment by this poikilothermic organism. (5) By using a graphic method, the minimal functional unit that preserves the full cooperativity (allosteric unit) was inferred to be the one containing 6 heme groups and its significance is discussed in connection with the structural hierarchy of the molecule.     

Exploration of the mechanism for LPFFD inhibiting the formation of β-sheet conformation of Aβ(1–42) in water

The main component of senile plaques found in AD brain is amyloid β-peptide (Aβ), and the neurotoxicity and aggregation of Aβ are associated with the formation of β-sheet structure. Experimentally, beta sheet breaker (BSB) peptide fragment Leu-Pro-Phe-Phe-Asp (LPFFD) can combine with Aβ, which can inhibit the aggregation of Aβ. In order to explore why LPFFD can inhibit the formation of β-sheet conformation of Aβ at atomic level, first, molecular docking is performed to obtain the binding sites of LPFFD on the Aβ(1–42) (LPFFD/Aβ(1–42)), which is taken as the initial conformation for MD simulations. Then, MD simulations on LPFFD/Aβ(1–42) in water are carried out. The results demonstrate that LPFFD can inhibit the conformational transition from α-helix to β-sheet structure for the C-terminus of Aβ(1–42), which may be attributed to the hydrophobicity decreasing of C-terminus residues of Aβ(1–42) and formation probability decreasing of the salt bridge Asp23-Lys28 in the presence of LPFFD.     

Regio and stereospecific synthesis of 11β-substituted 19-norsteroids: Influence of 11β-substitution on progesterone receptor affinity — (1)

The convenient synthesis of a series of lie-substituted 17-ethynyl-17β-hydroxy-4, 9-estradien-3-ones and their corresponding estradiols is reported. Relative affinities for the progestin and estrogen receptors showed very specific interactions between the progesterone receptor and the unsaturated substituents in the 11β-position of the steroid.     

Hemoglobins with multiple reactive sulphydryl groups: The reaction of dog hemoglobin with 5,5′-dithiobis (2-nitrobenzoate)

Dog hemoglobin has four sulphydryl groups per (tetramer) molecule located at the G18(111)a and F9(93)β positions. The two sulphydryls at the G18(111)a positions are unreactive toward nonmercurial sulphydryl reagents, but those at the F9(93)β positions are reactive toward these reagents. We have studied the kinetics of the reaction of dog hemoglobin with 5,5′-dithiobis (2-nitrobenzoic acid) as a function ofpH. At allpH values studied, the reaction is kinetically monophasic. Quantitative analysis of thepH dependence of the apparent second-order rate constant shows that two ionizable groups are linked to the reaction of the sulphydryl group. TheirpK _a values are 5.57 and 9.0. These values are assigned to HisHC3(146)β and to the CysF9(93)β sulphydryl. We find that dog carbonmonoxyhemoglobin is significantly—almost an order of magnitude—less reactive than the aquomet, azidomet, and oxy derivatives. This result may be due to a greater tendency (at acidpH) for the salt bridge between HisHC3(146)β and AspFG1(94)β to form in the carbonmonoxy than in the other derivatives. Formation of this salt bridge is known to hinder access to the CysF9(93)β sulphydryl [Perutz, M. F. (1970),Nature 228, 734–739].     

Hemoglobin binding with haptoglobin: Delineation of the haptoglobin binding site on the α-chain of human hemoglobin

Previous studies from this laboratory employing a comprehensive synthetic overlapping peptide strategy showed that the -chain of human hemoglobin (Hb) contains a single haptoglobin (HP) binding region residing within residues 121–135. The present study describes a precise delineation of this Hp-binding site on the -chain. Two overlapping peptides (111–125 and 121–135) spanning this region and a panel of five peptides decreasing at the C-terminal from residue 135 by decrements of two residues (119–135, 119–133, 119–131, 119–129, and 119–127) were synthesized, purified, and characterized. Quantitative radiometric titration of¹²⁵I-labeled human HP (type 2-1) with adsorbents of each of these synthetic peptides showed that the peptide 119–127 retained a Hp-binding activity equivalent to that of peptide 121–135. This finding indicated that Lys-127 marked the C-terminal boundary of the binding site. Another panel of eight peptides was then synthesized, which had their C-terminus fixed at Lys-127 and increased at the N-terminus by one-residue increments from residue 122 up to residue 115 (122–127, 121–127, 120–127, 119–127, 118–127, 117–127, 116–127, and 115–127). The binding of¹²⁵I-Hp to adsorbents of these peptides demonstrated that the N-terminal boundary of the site did not extend beyond Valine 121. It is, therefore, concluded that the Hp-binding site on the -chain of human Hb comprises residues 121–127.     

Primary structure of the hemoglobin α-chain of rose-ringed parakeet (Psittacula krameri)

The structure of the hernoglobin α-chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete α-chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian α-chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.     

Influence of GABA(A) Receptor α Subunit Isoforms on the Benzodiazepine Binding Site

Classical benzodiazepines, such as diazepam, interact with α_xβ₂γ₂ GABA_A receptors, x = 1, 2, 3, 5 and modulate their function. Modulation of different receptor isoforms probably results in selective behavioural effects as sedation and anxiolysis. Knowledge of differences in the structure of the binding pocket in different receptor isoforms is of interest for the generation of isoform-specific ligands. We studied here the interaction of the covalently reacting diazepam analogue 3-NCS with α₁S204Cβ₂γ₂, α₁S205Cβ₂γ₂ and α₁T206Cβ₂γ₂ and with receptors containing the homologous mutations in α₂β₂γ₂, α₃β₂γ₂, α₅β_1/2γ₂ and α₆β₂γ₂. The interaction was studied using radioactive ligand binding and at the functional level using electrophysiological techniques. Both strategies gave overlapping results. Our data allow conclusions about the relative apposition of α₁S204Cβ₂γ₂, α₁S205Cβ₂γ₂ and α₁T206Cβ₂γ₂ and homologous positions in α₂, α₃, α₅ and α₆ with C-atom adjacent to the keto-group in diazepam. Together with similar data on the C-atom carrying Cl in diazepam, they indicate that the architecture of the binding site for benzodiazepines differs in each GABA_A receptor isoform α₁β₂γ₂, α₂β₂γ₂, α₃β₂γ₂, α₅β_1/2γ₂ and α₆β₂γ₂.     

Polysaccharide conformation: Effect of side-group geometry on four diequatorially (1→4)-linked polysaccharides

A systematic approach to the stereochemical aspect of the conformational analysis of the polysaccharides cellulose, polyglucuronic acid, mannan, and polymannuronic acid has been undertaken. A more-exact treatment was given of the main side-groups, and differences from the previously used approximate method were found. A comparison of the flexibility of the four polysaccharides indicates that the polyuronic acids are more flexible than the corresponding glycans and that the mannopyranoses are more flexible than the glucopyranoses. The freedom of rotation of the main side-groups in the conformation of lowest overall potential energy was investigated and found to be restricted, but not sufficiently to cause localization.     

Influence of glucose-templated proline mimetics on the β-turn conformation of the peptide fragment Ac-Leu-d-Phe-Pro-Val-NMe2 found in Gramicidin S

The synthesis of tetrapeptide-based β-turn mimetics containing spirocyclic glucose-templated 3-hydroxyproline hybrids Glc3′(S)-5′(R)(CH₂OH)HypH and Glc3′(S)-5′(S)(CH₂OH)HypH as proline mimetics is presented. NMR-based conformational analysis of Ac-Leu-d-Phe-[Glc3′(S)-5′(R)(CH₂OH)HypH]-Val-NMe₂ and Ac-Leu-d-Phe-[Glc3′(S)-5′(S)(CH₂OH)HypH]-Val-NMe₂ demonstrates the presence of β-turn conformations. Different turn structures were observed by changing the stereochemistry at 5′-position of Glc3′(S)-5′(R)(CH₂OH)HypH. The major prolyl amide cis isomer of glucose-protected tetrapeptide Ac-Leu-d-Phe-[Glc(MOM)₄3′(S)-5′(R)(CH₂OMOM)HypH]-Val-NMe₂11 and glucose unprotected Ac-Leu-d-Phe-[Glc3′(S)-5′(R)(CH₂OH)HypH]-Val-NMe₂13 forms a type VI β-turn conformation. In contrast, the major prolyl amide trans rotamer of tetrapeptide Ac-Leu-d-Phe-[Glc(MOM)₄3′(S)-5′(S)(CH₂OMOM)HypH]-Val-NMe₂12 conserves a similar β-turn conformation as the Gramicidin S-based peptide fragment Ac-Leu-d-Phe-Pro-Val-NMe₂16.