Amino acids of ricin and its polypeptides

Ricin and its corresponding polypeptides (A & B chain) were purified from castor seed. The molecular weight of ricin subunits were 29,000 and 28,000 daltons. The amino acids in ricin determined were Asp45 The22 Ser40 Glu53 Cys4 Gly96 His5 Ile21 Leu33 Lys20 Met4 Phe13 Pro37 Tyr11 Ala45 Val23 Arg20 indicating that ricin contains approximately 516 amino acid residues. The amino acids of the two subunits of ricin A and B chains were Asp23 The12 Ser21 Glu29 Cys2 Gly48 His3 Ile12, Leu17 Lys10 Met2 Phe6 Pro17 Tyr7 Ala35 Val13 Arg13 while in B chain the amino acids were Asp22 The10 Ser19 Glu25 Cys2 Gly47 His1 Ile10, Leu15 Lys11 Met1 Phe7 Pro6 Tyr5 Ala32Val11 Arg10. The total helical content of ricin came around 53.6% which is a new observation.     

Control of the stability of Hydrogenobacter thermophilus cytochrome C(552) through alteration of the basicity of the N-terminal amino group of the polypeptide chain

In the denatured state of Hydrogenobacter thermophilus cytochrome c(552) (HT), the N-terminal amino group of the polypeptide chain is coordinated to the heme Fe in place of the axial Met, the His-N(term) form being formed [Tai, H., Munegumi, T., Yamamoto, Y. Inorg. Chem. 2009, 48, 331-338]. Since the His-N(term) form can be considered as an ordered residual structure in the denatured protein, its stability significantly influences the energy of the denatured state. In this study, the His-N(term) forms of the wild-type HT and its mutants possessing a series of amino acid residues at the N-terminal, such as N1D, N1E, and N1G, have been characterized to elucidate the physicochemical properties of the N-terminal residue responsible for the control of the thermodynamic stability of the His-N(term) form. The study revealed that the thermodynamic stability of the His-N(term) form depends highly on the basicity of the N-terminal amino group of the polypeptide chain in such a manner that an increase in the pK(a) value of the N-terminal amino group by 1 unit results in stabilization of the bond between heme Fe and the N-terminal amino group (Fe-N(term) bond) in the His-N(term) form by ～4 kJ mol(-1). The empirical hard and soft acid and base principle could account for the observed relationship between the pK(a) value of the N-terminal amino group and the stability of the Fe-N(term) bond in the His-N(term) form. In addition, the study demonstrated that the overall stability of the protein can be manipulated through the energy of the denatured protein by changing the thermodynamic stability of the His-N(term) form. Consequently, the overall stability of the protein has been shown to be controlled through alteration of the basicity of the N-terminal amino group of the polypeptide chain. These findings provide new insights into the stabilizing interactions in the denatured protein, which are relevant as to characterization of the protein stability and folding.     

EPR and optical spectroscopic studies of Met80X mutants of yeast ferricytochrome c. Models for intermediates in the alkaline transition

The ferric forms of Met80X mutants of yeast iso-1-cytochrome c (X = Ala, Ser, Asp, and Glu) display EPR and optical spectra that are strongly pH dependent. At low pH values (pH approximately 5) the sixth coordination sites are filled by H(2)O that, on elevating the pH, is replaced by OH(-) in the cases of Met80Ala and -Ser (pK approximately 5.6 and 5.9, respectively) and by a lysine amino group in the cases of Met80Asp and -Glu (pK approximately 9.3 and 11.6, respectively). The ligand sets and the pK values of the transitions are rationalized in terms of the structure of the heme pocket, and a possible mechanism of the "trigger" in the alkaline transition of the native protein is suggested.     

NMR investigation of the electrostatic effect in binding of a neuropeptide, achatin-I, to phosphatidylcholine bilayers

Achatin-I (Gly1-d-Phe2-Ala3-Asp4), known as a neuropeptide containing a d-amino acid, binds to the surface of a zwitterionic phosphatidylcholine (PC) membrane only when the peptide N-terminal amino group is in the ionized state, NH3+ (Kimura, T.; Okamura, E.; Matubayasi, N.; Asami, K.; Nakahara, M. Biophys. J. 2004, 87, 375-385). To gain mechanistic insights into how the binding equilibrium is delicately controlled by the ionization state of the N-terminal amino group, peptide-lipid binding interactions are investigated by selectively enriched 15N (at the N-terminus) and natural-abundance 13C NMR spectroscopy. Upon binding to the PC membrane, the 15N NMR of the N-terminal NH3(+) shifts upfield. This observation supports a mechanism that the role of the N-terminal NH3(+) in stabilizing the binding state is through electrostatic attraction with a headgroup negative charge, i.e., PO4(-). Interestingly, when the side chain beta-carboxyl group in Asp4 is deionized at acidic pH, the 15N signal of the N-terminal NH3(+) exhibits no significant chemical-shift change upon membrane binding of achatin-I. The Asp4 side chain thus regulates efficiency of the electrostatic binding between the peptide N-terminal NH3(+) and the lipid headgroup PO4(-). 13C chemical shifts in the hydrophobic D-Phe2 residue are largely perturbed upon membrane binding, in the case where the side chain beta-CO2(-) in Asp4 is deionized; the deionization of Asp4 beta-CO2(-) increases the net hydrophobicity of achatin-I with a reduction of both the electrostatic hydration and the electrostatic attraction with the headgroup N(CH3)3(+) in the most superficial region of the PC membrane, resulting in deeper anchoring of the phenyl ring. Hence, the electrostatic effect of the side chain beta-CO2(-) in Asp4 floats achatin-I on the PC membrane surface, and the binding equilibrium is sensitively controlled by the ionization state of the N-terminal NH3(+).     

Further studies on the fragmentation of protonated ions of peptides containing aspartic acid, glutamic acid, cysteine sulfinic acid, and cysteine sulfonic acid

Here we examined the fragmentation, on a quadrupole ion-trap mass spectrometer, of the protonated ions of a group of peptides containing one arginine and two different acidic amino acids, one being aspartic acid (Asp) or glutamic acid (Glu) and the other being cysteine sulfinic acid [C(SO2H)] or cysteine sulfonic acid [C(SO3H)]. Our results showed that, upon collisional activation, the cleavage of the peptide bond C-terminal to C(SO2H) is much more facile than that of the peptide bond C-terminal to Asp, Glu, or C(SO3H). There is no significant difference, however, in susceptibility to cleavage of peptide bonds that are C-terminal to Asp, Glu, and C(SO3H). To understand these experimental observations, we carried out B3LYP/6-31G* density functional theory calculations for a model cleavage reaction of GXG --> b2 + Gly, in which X is Asp, Glu, C(SO2H), or C(SO3H). Our calculation results showed that the cleavage reaction is thermodynamically more favorable when X = C(SO2H) than when X = Asp or C(SO3H). We attributed the less facile cleavage of the amide bond after Glu to that the formation of a six-membered ring b ion for Glu-bearing peptides is kinetically not as favorable as the formation of a five-membered ring b ion for peptides containing the other three acidic amino acids. The results from this study may provide useful tools for peptide sequencing.     

Direct test of the Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins

The Gaussian-chain model for treating residual charge-charge interactions was critically tested by recent experimental pK(a) results for individual Asp, Glu, and His residues in the unfolded drkN SH3 domain. Predicted pK(a)'s were in good agreement with experiment. The clustering of Asp and Glu residues along the sequence was suggested to limit pK(a) shifts and contribute to the folding stability by destabilizing the unfolded state.     

Direct NMR observation and pKa determination of the Asp102 side chain in a serine protease

The pK(a) value of aspartic acid in the catalytic triad of serine proteases has been a pivotal element in essentially every mechanism proposed for these enzymes over the past 40 years, but has, until now, eluded direct determination. Here, we have used the multinuclear 3D-NMR pulse programs HCACO and HCCH-TOCSY to directly identify and study the side-chain resonances of the aspartate and glutamate residues in uniformly (13)C-labeled α-lytic protease. Resonances from four of the six residues were detected and assigned, including that of Asp(102), which is notably the weakest of the four. pH titrations have shown all of the carboxylate (13)C signals to have unusually low pK(a) values: 2.0, 3.2, and 1.7 for Glu(129), Glu(174), and Glu(229), respectively, and an upper limit of 1.5 for Asp(102). The multiple H-bonds to Asp(102), long known from X-ray crystal studies, probably account for its unusually low pK(a) value through preferential stabilization of its anionic form. These H-bonds probably also contribute to the weakness of the NMR resonances of Asp(102) by restricting its mobility. The Asp(102)(13)C(γ) atom responds to the ionization of His(57) in the resting enzyme and to the inhibitor-derived oxyanion in a chloromethyl ketone complex, observations that strongly support the assignment. The low pK(a) value of Asp(102) would appear to be incompatible with mechanisms involving strong Asp(102)-His(57) H-bonds or high pK(a) values, but is compatible with mechanisms involving normal Asp(102)-His(57) H-bonds and moving His(57) imidazole rings, such as the reaction-driven ring flip.     

Quantification of taurine and amino acids in mice single fibrosarcoma cell by microchip electrophoresis coupled with chemiluminescence detection

A method based on MCE coupled with chemiluminescence (CL) detection was developed for the determination of taurine (Tau) and amino acids including alanine (Ala), glycine (Gly), tryptophan (Trp), glutamic acid (Glu) and aspartic acid (Asp) present in mice single fibrosarcoma (S180) cells. Cell injection, loading, cytolysis, electrophoretic separation and CL detection were integrated onto a simple double‐T microfluidic chip. The intracellular constituents were electrophoretically separated within 150 s. The CL detection was based on the enhancement effects of Tau and amino acids on the CL reaction of luminol with H₂O₂ and Cu²⁺. The average amounts of Tau, Trp, Gly, Ala, Glu and Asp in per S180 cell from a cell population were 4.73, 1.23, 2.65, 1.94, 1.61 and 1.99 fmol. Ten S180 cells were analyzed, and the contents of Tau, Trp, Gly, Ala, Glu and Asp in mice single S180 cells were found to be in the range of 1.78–8.84, 0.95–2.31, 1.08–6.87, 1.03–4.05, 0.84–2.61 and 0.82–3.68 fmol, respectively. This work demonstrates that MCE coupled with CL detection is a useful analytical tool that is simple, quick and highly sensitive for single‐cell analysis.     

Unraveling A Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

When the major ampulate spidroins (MaSp1) are called upon to form spider dragline silk, one of nature's most amazing materials, a small drop in pH must occur. Using a state-of-the-art simulation technique, constant pH molecular dynamics, we discovered a few residues that respond to the pH signal in the dimerization of the N-terminal domain (NTD) of MaSp1 which is an integral step in the fiber assembly. At neutral pH the deprotonation of Glu79 and Glu119 leads to water penetration and structural changes at the monomer-monomer binding interface. At strongly acidic pH, the protonation of Asp39 and Asp40 weakens the electrostatic attraction between the monomers. Thus, we propose a "trap-and-trigger" mechanism whereby the intermolecular salt-bridges at physiologically relevant pH conditions always act as a stabilizing "trap" favoring dimerization. As pH is lowered to about 6, Glu79 and Glu119 become protonated, triggering the dimerization and subsequent silk formation. We speculate that this type of mechanism is operative in many other pH-sensitive biological processes.     

Value of high-performance liquid chromatographic analysis of amino acids in the determination of Panax ginseng radix extract effect in cultured neurons

The present research describes a reversed-phase high-performance liquid chromatographic (RP-HPLC) method that allows the determination of several amino acids in primary cultured cortical neurons of rats. The concentration of amino acids was determined by using pre-column derivatization with dansyl chloride and UV-diode array detection. Data show that Panax ginseng radix extract (GS) can modulate amino acid release in neurons. The levels of glutamate (Glu), aspartate (Asp), gamma-aminobutyric acid (GABA) and glycine (Gly) in the GS-treated groups were higher than in the non-treated groups dose-dependentwise. In this case, Glu and GABA were the most released amino acids (74.43% +/- 0.97 and 88.41% +/- 4.12 at ginseng dose 0.01 mg/ml after 1h from treatment, respectively). The values obtained in the determination of the analytical parameters (linearity, precision, limit of detection and accuracy) confirm the quality of the method. The average recoveries for intra and inter-day assay (n = 5) were 101.18 and 102.38 for Asp, 99.35 and 98.44 for Glu, 99.59 and 99.66 for Gly, and 100.06 and 100.37 for GABA. These data proved that the method yields accurate results, with RSD lower than 2.2%. The precision of the method was estimated on the basis of RSD of six injections at two different concentrations of amino acids. This technique is useful in studying the GS-mediated modulation of the dynamic equilibrium of amino acids and neurotransmission in neurons.     

天花粉蛋白的化学 III:溴化氰降解片段CBa的氨基酸顺序

The results from the study on the separation, purification, amino acid composition and amino acid sequence of CBa, one of the four CNBr degradation fragments of crystalline trichosanthin, are presented. Its amino acid composition is: Asp3, Thr2, Ser2, Hse1, Glu2, Gly2, Ala6, Val1, Tyr3, Phe3, Lys2, Arg1. The sequence of the CBa is Gly-Tyr-Arg-Ala-Gly-Asp-Thr-Ser- Tyr-Phe-Phe-Asn-Glu-Ala-Ser-Ala-Thr-Glu-Ala-Ala-Lys-Tyr-Val- Phe-Lys-Asp-Ala-Hso.     

大鼠服用朱砂后脑内氨基酸类递质含量的变化

研究了朱砂对大鼠脑组织中氨基酸类神经递质含量的影响.将32只Wistar大鼠随机分为低、中、高剂量组和对照组,朱砂灌胃给药14天后,采用高效液相色谱法测定大鼠脑组织中谷氨酸(Glu)、天门冬氨酸(Asp)、甘氨酸(Gly)、γ-氨基丁酸(GABA)和牛磺酸(Tau)的含量,并计算兴奋毒性指数(EI)的变化.与对照组相比较,脑组织中氨基酸类神经递质含量均呈下降趋势,其中Asp和Gly的中、高剂量组差异有统计学意义(P0.05),Tau和GABA的高剂量组有统计学差异(P0.05),Glu和EI所有剂量组均有统计学差异(P0.05).朱砂对氨基酸类神经递质具有一定的抑制作用.     

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all‐atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side‐chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met‐enkephalin (CHO‐Tyr‐Gly‐Gly‐Phe‐Met‐NH₂) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard‐Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H‐Gly‐Tyr‐Asp‐Pro‐Glu‐Thr‐Gly‐Thr‐Trp‐Gly‐OH) reasonably reproduced a native‐like β‐hairpin structure in water although the C‐terminal and side‐chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Probing the formation of stable tertiary structure in a model miniprotein at atomic resolution: determinants of stability of a helical hairpin

The minimal model system to study the basic principles of protein folding is the hairpin. The formation of beta-hairpins, which are the basic components of antiparallel beta-sheets, has been studied extensively in the past decade, but much less is known about helical hairpins. Here, we probe hairpin formation between a polyproline type-II helix and an alpha-helix as present in the natural miniprotein peptide YY (PYY). Both turn sequence and interactions of aromatic side chains from the C-terminal alpha-helix with the pockets formed by N-terminal Pro residues are shown by site-directed mutagenesis and solution NMR spectroscopy in different solvent systems to be important determinants of backbone dynamics and hairpin stability, suggesting a close analogy with some beta-hairpin structures. It is shown that multiple relatively weak contacts between the helices are necessary for the formation of the helical hairpin studied here, whereas the type-I beta-turn acts like a hinge, which through certain single amino acid substitutions is destabilized such that hairpin formation is completely abolished. Denaturation and renaturation of tertiary structure by temperature or cosolvents were probed by measuring changes of chemical shifts. Folding of PYY is both reversible and cooperative as inferred from the sigmoidal denaturation curves displayed by residues at the interface of the helical hairpin. Such miniproteins thus feature an important hallmark of globular proteins and should provide a convenient system to study basic aspects of helical hairpin folding that are complementary to those derived from studies of beta-hairpins.     

Synthesis of Amino Acid‐comprising Sialyltransferase Inhibitors and Their Antimetastatic Activities against Human Breast Cancer Cells

The amino acid‐containing lithocholic acids (LCA) represent a new class of human sialyltransferase (ST) inhibitors. In this study, we have reported their design, synthesis, and inhibitory activity against human STs. Among these derivatives, D ‐Glu‐LCA 7 , L ‐Asp‐L ‐Asp‐LCA 13 , and L ‐Asp‐L ‐Asp‐Gly‐Gly‐LCA 22 with specific amino acid sequence were the most active ones with IC₅₀ values of 2.3–5.6 and 4.2‐6.2 μM toward α‐2,3‐ST and α‐2,6‐ST, respectively. The current study demonstrates that the new class of ST in‐ hibitors inhibit cell migration in breast cancer cells by preventing closure of the wound rather than involv‐ ing a direct antiproliferative effect.     

Determination of neurotransmitters in PC 12 cells by microchip electrophoresis with fluorescence detection

A sensitive fluorescence detection system with an Hg-lamp as the excitation source and a photon counter as the detector for microchip CE (MCE) has been developed. O-Phthaldialdehyde (OPA, lambda(ex) = 340 nm) was employed to label the catecholamine neurotransmitters such as dopamine (DA), norepinephrine (NE), and amino acid neurotransmitters including alanine (Ala), taurine (Tau), glycine (Gly), glutamic acid (Glu), and aspartic acid (Asp). The separation of seven derivatized neurotransmitters was successfully performed in MCE and the detection limits (S/N = 3) for DA, NE, Ala, Tau, Gly, Glu, and Asp were 0.85, 0.49, 0.23, 0.15, 0.13, 0.18, and 0.29 fmol, respectively. The system was then successfully applied for separation and determination of neurotransmitters in rat pheochromocytoma (PC 12) cells, and the average amounts of analyte per cell from a cell population were 2.5 fmol for DA, 3.3 fmol for Ala, 8.2 fmol for Tau, 4.0 fmol for Gly, and 1.9 fmol for Glu, respectively. By single-cell injection mode, electrophoresis separation and quantitative measurement of Glu in individual PC 12 cells was obtained. The average value of Glu per cell from single PC 12 cells analysis was found to be 3.5 +/- 3.1 fmol.     

Theoretical study toward understanding the catalytic mechanism of pyruvate decarboxylase

Density functional calculations are employed to explore the mechanisms of all elementary reaction steps involved in the catalytic cycle of pyruvate decarboxylase (PDC). Different models are constructed for mimicking the involvement of some key residues in a certain step. The effect of the protein framework on the potential energy profiles of active site models is approximately modeled by fixing some freedoms, based on the crystal structure of the PDC enzyme from Saccharomyces cerevisiae (ScPDC). Our calculations confirm that Glu51 is the most important residue in the formation of the ylide and the release of acetaldehyde via the proton relay between Glu51, N1', and the 4'-amino group of thiamine diphosphate. The presence of Glu477 and Asp28 residues makes the decarboxylation of lactylthiamin diphosphate (LThDP) an endothermic process with a significant free energy barrier. The protonation of the alpha-carbanion to form 2-(1-hydroxyethyl)-thiamin diphosphate is found to go through a concerted double proton transfer transition state involving both Asp28 and His115 residues. The final step, acetaldehyde release, is likely to proceed through a concerted transition state involving carbon-carbon bond-breaking and the deprotonation of the alpha-hydroxyl group. The decarboxylation of LThDP and the protonation of the alpha-carbanion are two rate-limiting steps, relative to the facile occurrence of the ylide formation and acetaldehyde release. The catalytic roles of residues Glu51, Glu477, Asp28, and Gly417 in the active site of ScPDC in individual steps elucidated from the present study are in good agreement with those derived from site-directed mutagenesis.     

Analysis of amino acids in human vascular endothelial (ECV-304) cells by microchip electrophoresis with fluorescence detection

A rapid and sensitive method was developed for the analysis of amino acids by microchip electrophoresis with Hg-lamp excitation fluorescence detection. Fluorescein-isothiocyanate (FITC) was chosen to estimate the sensitivity of this system, and the detection limit (S/N = 3) with FITC was 1.7 nM, which showed that the system was sensitive as well as simple. Two derivatizing agents, FITC and ortho-phthalaldehyde (OPA) were employed to label amino acids and were compared in the same fluorescence detection system with an Hg lamp as the excitation source. The separation parameters were optimized in detail. Optimum separation of OPA-labeled amino acids was obtained in less than 200 s with 20 mM borate buffer (pH 9.0) containing 20% acetonitrile and 10 mM beta-cyclodextrin. Detection limits for amino acids (alanine (Ala), taurine (Tau), glycine (Gly), glutamic acid (Glu), and aspartic acid (Asp)) of 0.38-1.0 muM were achieved. The method was successfully applied to analysis of amino acids in human vascular endothelial cells (ECV-304). The average amount of amino acids in single ECV-304 cells is estimated to be 5.84 fmol for Ala, 2.78 fmol for Tau, 1.15 fmol for Gly, 3.10 fmol for Glu, and 1.30 fmol for Asp.     

Synthesis and screening of libraries of synthetic tripodal receptor molecules with three different amino acid or peptide arms: identification of iron binders

A novel selectively deprotectable triazacyclophane scaffold was used for the design and split-mix synthesis of two libraries of solid-phase bound tripodal synthetic receptors possessing three different amino acid or peptidic arms. In the synthesis of the first library, the two outer arms consisted of amino acid Ala, Arg, Asp, Gln, Gly, Lys, Phe, Ser, Tyr, or Val and the middle arm consisted of amino acid Asn, Glu, His, Leu, or Pro. The second library contained amino acid and/or (di)peptide arms. The arms were different in all library members. The first outer arm consisted of amino acid(s) Ala, Arg, Gln, Phe, or Ser, the second outer arm consisted of amino acid(s) Asp, Gly, Lys, Tyr, or Val, and the middle arm consisted of amino acid(s) Asn, Glu, His, Leu, or Pro, leading to a 27 000 member library of synthetic tripodal receptor molecules. In on-bead screening experiments, a remarkable selectivity of some library members for Fe(3+) was observed and decoding of their structures by Edman degradation revealed consensus sequences with structural resemblance to non-heme iron proteins.     

Abnormal levels of seven amino neurotransmitters in depressed rat brain and determination by HPLC‐FLD

The determination of amino acids with actions like neurotransmitters or modulators has been increasingly important for diagnosis in many neuropsychiatric diseases. A rapid and simple high‐performance liquid chromatography with fluorescence detection method was developed for simultaneous determination of seven amino acids: aspartate (Asp), glutamate (Glu), serine (Ser), glutamine (Gln), glycine (Gly), taurine (Tau) and γ‐aminobutyric` acid (GABA). Homoserine was used as an internal standard. The analysis was performed on a BDS column with methanol and 50 mm sodium acetate solution (pH 6.5) using a simple gradient elution. Several parameters of the developed method were validated including linearity, accuracy, precision, extraction recovery and stability, which were within the acceptable range. The method was successfully applied to determination of real samples: hippocampus and cortex in depressed rats exposed to chronically unpredictable stress in order to study if there existed differences in the seven amino acids levels between depressed rats and control. The results showed that Asp, Gly, Tau and GABA significantly decreased with increasing Gln in the hippocampus of depressed rats, compared with that of the control group, among which obviously lower level of Asp and higher level of Gln in cortex were observed. The analytical method and the results could be useful for clinical diagnosis and further insight into pathophysiological mechanism of depression.