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.     

Electron capture dissociation product ion abundances at the X amino acid in RAAAA-X-AAAAK peptides correlate with amino acid polarity and radical stability

We present mechanistic studies aimed at improving the understanding of the product ion formation rules in electron capture dissociation (ECD) of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry. In particular, we attempted to quantify the recently reported general correlation of ECD product ion abundance (PIA) with amino acid hydrophobicity. The results obtained on a series of model H-RAAAAXAAAAK-OH peptides confirm a direct correlation of ECD PIA with X amino acid hydrophobicity and polarity. The correlation factor (R) exceeds 0.9 for 12 amino acids (Ile, Val, His, Asn, Asp, Glu, Gln, Ser, Thr, Gly, Cys, and Ala). The deviation of ECD PIA for seven outliers (Pro is not taken into consideration) is explained by their specific radical stabilization properties (Phe, Trp, Tyr, Met, and Leu) and amino acid basicity (Lys, Arg). Phosphorylation of Ser, Thr, and Tyr decreases the efficiency of ECD around phosphorylated residues, as expected. The systematic arrangement of amino acids reported here indicates a possible route toward development of a predictive model for quantitative electron capture/transfer dissociation tandem mass spectrometry, with possible applications in proteomics.     

Effect of side chains on competing pathways for beta-scission reactions of peptide-backbone alkoxyl radicals

High-level quantum chemistry calculations have been carried out to investigate beta-scission reactions of alkoxyl radicals located at the alpha-carbon of a peptide backbone. This type of alkoxyl radical may undergo three possible beta-scission reactions, namely C-C beta-scission of the backbone, C-N beta-scission of the backbone, and C-R beta-scission of the side chain. We find that the rates for the C-C beta-scission reactions are all very fast, with rate constants of the order 10(12) s(-1) that are essentially independent of the side chain. The C-N beta-scission reactions are all slow, with rate constants that range from 10(-0.7) to 10(-4.5) s(-1). The rates of the C-R beta-scission reactions depend on the side chain and range from moderately fast (10(7) s(-1)) to very fast (10(12) s(-1)). The rates of the C-R beta-scission reactions correlate well with the relative stabilities of the resultant side-chain product radicals (*R), as reflected in calculated radical stabilization energies (RSEs). The order of stabilities for the side-chain fragment radicals for the natural amino acids is found to be Ala < Glu < Gln approximately Leu approximately Met approximately Lys approximately Arg < Asp approximately Ile approximately Asn approximately Val < Ser approximately Thr approximately Cys < Phe approximately Tyr approximately His approximately Trp. We predict that for side-chain C-R beta-scission reactions to effectively compete with the backbone C-C beta-scission reactions, the side-chain fragment radicals would generally need an RSE greater than approximately 30 kJ mol(-1). Thus, the residues that may lead to competitive side-chain beta-scission reactions are Ser, Thr, Cys, Phe, Tyr, His, and Trp.     

磷酸三乙胺-乙腈流动相体系反相分离2，4-二硝基氟苯-氨基酸衍生物

从两个方面改进了反相分离2,4-二硝基氟苯-氨基酸衍生物测定氨基酸的分析方法:一是使用高缓冲容量pH 2.75和6.50的磷酸三乙胺-乙腈流动相体系代替醋酸盐/乙腈流动相体系;另一个是强调了衍生反应的操作细节。以含精、丝、天冬、谷、苏、甘、丙、脯、组、蛋、缬、色、苯丙、亮、异亮、赖、酪氨酸注射液为目标试样,对方法进行认证,线性不低于0.9999(对谷氨酸、赖氨酸和酪氨酸不低于0.9998),准确度（回收率）为100±1%,精密度（RSD）低于0.5%,均优于以往的方法。方法适用于在一般液相色谱实验室进行氨基酸注射液和原料药的分析,无需专用氨基酸分析仪。     

Trypsin inhibiting material from Ascaris lumbricoides var. suum. I. Preparation of pure trypsin inhibitors

The purification of a trypsin inhibitor from Ascaris lumbricoides var. suum is described. The electrophoretically pure preparation which inhibits trypsin in a specific manner is a relatively small peptide containing 5 Asp, 4 Thr, 1 Ser, 11 Glu, 6 Pro, 6 Gly, 5 Ala, 2 Val, 10 (Cys)_1/2, 3 Ile, 2 Phe, 7 Lys, 3 Arg and 1 Try.     

Zinc(II) complexes of ubiquitin: speciation, affinity and binding features

Intraneuronal inclusions consisting of hypermetallated, (poly-)ubiquitinated proteins are a hallmark of neurodegeneration. To highlight the possible role played by metal ions in the dysfunction of the ubiquitin-proteasome system, here we report on zinc(II)/ubiquitin binding in terms of affinity constants, speciation, preferential binding sites and effects on protein stability and self-assembly. Potentiometric titrations allowed us to establish that at neutral pH only two species, ZnUb and Zn(2)Ub, are present in solution, in line with ESI-MS data. A change in the diffusion coefficient of ubiquitin was observed by NMR DOSY experiments after addition of Zn(II) ions, and thus indicates metal-promoted formation of protein assemblies. Analysis of (1)H, (15)N, (13)Cα and (13)CO chemical-shift perturbation after equimolar addition of Zn(II) ions to ubiquitin outlined two different metal-binding modes. The first involves a dynamic equilibrium in which zinc(II) is shared between a region including Met1, Gln2, Ile3, Phe4, Thr12, Leu15, Glu16, Val17, Glu18, Ile61 and Gln62 residues, which represent a site already described for copper binding, and a domain comprising Ile23, Glu24, Lys27, Ala28, Gln49, Glu51, Asp52, Arg54 and Thr55 residues. A second looser binding mode is centred on His68. Differential scanning calorimetry evidenced that addition of increasing amounts of Zn(II) ions does not affect protein thermal stability; rather it influences the shape of thermograms because of the increased propensity of ubiquitin to self-associate. The results presented here indicate that Zn(II) ions may interact with specific regions of ubiquitin and promote protein-protein contacts.     

Translational diffusion constants of the amino acids: measurement by NMR and their use in modeling the transport of peptides

In this work, the translational self-diffusion constants, DT's, of 12 amino acids (Ala, Arg, Asn, Asp, Cys, Glu, His, Ile, Lys, Met, Phe, and Ser) are measured by field gradient NMR and extrapolated to infinite dilution. The experiments were carried out in D2O at 298 K at pD approximately =3.5 in 50 mM sodium phosphate buffer. Of these 12 amino acids, 6 are being reported for the first time (Asp, Cys, Glu, His, Lys, and Met) and the remaining 6 (Ala, Arg, Asn, Ile, Phe, and Ser) are compared with DT's from the literature. When corrected for differences in solvent viscosity and temperature, the discrepancy between DT's measured in the present work and those reported previously is always <8%, which is reasonable given the range of values reported previously by different groups. With the present work, DT's for all of the amino acids are now available. These diffusion constants are then used in modeling studies of the diffusion and free solution electrophoretic mobility, mu, of several model peptides. For this set of peptides, it is shown that modeling using revised input parameters results in improved agreement between model and experimental mobilities.     

THE DISTRIBUTION FUNCTION OF RESIDUE-RESIDUE CONTACTS IN PROTEIN MOLECULES

In protein molecules each residue has a different ability to form contacts.In this paper,we calculated the number of contacts per residue and investigated the distribution of residue-residue contacts from 495 globular protein molecules using Contacts of Structural Units(CSU)software.It was found that the probability P(n)of amino acid residues having n pairs of contacts in all contacts fits Gaussian distribution very well.The distribution function of residue-residue contacts can be expressed as:P(n)=P_0+aexp[-b(n-n_c)~2].In our calculation,P_0=-0.06,α=11.4,b=-0.04 and n_c=9.0.According to distribution function,we found that those hydrophobic(H)residues including Leu,Val,Ile,Met,Phe,Tyr,Cys,and Trp residues have large values of the most probable number of contact n_c,and hydrophilic(P)residues including Ala,Gly,Thr, His,Glu,Gln,Asp,Asn,Lys,Ser,Arg,and Pro residues have the small ones.We also compare with Fauchere-Pliska hydrophobicity scale(FPH)and the most probable number of contact n_c for 20 amino acid residues,and find that there exists a linear relationship between Fauchere-Pliska hydrophobicity scale(FPH)and the most probable number of contact n_c, and it is expressed as:n_c=a+b×FPH,here α=8.87,and b=1.15.It is important to further explain protein folding and its stability from residue-residue contacts.     

On the sodium and lithium ion affinities of some α-amino acids

The decomposition of 59 different cluster ions (generated by fast atom bombardment) consisting of two different amino acids and a sodium ion was analysed. The only fragment ions of significant abundance could be assigned to sodium ion-bound amino acids. Assuming that the most abundant ion in the fragment ion spectrum corresponds to the amino acid with the highest sodium ion affinity (SIA), the 20 common α-amino acids could be ordered with increasing sodium ion affinity as follows: Gly, Ala, Cys, Val, (Leu, Ile), Ser, Met, Thr, (Phe, Pro), Asp, Tyr, (Glu, Lys), Trp, Asn, Gln, His, Arg. Quantitative determinations were carried out by comparison of the lithium ion affinity (LIA) of Ala with that of dimethylformamide (DMF) in a fragment ion scan of the ion-bound dimer Ala—Li⁺—DMF. LIA(Ala) was calculated from LIA(Ala) = LIA(DMF) – (1/C)ln[I(AlaLi⁺)/I(DMF—Li⁺)], where the constant C was estimated from measurements of proton-bound amine–amino acid clusters. From fragment ion analysis of nine other Li⁺-bound α-amino acid dimers, the following lithium ion affinities were obtained: Gly 51.0, Ala 52.6, Sar 53.5, α-aminobutyric acid 53.7, glycine methyl ester 54.7 and Val 54.8. SIA(Ala) was estimated to be 75% of the lithium ion affinity and from fragment ion analysis of ten Na⁺-bound α-amino acid dimers the following sodium ion affinities were obtained: Gly 37.9, Ala 39.4, α-aminobutyric acid 40.3, Val 41.0, glycine methylster 41.0 and Sar 41.2.     

Characterization of amino acids in silk sericin protein from Gonometa rufobrunnae by MEKC with phenyl isothiocyanate derivatization

An MEKC method was developed for the separation and characterization of phenyl-isothiocyanate (PITC)-labeled amino acids derived from Gonometa rufobrunnae silkworm after microdialysis sample cleanup. The influence of the buffer and SDS concentration on the resolution of the amino acids was investigated. A buffer system consisting of 25 mM phosphate, 10 mM borate buffer at pH 9.00, and 70 mM SDS showed the best results, with 13 PITC-amino acid derivatives being resolved out of 15 possible amino acids that were under study. Microdialysis sampling demonstrated its efficiency as a sample cleanup technique. Sericin protein from G. rufobrunnae was found to be characterized by at least 11 positively identified amino acids. These included His, Tyr, Ser, Ala, Phe, Lys, Gly, Arg, Cys, Glu, and Asp. Leu/Met and Val/Thr were coeluting pairs and hence could not be positively confirmed.     

Investigation of the interactions between ginsenosides and amino acids by mass spectrometry and theoretical chemistry

In order to evaluate the essence of the interactions of ginsenosides and proteins which are composed by α-amino acids, electrospray ionization mass spectrometry was employed to study the noncovalent interactions between ginsenosides (Rb₂, Rb₃, Re, Rg₁ and Rh₁) and 18 kinds of α-amino acids (Asp, Glu, Asn, Phe, Gln, Thr, Ser, Met, Trp, Val, Gly, Ile, Ala, Leu, Pro, His, Lys and Arg). The 1:1 and 2:1 noncovalent complexes of ginsenosides and amino acids were observed in the mass spectra. The dissociation constants for the noncovalent complexes were directly calculated based on peak intensities of ginsenosides and the noncovalent complexes in the mass spectra. Based on the dissociation constants, it can be concluded that the acidic and the basic amino acids, Asp, Glu, Lys and Arg, bound to ginsenosides more strongly than other amino acids. The experimental results were verified by theoretical calculations of parameters of noncovalent interaction between ginsenoside Re and Arg which served as a representative example. Two kinds of binding forms, “head–tail” (“H–T”) and “head–head” (“H–H”), were proposed to explain the interaction between ginsenosides and amino acids. And the interaction in “H–T” form was stronger than that in “H–H” form.     

Cascade Dissociations of Peptide Cation-Radicals. Part 1. Scope and Effects of Amino Acid Residues in Penta-, Nona-, and Decapeptides

Amino acid residue-specific backbone and side-chain dissociations of peptide z ions in MS(3) spectra were elucidated for over 40 pentapeptides with arginine C-terminated sequences of the AAXAR and AAHXR type, nonapeptides of the AAHAAXX"AR and AAHAXAX"AR type, and AAHAAXX"AAR decapeptides. Peptide z(n) ions containing amino acid residues with readily transferrable benzylic or tertiary β-hydrogen atoms (Phe, Tyr, His, Trp, Val) underwent facile backbone cleavages to form dominant z(n-2) or z(n-3) ions. These backbone cleavages are thought to be triggered by a side-chain β-hydrogen atom transfer to the z ion C(α) radical site followed by homolytic dissociation of the adjacent C(α)-CO bond, forming x(n-2) cation-radicals that spontaneously dissociate by loss of HNCO. Amino acid residues that do not have readily transferrable β-hydrogen atoms (Gly, Ala) do not undergo the z(n) → z(n-2) dissociations. The backbone cleavages compete with side-chain dissociations in z ions containing Asp and Asn residues. Side-chain dissociations are thought to be triggered by α-hydrogen atom transfers that activate the C(β)-C(γ) or C(β)-heteroatom bonds for dissociations that dominate the MS(3) spectra of z ions from peptides containing Leu, Cys, Lys, Met, Ser, Arg, Glu, and Gln residues. The Lys, Arg, Gln, and Glu residues also participate in γ-hydrogen atom transfers that trigger other side-chain dissociations.     

大亚湾沉积物中氨基酸的垂直分布——沉积物柱样W0中的水解氨基酸

测定了采自大亚湾近岸海域的一个长60cm的沉积物柱样W0中15种水解氨基酸的含量；结果表明，15种水解氨基酸含量均随深度而下降，其中苏氨酸、丝氨酸、甘氨酸、丙氨酸、精氨酸、缬氨酸、苯丙氨酸、亮氨酸、异亮氨酸的含量以及水解氨基酸总量随深度的变化可用指数方程c＝c0e^-kx加以描述；天冬氨酸、谷氨酸、丝氨酸、甘氨酸、丙氨酸和缬氨酸是大亚湾沉积物中最丰富的氨基酸。     

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.     

STATISTICAL PROPERTIES OF LONG-RANGE CONTACTS IN GLOBULAR PROTEINS

The analysis of residue-residue contacts in protein structures can shed some light on our understanding of the folding and stability of proteins. In this paper, we study the statistical properties of long-range and short-range residue-residue contacts of 91 globular proteins using CSU software and analyze the importance of long-range contacts in globular protein structure. There are many short-range and long-range contacts in globular proteins, and it is found that the average number of long-range contacts per residue is 5.63 and the percentage of residue-residue contacts which are involved in long-range ones is 59.4%. In more detail, the distribution of long-range contacts in different residue intervals is investigated and it is found that the residues occurring in the interval range of 4-10 residues apart in the sequence contribute more long-range contacts to the stability of globular protein. The number of long-range contacts per residue, which is a measure of ability toform residue-residue contacts, is also calculated for 20 different amino acid residues. It is shown that hydrophobic residues (including Leu, Val, Ile, Met, Phe, Tyr, Cys and Trp) having a large number of long-range contacts easily form long-range contacts, while the hydrophilic amino acids (including Ala, Gly, Thr, His, Glu, Gln, Asp, Asn, Lys, Ser, Arg, and Pro) form long-range contacts with more difficulty. The relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of short-range and long-range contacts per residue for 20 amino acid residues is also studied. An approximately linear relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of long-range contacts per residue CL is found and can be expressed as     

球状蛋白质分子中氨基酸紧密接触对性质的研究

采用CSU软件 (Contactsofstructuralunits) ,对 61种球状蛋白质分子中氨基酸紧密接触对 (Residue residuecontact)进行了研究 .重点研究了不同氨基酸在形成远程紧密接触对 (Long rangecontact)和近程紧密接触对 (Short rangecontact)时的不同能力 .发现氨基酸Leu,Val,Ile,Met,Phe,Tyr,Cys,Trp(疏性氨基酸 ,H)比较容易形成远程紧密接触对 ,氨基酸Glu,Gln ,Asp ,Asn,Lys,Ser,Arg,Pro(亲水氨基酸 ,P)比较难形成远程紧密接触对 ,而氨基酸Ala,Gly,Thr,His(中性氨基酸 ,N)在形成远程紧密接触对时能力一般 .它们平均每个氨基酸可形成 6 0 3 ,3 64和 4 43个远程紧密接触对 .同时它们在形成近程紧密接触对时能力非常接近 ,平均每个氨基酸可形成的近程紧密接触对数目在 2 3 4～ 2 85变化 ,差别非常小 .亲水氨基酸 (P) ,中性氨基酸 (N)和疏水性氨基酸 (H)在蛋白质分子结构稳定性上起着不同的作用     

Effects of Different Amino Acids in Culture Media on Surfactin Variants Produced by <Emphasis Type="Italic">Bacillus subtilis</Emphasis> TD7

Surfactin produced by Bacillus subtilis has different variants, which are affected by the composition of substrate available. To demonstrate the effects of amino acids on surfactin variants, B. subtilis TD7 was cultivated under the same conditions but with different amino acids supplied in media, respectively, and the type as well as the proportion of surfactin variants produced was analyzed with electrospray ionization mass spectrometry and gas chromatography–mass spectrometry. The result shows that the addition of different amino acids significantly influences the proportion of surfactin variants with different fatty acids. When Arg, Gln, or Val was added to the culture medium of B. subtilis TD7, the proportion of produced surfactin variants with even β-hydroxy fatty acids significantly increased, while the addition of Cys, His, Ile, Leu, Met, Ser, or Thr enhanced the proportion of surfactin variants with odd β-hydroxy fatty acids markedly. This result may be of some reference value in enhancing the production of specific surfactin variants as well as in the research on the relationship between culture media and the corresponding products of a certain bacterium.     

Revising the proton affinity scale of the naturally occurring α-amino acids

The proton affinities (PA) of the 20 naturally occurring alpha-amino acids (AA) have been determined computationally by means of density functional theory (DFT) and high-level G2(MP2) calculations. These theoretical PAs, together with data that have appeared since 1997 in the literature, are used to validate the most reasonable currently available PA scale for AAs (Harrison, A. G. Mass Spectrom. Rev. 1997, 16, 201-217.). Significant scatter is observed for the PAs of Ser, Asp, Phe, Asn, Met, Pro, Gln, Glu, Trp, His, Lys, and Arg, many of which have a basic side-chain functionality. Critical review of the available data leads to new consensus PAs for Asn, Gln, Met, and Arg of 222.4, 230.5, 223.7, and 250.2 kcal/mol, respectively.     

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.     

A meanfield approach to the thermodynamics of a protein-solvent system with application to the oligomerization of the tumor suppressor p53

The thermodynamic stability and oligomerization status of the tumor suppressor p53 tetramerization domain have been studied experimentally and theoretically. A series of hydrophilic mutations at Met-340 and Leu-344 of human p53 were designed to disrupt the hydrophobic dimer-dimer interface of the tetrameric oligomerization domain of p53. Meanfield calculations of the free energy of the solvated mutants as a function of interdimer distance were compared with experimental data on the thermal stability and oligomeric state [tetramer, dimer, or equilibrium mixture of both] of each mutant. The calculations predicted a decreasing stability and oligomeric state for the following amino acids at residue 340: Met [tetramer] > Ser Asp, His, Gin, > Glu, Lys [dimer], whereas the experimental results showed the following order: Met [tetramer] > Ser > Gln > His, Lys > Asp, Glu [dimers]. For residue 344, the calculated trend was Leu [tetramer] > Ala > Arg, Gln, Lys [dimer], and the experimental trend was Leu [tetramer] > Ala, Arg, Gln, Lys [dimer]. The discrepancy for the lysine side chain at residue 340 is attributed to the dual nature of lysine, both hydrophobic and charged. The incorrect prediction of stability of the mutant with Asp at residue 340 is attributed to the fact that within the meanfield approach, we use the wild-type backbone configuration for all mutants, but low melting temperatures suggest a softening of the α-helices at the dimer-dimer interface. This initial application of meanfield theory toward a protein-solvent system is encouraging for the application of the theoretical model to more complex systems.