Sequence composition and environment effects on residue fluctuations in protein structures

Structure fluctuations in proteins affect a broad range of cell phenomena, including stability of proteins and their fragments, allosteric transitions, and energy transfer. This study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per-residue elastic network model accounting for the nonhomogeneous protein mass distribution and the interatomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues in agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups: (i) highly fluctuating-Gly, Ala, Ser, Pro, and Asp, (ii) moderately fluctuating-Thr, Asn, Gln, Lys, Glu, Arg, Val, and Cys, and (iii) weakly fluctuating-Ile, Leu, Met, Phe, Tyr, Trp, and His. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences, and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu, and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.     

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.     

牛视紫红质蛋白质中视黄醛的活性位点

视紫红质蛋白是一个跨膜蛋白, 视黄醛(RET)在该蛋白中的活性结合位点涉及到视觉过程机理, 与一些眼科疾病病理有关. 基于牛视紫红质蛋白1U19的蛋白质晶体结构数据, 采用密度泛函理论的B3LYP方法计算RET-Lys296残基与视黄醛分子周围半径为0.6 nm的空间范围30个氨基酸残基相互作用和结合能. 数值显示1U19蛋白中的残基Glu113、Glu181和Glu122是质子化的RET-Lys296残基的活性结合位点, 结合能分别为-333.38、-205.67和-194.56 kJ·mol-1. 这些氨基酸残基带有一个负电荷, 与质子化的RET-Lys296残基发生强烈的离子静电相互作用. 另外几个残基Ala292、Cys187、Phe293、Pro291以及Trp265等与质子化RET-Lys296残基也有相互吸引作用. 当RET-Lys296残基非质子化, 上述相互作用消失, 促使视黄醛分子与视蛋白分离. 研究发现残基Glu113和Glu181周围各自有一个结晶水分子通过双氢键形式起着稳定作用.     

A linear free-energy correlation in the low-energy tandem mass spectra of protonated tripeptides Gly–Gly–Xxx

The backbone cleavages of protonated tripeptide ions of the series Gly—Gly—Xxx, where Xxx ? Gly, Ala, Val, d-Leu, l-Leu, Ile, Phe, Tyr, Trp, Pro, Met and Glu, were studied in a hybrid tandem mass spectrometer. C-Terminal y-type ions and N-terminal a- and b-type ions were noted. A linear relationship between log (y₁/b₂) and the proton affinity of the C-terminal amino acid substituents was found: as the proton affinity of the C-terminal residue increases, the fraction of y₁ ion formation increases. When the C-terminal substituent was more basic than Trp, the b₂ ion was not observed. It is likely that the site of protonation changes from peptide bond to side-chain for just these residues, Lys, His and Arg.     

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     

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.     

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.     

A scoring function for docking ligands to low-resolution protein structures

We present a docking method that uses a scoring function for protein-ligand docking that is designed to maximize the docking success rate for low-resolution protein structures. We find that the resulting scoring function parameters are very different depending on whether they were optimized for high- or low-resolution protein structures. We show that this docking method can be successfully applied to predict the ligand-binding site of low-resolution structures. For a set of 25 protein-ligand complexes, in 76% of the cases, more than 50% of ligand-contacting residues are correctly predicted (using receptor crystal structures where the binding site is unspecified). Using decoys of the receptor structures having a 4 A RMSD from the native structure, for the same set of complexes, in 72% of the cases, we obtain at least one correctly predicted ligand-contacting residue. Furthermore, using an 81-protein-ligand set described by Jain, in 76 (93.8%) cases, the algorithm correctly predicts more than 50% of the ligand-contacting residues when native protein structures are used. Using 3 A RMSD from native decoys, in all but two cases (97.5%), the algorithm predicts at least one ligand-binding residue correctly. Finally, compared to the previously published Dolores method, for 298 protein-ligand pairs, the number of cases in which at least half of the specific contacts are correctly predicted is more than four times greater.     

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.     

Amino acid-amino acid interactions studied by charge-transfer chromatography

The interaction between amino acids was studied by charge-transfer reversed-phase thin-layer chromatography. The dependence of the lipophilicity of Trp on the concentration of other amino acids in the eluent was considered to be linearly related to the strength of interaction. Arg, Asn, Glu, Met, Phe and Thr interacted with Trp; Ala, Gly and Ser showed no interaction. Stepwise regression analysis indicated that the pK value of the amino acid side-chain and the lipophilicity of the amino acid had the greatest impact on the interaction, suggesting the simultaneous presence of weak hydrophilic and hydrophobic bonding forces between amino acids. Sodium acetate in the eluent increased the interactive strength between Phe and Trp; acetic acid and sodium chloride did not influence the interaction significantly. No significant difference was found between the effects of L- and D-Asn.     

Furcatin 水解酶的三维结构模建和与furcatin 的对接研究

利用同源模建和动力学模拟方法，模建了furcatin水解酶（FH）的三维结构．并在这基础上，分析了活性位点的组成和结构．研究了furcatin与FH的对接．结果表明，Ser84，Arg146，Thr189，Thr234和Gly372在复合物的形成过程中起重要的作用．其中，Ser84，Argl46和Thr189是在FH的活性口袋的二糖部分的亚单位一1中重要的氨基酸，Thr234和Gly372是亚单位-2中重要的氨基酸．     

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.     

The recognition of nucleotides with model beta-hairpin receptors: investigation of critical contacts and nucleotide selectivity

[reaction: see text] We have investigated the factors that contribute to binding of ATP by a designed 12-residue beta-hairpin peptide, WKWK, and have determined its selectivity for binding to the naturally occurring nucleotide triphosphates. We have previously shown that WKWK creates an ATP binding pocket on one face of the beta-hairpin consisting of two Trp and two Lys residues. Mutation of the two Lys residues on the binding face of the beta-hairpin resulted in a lower affinity, indicating that each is involved in ATP binding and that each residue contributes approximately -1.5 kcal/mol to the energy of complexation. Replacement of either Trp residue of the ATP binding pocket with Phe or Leu destabilizes the complex formed with ATP by approximately 1 kcal/mol, indicating that both Trp residues participate in interactions with ATP. For binding to the nucleotide triphosphates, the order of binding affinity was shown to follow dTTP > GTP > ATP > CTP, with differences in binding energies spanning as much as 1.6 kcal/mol. NMR analysis demonstrates that both aromatic interactions with the Trp side chains and CH-pi interactions between the ribose protons and the Trp residues may contribute significantly to binding. The results from our model system provide useful thermodynamic information regarding protein-nucleic acid interactions that occur at the surface of a beta-sheet.     

Neocarzinostatin: selective tryptophan oxidation and neocarzinostatin-chromophore binding to apo-neocarzinostatin

Neocarzinostatin (NCS), an antitumor protein antibiotic, is composed of apo-neocarzinostatin (apo-NCS) and neocarzinostatin-chromophore (NCS-chr), the principle of the biological activities of NCS. Apo-NCS having two tryptophan (Trp) residues at positions (39 and 83) was chemically modified by N-bromosuccinimide in a study on the correlation of the binding site(s) of NCS-chr. Selective oxidation of Trp residues was observed when NCS was titrated with N-bromosuccinimide. In contrast, non-selective oxidation of the two Trps on apo-NCS was observed and both Trp (39 and 83) of apo-NCS were titrated with N-bromosuccinimide. After selective oxidation, the remaining Trp residue of NCS was assigned as Trp (83). These results clearly indicate that the Trp (83) residue of apo-NCS changed from the "reactive type" to the "non-reactive type" after the binding of NCS-chr with apo-NCS. The fluorescence emission intensity of apo-NCS generated from the Trp (39) residue was quenched by NCS-chr. These data suggest that NCS-chr directly interacts with the Trp (39) residue and that a beta-sheeted loop containing the Trp (83) residue of apo-NCS changes the high-order structure upon binding with NCS-chr.     

In silico mutagenesis and docking studies of Pseudomonas aeruginosa PA-IIL lectin predicting binding modes and energies

This article is focused on the application of two types of docking software, AutoDock and DOCK. It is aimed at studying the interactions of a calcium-dependent bacterial lectin PA-IIL (from Pseudomonas aeruginosa) and its in silico mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of both docking software applied on a studied problem was evaluated as well. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry and partially also in predicting the preference changes caused by mutation. Obtaining a reasonable in silico method for the prediction of lectin-saccharide interactions may be possible in the future.     

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.     

Essential of Proline and Valine Residues in the Peptide Derived from Lactoferrin for Angiotensin Converting Enzyme Inhibition

We synthesized Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu, the peptide contained in lactoferrin (Lf), to identify the angiotensin converting enzyme (ACE) inhibition. In an attempt to know the structure‐activity relationship of this peptide, we replaced Pro (the third amino acid residues from N‐terminal) or Val (the fourth amino acid residues from N‐terminal) with Ala (neutral amino acid), Glu (acidic amino acid) or Lys (basic amino acid) to produce six peptides. From the in vitro ACE inhibition (IC₅₀) of these synthesized peptides, the original peptide (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu) showed higher ACE inhibition than the replaced six peptides. Thus, replacement of Pro at the third amino acid residues or Val at the fourth position with Ala, Glu or Lys revealed the ACE inhibition to be lower than the original form of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu. Otherwise, we added one peptide at the C‐terminal of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu and found both products with an addition of Val (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Val) or Ile (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Ile) showing a lower ACE inhibition than the original one. The ACE inhibitions produced by both replaced peptides were without significance. Also, deletion of the last peptide at the C‐terminal (Leu‐Arg‐Pro‐Val‐Ala‐Ala) failed to produce a marked change of ACE inhibition as compared to the original one. These results suggest that Pro and Val are essential in the peptide for inhibition of ACE activity.     

An E.P.R. study of peptides after U.V. irradiation

Abstract— Various peptides of Gly, Ala, Phe, Tyr, and Trp have been irradiated with U.V. light in the solid state or in frozen aqueous solution. The radicals produced were studied by E.P.R. spectroscopy at low temperature and at room temperature. Radicals seem to occur preferentially on Gly or Ala when in the C-terminal position and there is evidence for a photosensitization of these amino acids by aromatic amino acids.     

氨基酸分析法研究蒙古国博格达汗宫建筑彩画的胶料种类

为了鉴定博格达汗宫建筑彩画使用的胶料,采用氨基酸分析法测定了古代常用胶料(鸡蛋、动物胶及奶类)的氨基酸组成比.分析3类胶料,发现各胶料的氨基酸组成特点,其中动物胶含羟脯氨酸,且甘氨酸平均含量高达20.45%;鸡蛋中天冬氨酸与脯氨酸的比值较高,平均值为2.29;奶类中谷氨酸与丙氨酸的比值较高,平均值为5.01.在此基础上,分析了蒙古国博格达汗宫建筑彩画样品,对样品的氨基酸组成比进行主成分分析,确定了样品胶料的种类.同时,以动物胶特有的氨基酸--羟脯氨酸(含量均值13.6%)为研究对象,估算出文物样品使用胶料的配方为鸡蛋胶原/动物胶胶原(1.5∶ 1),得出了蒙古国博格达汗宫建筑彩画是采用以鸡蛋为主、动物胶为辅的混合胶料的结论.     

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.