Different contribution of conserved amino acids to the global properties of triosephosphate isomerases

It is generally assumed that the amino acids that exist in all homologous enzymes correspond to residues that participate in catalysis, or that are essential for folding and stability. Although this holds for catalytic residues, the function of conserved noncatalytic residues is not clear. It is not known if such residues are of equal importance and have the same role in different homologous enzymes. In humans, the E104D mutation in triosephosphate isomerase (TIM) is the most frequent mutation in the autosomal diseases named “TPI deficiencies.” We explored if the E104D mutation has the same impact in TIMs from four different organisms (Homo sapiens, Giardia lamblia, Trypanosoma cruzi, and T. brucei). The catalytic properties were not significantly affected by the mutation, but it affected the rate and extent of formation of active dimers from unfolded monomers differently. Scanning calorimetry experiments indicated that the mutation was in all cases destabilizing, but the mutation effect on rates of irreversible denaturation and transition‐state energetics were drastically dependent on the TIM background. For instance, the E104D mutation produce changes in activation energy ranging from 430 kJ mol^?1 in HsTIM to ?78 kJ mol^?1 in TcTIM. Thus, in TIM the role of a conserved noncatalytic residue is drastically dependent on its molecular background. Accordingly, it would seem that because each protein has a particular sequence, and a distinctive set of amino acid interactions, it should be regarded as a unique entity that has evolved for function and stability in the organisms to which it belongs. Proteins 2014; 82:323–335. © 2013 Wiley Periodicals, Inc.     

The effect of specific proline residues on the kinetic stability of the triosephosphate isomerases of two trypanosomes

The effect of specific residues on the kinetic stability of two closely related triosephosphate isomerases (from Trypanosoma cruzi, TcTIM and Trypanosoma brucei, TbTIM) has been studied. Based on a comparison of their β‐turn occurrence, we engineered two chimerical enzymes where their super secondary β‐loop‐α motifs 2 ((βα)₂) were swapped. Differential scanning calorimetry (DSC) experiments showed that the (βα)₂ motif of TcTIM inserted into TbTIM (2Tc) increases the kinetic stability. On the other hand, the presence of the (βα)₂ motif of TbTIM inserted into TcTIM (2Tb) gave a chimerical protein difficult to purify in soluble form and with a significantly reduced kinetic stability. The comparison of the contact maps of the (βα)₂ of TbTIM and TcTIM showed differences in the contact pattern of residues 43 and 49. In TcTIM these residues are prolines, located at the N‐terminal of loop‐2 and the C‐terminal of α‐helix‐2. Twelve mutants were engineered involving residues 43 and 49 to study the effect over the unfolding activation energy barrier (E_A). A systematic analysis of DSC data showed a large decrease on the E_A of TcTIM (ΔE_A ranging from 468 to 678 kJ/mol) when the single and double proline mutations are present. The relevance of Pro43 to the kinetic stability is also revealed by mutation S43P, which increased the free energy of the transition state of TbTIM by 17.7 kJ/mol. Overall, the results indicate that protein kinetic stability can be severely affected by punctual mutations, disturbing the complex network of interactions that, in concerted action, determine protein stability. Proteins 2017; 85:571–579. © 2016 Wiley Periodicals, Inc.     

Genetic code preferentially conserves long-range interactions among the amino acids

The physical properties of amino acids were investigated in order to evaluate their possible relationship to the assignment of codons for amino acids in the genetic code. A comparison of the interconversion probability between amino acids and the distances between the amino acids for individual physical properties revealed a striking hierarchy among the physical properties. Surprisingly, it is the long-range/solvent interactions and not the short-range/stereochemical properties which are preferentially conserved in the genetic code.     

腐生型眼虫Astasia longa两种TIM同工酶cDNA的克隆和分析

利用 3′ RACE和 5′ RACE技术 ,从腐生型眼虫长变胞藻 (Astasialonga)克隆了磷酸丙糖异构酶(TIM)的两个同工酶cDNA全序列。分析表明 :它们分别编码定位于细胞质的胞质型TIM (cTIM)和定位于质体的质体型TIM (pTIM) ;后者的N端具有引导该酶定位到质体中去的典型“前导序列”。根据这些事实我们推测腐生型眼虫A .longa质体中可能存在功能性的TIM ,并进一步认为该质体可能不只是一般意义上的“叶绿体退化的残迹” ,而仍是一种至少有TIM参与其代谢活动的功能性细胞器     

Logic of the genetic code: Conservation of long-range interactions among amino acids as a prime factor

Any statement on the optimality of the existing code ought to imply that this code is ideal for conserving a certain hierarchy of properties while implying that other codes may have been better suited for conservation of other hierarchies of properties. We have evaluated the capability of mutations in the genetic code to convert one amino acid into another in relation to the consequent changes in physical properties of those amino acids. A rather surprising result emerging from this analysis is that the genetic code conserves long-range interactions among amino acids and not their short-range stereochemical attributes. This observation, based directly on the genetic code itself and the physical properties of the 20 amino acids, lends credibility to the idea that the genetic code has not originated by a frozen accident (the null hypothesis rejected by these studies) nor are stereochemical attributes particularly useful in our understanding of what makes the genetic code ‘tick’. While the argument that replacement of, say, an aspartate by a glutamate is less damaging than replacement by arginine makes sense, in order to subject such statements to rigorous statistical tests it is essential to define what constitutes a random sample for the genetic code. The present investigation describes one possible specification. In addition to obvious statistical considerations of testing hypotheses, this procedure points to the more exciting notion that alternative codes may have existed.     

Identification of two amino acids in activin A that are important for biological activity and binding to the activin type II receptors

Activins are members of the transforming growth factor-beta family of growth and differentiation factors. In this paper, we report the results of a structure-function analysis of activin A. The primary targets for directed mutagenesis were charged, individual amino acids located in accessible domains of the protein, concentrating on those that differ from transforming growth factor-beta2, the x-ray crystal structure of which is known. Based on the activities of the recombinant activin mutants in two bioassays, 4 out of 39 mutant proteins (D27K, K102A, K102E, and K102R) produced in a vaccinia virus system were selected for further investigation. After production in insect cells and purification of these four mutants to homogeneity, they were studied in bioassays and in cross-linking experiments involving transfected receptor combinations. Mutant D27K has a 2-fold higher specific bio-activity and binding affinity to an ActRIIA/ALK-4 activin receptor complex than wild type activin, whereas mutant K102E had no detectable biological activity and did not bind to any of the activin receptors. Mutant K102R and wild type activin bound to all the activin receptor combinations tested and were equipotent in bioassays. Our results with the Lys-102 mutants indicate that the positive charge of amino acid 102 is important for biological activity and type II receptor binding of activins.     

Identification of unique amino acids that modulate CYP4A7 activity

A multifamily sequence alignment of the rabbit CYP4A members with the known structure of CYP102 indicates amino acid differences falling within the so-called substrate recognition site(s) (SRS). Chimeric proteins constructed between CYP4A4 and CYP4A7 indicate that laurate activity is affected by the residues within SRS1 and prostaglandin activity is influenced by SRS2-3. Site-directed mutant proteins of CYP4A7 found laurate and arachidonate activity markedly diminished in the R90W mutant (SRS1) and somewhat decreased in W93S. While PGE(1) activity was only slightly increased, the mutant proteins H206Y and S255F (SRS2-3), on the other hand, exhibited remarkable increases in laurate and arachidonate metabolism (3-fold) above wild-type substrate metabolism. Mutant proteins H206Y, S255F, and H206Y/S255F but not R90W/W93S, wild-type CYP4A4, or CYP4A7 metabolized arachidonic acid in the absence of cytochrome b(5). Stopped-flow kinetic experiments were performed in a CO-saturated environment performed to estimate interaction rates of the monooxygenase reaction components. The mutant protein H206Y, which exhibits 3-fold higher than wild-type substrate activity, interacts with CPR at a rate at least 10 times faster than that of wild-type CYP4A7. These experimental results provide insight regarding the residues responsible for modulation of substrate specificity, affinity, and kinetics, as well as possible localization within the enzyme structure based on comparisons with homologous, known cytochrome P450 structures.     

Identification of post-translational modified amino acids

Summary Methylated lysines (N -mono-methylated, N -di-methylated and N -tri-methylated) have been identified after derivatization with orthophthaldialdehyde (OPA) by using pre-column and post-column derivatization techniques.Also the N -acetylated lysine and N -formylated lysine have been identified by OPA post-column derivatization techniques but only in free form due to their instability under acidic conditions which are used for protein hydrolysis.Additionally, all the modified amino acids mentioned above have been derivatized with DABITC/PITC, an Edman reagent, and identified as DABTH-derivatives on thin-layer polyamide sheets.     

Identification of trypanosomes isolated from reduviidae from north Chile

Examination of 54 Triatoma infestans from a village near the European Southern Observatory La Silla in Chile and of 9 Triatoma spinolai from the territory of the observatory showed that 10 T. infestans were infected with trypanosomatids. Mice were infected with in vitro cultures initiated with five different trypanosomatid isolates and treated with the immunosuppressive drug cyclophosphamide to increase the parasitemia of the flagellates. Evidence of the presence of T. cruzi was provided by a comparative biometrical analysis of blood trypomastigotes and the occurrence of intracellular amastigotes. Three methods for further identification were used: examination of kDNA ultrastructure, disc electrophoresis of soluble proteins and the Aaptos papillata II lectin induced agglutination. We obtained the following results for all isolates: (1) presence of a central band of the kDNA; (2) T. cruzi specific double bands of the protein patterns; (3) positive reaction with Aaptos papillata II. No differences between the five isolates from Chile and T. cruzi or T. cruzi-like strains from other countries could be observed. Based on these results an infection of the bugs with T. rangeli and T. conorhini could be excluded.     

Portal-drained viscera and hepatic fluxes of branched-chain amino acids do not account for differences in circulating branched-chain amino acids in rats fed arginine-deficient diets

Summary Concentrations and fluxes of amino acids across the portal-drained viscera (PDV) and liver were assessed in rats fed a meal of one of three arginine-deficient diets containing either alanine or the arginine precursors, ornithine or citrulline. A previous report included findings of seven arginine-related amino acids and indicated that only the citrulline-containing diet protected blood arginine concentrations. In the present report we extend these findings and note that the concentrations and fluxes of the non-arginine-related amino acids showed remarkable consistency across diet groups. However, total branched-chain amino acid (BCAA) concentrations of arterial blood were higher in rats fed the - Arg/+ Ala and the - Arg/+ Orn diets than in rats fed the control (+ Arg) diet. The elevated BCAA correlated with higher circulating concentrations of other essential amino acids but were inversely correlated with arginine concentrations. PDV and hepatic fluxes of BCAA were not different across diet groups, indicating that amino acid absorption and hepatic utilization of BCAA were generally comparable across diet groups. Hepatic concentrations of 14 of 22 measured amino acids, including total BCAA, were correlated with their arterial concentrations. The circulating concentrations and net PDV and hepatic fluxes of rats fed the control diet were comparable to our previous observations in fed rats and illustrate the role of the liver in utilization of diet-derived essential amino acids.Abbreviations PDV portal-drained viscera - BCAA branched-chain amino acids - SSA 5-sulfosalicylic acid - PBF portal blood flow - HBF hepatic blood flow - SELSM pooled standard errors of least squares means - TAA total amino acids - NEAA nonessential amino acids - EAA essential amino acids - LNAA large neutral amino acids Mention of a trade name, proprietary product or specific equipment does not constitute a guarantee by the US Department of Agriculture and does not imply its approval to the exclusion of other products that may be suitable.     

Identification of amino acids in human colipase that mediate adsorption to lipid emulsions and mixed micelles

The adsorption of colipase is essential for pancreatic triglyceride lipase activity and efficient dietary fat digestion. Yet, little is known about which specific amino acids in the hydrophobic surface of colipase influence adsorption. In this study, we systematically substituted alanine or tryptophan at residues implicated in adsorption of colipase to an interface. We expressed, purified recombinant colipase mutants and characterized the ability of each alanine mutant to restore activity to lipase in the presence of bile salts. The functions of L16A, Y55A, I79A and F84A colipase were most impaired with activities ranging from 20 to 60% of wild-type colipase. We next characterized the fluorescence properties of the tryptophan mutants in the absence and presence of bile–salt–oleic acid mixed micelles. We performed steady-state emission spectra to determine peak shift and I₃₃₀/I₃₅₀ ratio and acrylamide quenching curves to characterize the environment of the residues. The analysis supports a model of adsorption that includes residues Leu 34 and Leu 36 on the 2nd loop, Tyr 55 and Tyr 59 on the 3rd loop and Ile 75 and Ile 79 on the 4th loop. The analysis confirms that Phe 84 is not part of the adsorption surface and likely stabilizes the conformation of colipase. Contrary to the predictions of computer modeling, the results provide strong support for an essential role of Tyr 55 in colipase adsorption to mixed micelles. The results indicate that the adsorption of colipase to mixed micelles is mediated by specific residues residing in a defined surface of colipase.     

An intracellular aminopeptidase from Streptomyces rimosus that prefers basic amino acids

An aminopeptidase from the mycelia of Streptomyces rimosus was isolated in an electrophoretically homogeneous form. It was shown to be a monomeric, acidic protein (pI = 4.4, mol. wt. approx. 83,000), with optimal activity at pH 7.1–7.8 and at 35–41° C. The enzyme was fully inhibited by 0.1 mM EDTA or 1 mM o-phenanthroline; the activity was restored upon addition of 0.05 mM Co²⁺, Zn²⁺, or Ni²⁺. Amastatin, bestatin, and puromycin also inhibited the enzyme. The aminopeptidase hydrolyzed amino-acid-2-naphthylamides and various di- to heptapeptides. The highest catalytic coefficients (23 and 19 μM^–1 s^–1) were obtained with Arg- and Lys-2-naphthylamide, followed by Leu-, Phe- and Met-derivatives with one order of magnitude lower catalytic coefficients. Basic or bulky hydrophobic amino acids at the P₁ and/or P₁′ position of peptide substrates were preferred. Acidic amino acids and proline were not accepted. The affinity of the enzyme increased with the length of peptide. According to these properties, S. rimosus intracellular aminopeptidase is distinct from the extracellular leucine aminopeptidase of the same organism and can be classified as an Arg(Lys)-preferring metalloaminopeptidase. Received: 18 January 1996 / Accepted: 19 March 1996     

Chloroplast and cytosolic triosephosphate isomerases from spinach: purification,microsequencing and cDNA cloning of the chloroplast enzyme

Chloroplast and cytosolic triosephosphate isomerases from spinach were separated and purified to homogeneity. Both enzymes were partially sequenced by Edman degradation. Using degenerate primers designed against the amino acid sequences, a homologous probe for the chloroplast enzyme was amplified and used to isolate several full-size cDNA clones. Chloroplast triosephosphate isomerase is encoded by a single gene in spinach. Analysis of the chloroplast cDNA sequence in the context of its homologues from eukaryotes and eubacteria reveals that the gene arose through duplication of its pre-existing nuclear counterpart for the cytosolic enzyme during plant evolution.Abbreviations TPI triosephosphate isomerase - PEG polyethylene glycol - cp plastid - c cytosolic - SDS sodium dodecyl sulphate - PAGE polyacrylamide gel electrophoresis - PVP polyvinylpyrrolidone - PCR polymerase chain reaction - PGK 3-phosphoglycerate kinase     

Sterols, fatty acids and free amino acids from two Helvella species

Sterols, fatty acids and free amino acids of Helvella crispa and H. monachella were investigated. They contained traces of ergosterol and a high amount of ergosta 5.22-dien-3β-ol. Linoleic acid and l-Dopa are the most abundant fatty acid and free amino acid, respectively. The aqueous extract of H. monachella inhibits prostaglandin release by rat peritoneal leucocyres in vitro.     

Dynamic interactions of enzymes involved in triosephosphate metabolism

A steady-state kinetic analysis of the coupled reactions catalysed by the three-enzyme system, aldolase, glyceraldehyde-3-phosphate dehydrogenase and triosephosphate isomerase, was performed. The kinetic parameters of the progress curves of end-product formation calculated for noninteracting enzymes were compared with those measured in the two-enzyme and three-enzyme systems. Changes in the fluorescence anisotropy of labelled dehydrogenase upon addition of aldolase and/or isomerase were also measured. Glyceraldehyde-3-phosphate oxidation catalysed by glyceraldehyde-3-phosphate dehydrogenase in the presence of isomerase (which ensures rapid equilibration of the triosephosphates) follows single first-order kinetics. The rate constant depends simply on the concentration of the dehydrogenase, indicating no kinetically significant isomerase-dehydrogenase interaction. Fluorescence anisotropy measurements also fail to reveal complex formation between the two enzymes. The steady-state velocity of 3-phosphoglycerate formation from fructose 1, 6-bisphosphate in the reactions catalysed by aldolase and dehydrogenase is not increased twofold on addition of the isomerase, even though a 1:2 stoichiometry of fructose 1,6-bisphosphate/glyceraldehyde 3-phosphate is expected. In fact, by increasing the concentration of the isomerase, the steady-state velocity actually decreases. This effect of the isomerase may be a kinetic consequence of an aldolase-isomerase interaction, which results in a decrease of aldolase activity. Furthermore, the fluorescence anisotropy of labelled dehydrogenase, measured at different aldolase concentrations, is significantly lower when the sample contains isomerase. The decrease in the steady-state velocity of the consecutive reactions caused by the elevation of isomerase concentration could be negated by increasing the dehydrogenase concentrations in the three-enzyme system. All of these observations fit the assumption that the amount of aldolase-dehydrogenase complex is reduced due to competition of isomerase with dehydrogenase. The alternate binding of dehydrogenase and isomerase to aldolase may regulate the flux rate of glycolysis.     

Identification of amino acids in the leader peptide of Methanococcus voltae preflagellin that are important in posttranslational processing

Archaeal flagellins are made initially as preproteins with short, positively charged leader peptides. Analysis of all available archaeal preflagellin sequences indicates that the -1 position is always held by a glycine while the -2 and -3 positions are almost always held by charged amino acids. To evaluate the importance of these and other amino acids in the leader peptides of archaeal flagellins for processing by a peptidase, Methanococcus voltae mutant FlaB2 preflagellin genes were generated by PCR and the proteins tested in a methanogen preflagellin peptidase assay that detects the removal of the leader peptide from preflagellin. When the -1 position was changed from glycine to other amino acids tested, no cleavage was observed by the peptidase, with the exception of a change to alanine at which poor, partial processing was observed. Amino acid substitutions at the -2 lysine position resulted in a complete loss of processing by the peptidase, while changes at the -3 lysine resulted in partial processing. A mutant preflagellin with a leader peptide shortened from 12 amino acids to 6 amino acids was not processed. When the invariant glycine residue present at position +3 was changed to a valine, no processing of this mutant preflagellin was observed. The identification of critical amino acids in FlaB2 required for proper processing suggests that a specific preflagellin peptidase may cleave archaeal flagellins by recognition of a conserved sequence of amino acids.     

Steric and electrostatic interactions govern nanofiltration of amino acids

Crossflow nanofiltration experiments were performed to investigate the factors influencing the removal of amino acids by a commercially available polymeric thin-film composite membrane. The removals of five monoprotic (Ala, Val, Leu, Gly, and Thr), one diprotic (Asp), and one dibasic (Arg) amino acids in a range of permeate fluxes, feed pH values, and ionic strengths were analyzed using a phenomenological model of membrane transport. At any given pH and ionic strength, reflection coefficients (rejection at asymptotically infinite flux) of monoprotic amino acids increased with molar radius demonstrating the role of steric interactions on their removal. Additionally, consistent with Donnan exclusion, higher reflection coefficients were obtained when the membrane and the amino acids both carried the same nature of charge (positive or negative). In other words, both co-ion repulsion and molecular size determined amino acids removal. Importantly, the removal of effectively neutral amino acids were significantly higher than neutral sugars and alcohols of similar size demonstrating that even near their isoelectric point, zwitterionic characteristics preclude them from being considered as strictly neutral.