Design and properties of [Met35(O)]Aβ42-lactam(Asp23/Lys28) possessing a lactam tether as a salt-bridge surrogate

A characteristic feature of higher-order structures of amyloid β peptide (Aβ) aggregates observed in Alzheimer disease is the salt-bridge between the side-chains of Asp²³ (carboxylate) and Lys²⁸ (ammonium). We synthesized an [Met³⁵(O)]Aβ42 possessing a covalently bound lactam tether as an Asp²³/Lys²⁸ salt-bridge surrogate (compound 3). The lactam tether of 3 markedly promoted the formation of stable protofibril-like species that exhibited amyloidogenic properties such as a cross-β-sheet structure and cytotoxicity. This finding is consistent with reports that the Asp²³/Lys²⁸ salt-bridge of Aβ42 is transiently formed in aggregation intermediates.     

Potent antiobesity effect of a short-length peptide YY-analogue continuously administered in mice

The gastrointestinal peptide, peptide YY_3–36 (PYY_3–36) and its shorter peptide analogues have been reported to reduce appetite by activating the neuropeptide Y2 receptor (Y2R), which is associated with obesity and other metabolic diseases. A 14-amino acid PYY analogue, Ac-[d-Pro²⁴,Cha^27,28,36,Aib³¹]PYY(23–36) (3), showed high binding affinity and agonist activity for the Y2R, similar to that of PYY_3–36, but had weak anorectic activity upon continuous administration in lean mice. Three amino acid substitutions [Pya(4)²⁶, Aib²⁸, Lys³⁰], which contributed to the decreased hydrophobicity of 3, efficiently increased its anorectic activity. The compound containing these three amino acids, Ac-[d-Pro²⁴,Pya(4)²⁶,Cha^27,36,Aib^28,31,Lys³⁰]PYY(23–36) (22), exerted more potent and durable food intake suppression than that by PYY_3–36 in lean mice, as well as excellent Y2R agonist activity (EC₅₀: 0.20 nM) and good subcutaneous bioavailability (66.6%). The 11-day continuous administration of 22 at 1 mg/kg/day successfully produced antiobese and antidiabetic effects, with more than 20% body weight loss in obese and Type 2 diabetes ob/ob model mice.     

Theoretical studies on protein-nucleic acid interactions. I. Interaction of positively charged amino acids with nucleic acid fragments

Coulombic interactions between the side chains of charged amino acids (Arg⁺, Lys⁺, and His⁺) and negatively charged phosphate groups of nucleic acid fragments have been studied theoretically. Diribose monophosphate and dideoxyribose monophosphate are chosen as model systems for single-stranded RNA and DNA, respectively. The interaction energies have been calculated by second-order perturbation theory using simplified formulas for individual terms. The interaction energy in this formalism is a sum of electrostatic, polarization, dispersion, and repulsive energies. Our results show that about 90% of the total interaction energy is contributed by the electrostatic term alone. Contribution from the repulsive term exceeds that from the dispersion term. Calculated interaction energies suggest that Lys⁺ and His⁺ form more stable complexes with RNA than with single-stranded DNA. On the other hand, Arg⁺ has a higher affinity for DNA than for RNA. The affinity of nucleic acids for the three amino acids is in the order Lys⁺ > His⁺ > Arg⁺. Further, the basic amino acid residues form more stable complexes with A-DNA than with B-DNA. The role of the Coulombic interactions in the specific recognition of nucleic acids by proteins is discussed.     

Positively charged amino acids flanking a sumoylation consensus tetramer on the 110 kDa tri-snRNP component SART1 enhance sumoylation efficiency

Covalent attachment of Small Ubiquitin-like MOdifiers (SUMOs) to the ε-amino group of lysine residues in target proteins regulates many cellular processes. Previously, we have identified the 110 kDa U4/U6.U5 tri-snRNP component SART1 as a target protein for SUMO-1 and SUMO-2. SART1 contains lysines on positions 94, 141, 709 and 742 that are situated in tetrameric sumoylation consensus sites. Recombinant SART1 was produced in E. coli, conjugated to SUMO-2 in vitro, digested by trypsin and analysed by MALDI-ToF, MALDI-FT-ICR or nanoLC-iontrap MS/MS. We found that Lys⁹⁴ and Lys¹⁴¹ of SART1 were preferentially conjugated to SUMO-2 monomers and multimers in vitro. In agreement with these results, mutation of Lys⁹⁴ and Lys¹⁴¹, but not Lys⁷⁰⁹ and Lys⁷⁴², resulted in a reduced sumoylation of SART1 in HeLa cells. A detailed characterization of the four sumoylation sites of SART1 using full-length recombinant SART1 and a peptide sumoylation approach indicated that positively charged amino acids adjacent to the tetrameric sumoylation consensus site enhance the sumoylation of Lys⁹⁴. These results show that amino acids surrounding the classic tetrameric SUMO consensus site can regulate sumoylation efficiency and validate the use of an in vitro sumoylation-mass spectrometry approach for the identification of sumoylation sites.     

Chemical semisynthesis of aprotinin homologues and derivatives mutated inp′ positions

An extended concept for the replacement of amino acids in theP' region of aprotinin by chemical semisynthesis is presented. Either fragment condensation with dipeptides protected as tert-butyl ester or stepwise introduction of two single amino acid-tert-butyl esters into a partially esterified aprotinin derivative (with free Lys¹⁵-carboxyl group) lacking the amino acids Ala¹⁶ and Arg¹⁷ leads to aprotinin homologues and derivatives mutated in theP′ ₁ andP′ ₂ position. This method may complement the recently reported enzymatic synthesis by enabling access to aprotinin homologues and derivatives, which cannot be prepared enzymatically. The synthesis of [Ala¹⁷]BPTI and [seco-17/18]BPTI is described in detail.     

Solution and solid state behavior of Co2+, Ni2+ and Zn2+ tosylaminoacidate systems: Crystal and molecular structure of bis(N-tosylglycinato)tetraaquocobalt(II) and bis(N-tosyl-β-alaninato)tetraaquozinc(II) complexes

The interactions between N-tosylamino acids and cobalt(II), nickel(II) and zinc(II) ions in aqueous solution and in the solid state have been investigated. From concentrated aqueous solutions, compounds of general formula [M(II)(N-tosylaminoacidato)₂(H₂O)₄](M = Co(II), Ni(II) and N-tosylaminoacidato = N-tosylglycinate (Tsgly^?), N-tosyl-α- and -β-alaninate (Ts-α- and Ts-β-ala^?); M = Zn(II) and N-tosylaminoacidate = Tsgly^?, Ts-β-ala^?) and [Zn(II)(N- tosylaminoacidato)₂(H₂O)₂] were isolated and characterized by means of thermogravimetric, electronic and infrared spectra. For two of them: [Co(Tsgly)₂(H₂O)₄](I) and [Zn(Ts-β-ala)₂(H₂O)₄](II) the crystal and molecular structures were also determined. Both compounds crystallize in the monoclinic space group P2₁/c, with two formula units in a cell of dimensions: a = 13.007(6), b = 5.036(2), c = 18.925(7) Å, β = 102.33(3)° for (I) and a = 14.173(6), b = 5.469(2), c = 17.701(7) Å, β = 106.63(3)° for (II). The structures were solved by the heavy-atom method and refined by least-squares calculations to R = 0.031 and 0.064 for (I) and (II) respectively. The cobalt and zinc atoms lie in the centers of symmetry, each bonded to two amino- acid molecules through a carboxylic oxygen atom and four water molecules in a slightly tetragonally distorted octahedral geometry. The second carboxylic oxygen atom is not involved in metal coordination. Electronic and X ray-powder spectra suggest that the tetrahydrate complexes of Co²⁺, Ni²⁺ and Zn²⁺ ions of the same amino acids are isomorphous and isostructural. No coordinative interactions between ligand and metal ions were found in aqueous solution on varying the pH values before hydroxide precipitation.     

C-Terminal Truncations of the Saccharomyces cerevisiae PMA1 H+-ATPase Have Major Impacts on Protein Conformation,Trafficking, Quality Control,and Function

The C-terminal tail of yeast plasma membrane (PM) H⁺-ATPase extends approximately 38 amino acids beyond the final membrane-spanning segment (TM10) of the protein and is known to be required for successful trafficking, stability, and regulation of enzyme activity. To carry out a detailed functional survey of the entire length of the tail, we generated 15 stepwise truncation mutants. Eleven of them, lacking up to 30 amino acids from the extreme terminus, were able to support cell growth, even though there were detectable changes in plasma membrane expression, protein stability, and ATPase activity. Three functionally distinct regions of the C terminus could be defined. (i) Truncations upstream of Lys⁸⁸⁹, removing more than 30 amino acid residues, yielded no viable mutants, and conditional expression of such constructs supported the conclusion that the stretch from Ala⁸⁸¹ (at the end of TM10) to Gly⁸⁸⁸ is required for stable folding and PM targeting. (ii) The stretch between Lys⁸⁸⁹ and Lys⁹¹⁶, a region known to be subject to kinase-mediated posttranslational modification, was shown here to be ubiquitinated in carbon-starved cells as part of cellular quality control and to be essential for normal ATPase folding and stability, as well as for autoinhibition of ATPase activity during glucose starvation. (iii) Finally, removal of even one or two residues (Glu⁹¹⁷ and Thr⁹¹⁸) from the extreme C terminus led to visibly reduced expression of the ATPase at the plasma membrane. Thus, the C terminus is much more than a simple appendage and profoundly influences the structure, biogenesis, and function of the yeast H⁺-ATPase.     

Determination of hexahydrophthalic anhydride adducts to human serum albumin

Hexahydrophthalic anhydride (HHPA) is a highly sensitizing industrial chemical that is known to covalently bind to endogenous proteins. The aim of this study was to determine the binding sites of HHPA to human serum albumin (HSA). Conjugates between HSA and HHPA, at two different molar ratios, were synthesized under physiological conditions. The conjugates were digested with trypsin and Pronase E to obtain specific peptides and amino acids, which were separated by liquid chromatography (LC). Fractions containing modified peptides were detected through quantification of hydrolysable HHPA using LC coupled to a triple quadrupole mass spectrometer with electrospray ionization. Modified residues in albumin were identified by sequence analyses using nanoelectrospray quadrupole time-of-flight mass spectrometry. A total of 36 HHPA adducts were found in the HSA–HHPA conjugate with 10 times molar excess of added HHPA. In the conjugate with a molar ratio of 1:0.1 of added HHPA, seven HHPA adducts were found bound to Lys¹³⁷ (domain IB), Lys¹⁹⁰, Lys¹⁹⁹ and Lys²¹² (domain IIA), Lys³⁵¹ (domain IIB), and Lys⁴³² and Lys⁴³⁶ (domain IIIA). Moreover, several of these adducted albumin peptides were detected in nasal lavage fluid from one volunteer exposed to HHPA. The binding sites of HHPA to HSA have been determined, thus identifying potential allergenic chemical structures. This knowledge generates the possibility of developing methods for the biological monitoring of HHPA exposure by analysing tryptic peptides including these binding sites.     

Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design

Objectives

Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions.

Methods

Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations.

Results

The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions.

Conclusion

(1) The salt bridge interactions between acidic amino acids (Glu^- and Asp^-) and alkaline amino acids (Arg⁺, Lys⁺ and His⁺) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg⁺, Lys⁺ and His⁺) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.     

Limited tryptic digestion of recombinant human interleukin-2: Structure-binding relationships with the α chain of the interleukin-2 receptor

The surface topography and structural features of interleukin-2 (IL-2) in relation to its interaction with the α subunit of its receptor (IL-2Rα) have been probed by limited tryptic digestion followed by detailed structural analyses. Four sensitive cleavage sites in IL-2 (Lys⁸, Lys⁹, Lys³⁵, and Arg³⁸) were identified as surface amino acids, suggesting that they are potential binding sites for IL-2Rα. To examine the involvement of these residues in IL-2Rα binding, a truncated IL-2 molecule lacking the amino-terminal residues through Arg³⁸ was generated and it was found to be incapable of binding IL-2Rα in a solid-phase receptor binding sequencing assay. These studies have led to the conclusion that the IL-2Rα contact region of IL-2 includes residues Lys³⁵ and Arg³⁸. This finding is supported by the refined three-dimensional structure of IL-2 in which these residues are located outside of the compact bundle of four helices and thus are readily available for interaction with IL-2Rα.     

Analysis of the interferences in quantitation of a site-specifically PEGylated exendin-4 analog by the Bradford method

Protein modification has been found to affect the estimation of protein concentration in some of the traditional dye-based absorbance measurements. In this work, a distinct reduction in A₅₉₅ was observed during the quantitation of a PEGylated exendin-4 analogue (Ex4C) by the Bradford method and the PEGylation process was found to interfere with the measurement. Lys¹², Arg²⁰, and Lys²⁷ were further proved to be the major amino acids that functioned as dye-binding sites. The shielding effect produced by the large polymer was demonstrated to depend on the length of PEG that was used for modification.     

Theoretical studies on protein-nucleic acid interactions. II. Hydrogen bonding of amino acid side chains with bases and base pairs of nucleic acids

With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg⁺, Glu^?, and Asp^?) has been studied by a second-order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen-bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys⁺, Arg⁺, and His⁺) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G–X > C–X > A–X U–X or T–X, and G · C–X > A · T(U)–X, where X is one of these amino acid residues. It has been shown that Glu^? and Asp^? can recognize guanine in single-stranded nucleic acids; Arg⁺ can recognize G · C base pairs from A · T base pairs in double-stranded structures.     

ThepH dependence of the equilibrium constantK Hyd for the hydrolysis of the Lys15-Ala16 reactive-site peptide bond in bovine pancreatic trypsin inhibitor (aprotinin)

ThepH dependence of the equilibrium constant K_Hyd for the hydrolysis of the Lys¹⁵-Ala¹⁶ reactive-site peptide bond of the bovine pancreatic trypsin inhibitor (aprotinin) was investigated over thepH range 2.3–6.5. Solutions of aprotinin, modified aprotinin with the Lys¹⁵-Ala¹⁶ peptide bond cleaved and mixtures of both species were incubated with 10 mol% porcine β-trypsin. The state of equilibrium was determined by analytical cation-exchange HPLC. The K_Hyd values obtained did not exactly obey the simple equation of Dobry et al. (1952), which had to be used in an extended form with two additional parameters for a satisfactory fit. ThepH-independent equilibrium constant is 0.90 and thepK values of the Lys¹⁵ carboxyl group and of the Ala¹⁶ amino group are 3.10 and 8.22, respectively. ThepK of an additional group is apparently perturbed by the peptide-bond hydrolysis. It is 4.60 in the native and 4.40 in the modified aprotinin.     

Role of Lys281 in the <Emphasis Type="Italic">Dunaliella salina</Emphasis> (6-4) Photolyase Reaction

His³⁵⁴ and His³⁵⁸, two highly conserved histidines in Xenopus laevis (6-4) photolyase [equivalent to His⁴⁰¹ and His⁴⁰⁵, in Dunaliella salina (6-4) photolyase], are critical for photoreactivation. They act as a base and an acid, respectively. However, the remaining high repair activity when the pH value is higher than the pKa of histidine suggests the involvement of other basic amino acids in photoreactivation. According to the results of in vivo enzyme assay and three-dimension structural model of Dunaliella salina (6-4) photolyase we hypothesized that Lys²⁸¹ might be involved in the photoreactivation over the pH range from 10.0 to 11.0. To test this, we generated two mutant forms of the (6-4) photolyase, K281G and K281R mutant, by overlap extension polymerase chain reaction, and performed the enzyme assay with these mutants. From these results we conclude that the Lys²⁸¹, which is highly conserved in (6-4) photolyases, participates in the photoreactivation and acts as an acid to donate a proton to His⁴⁰¹ when the environmental pH is higher than the pKa value of histidine.     

tert-Butyl 1,5-bis(4-(benzo[d]isothiazol-3-yl)piperazin-1-yl)-1,5-dioxopentan-2-ylcarbamate urea/thiourea derivatives as potent H+/K+-ATPase inhibitors

Amino acids are known to possess variable efficacy against ulceration. Considering the good antiulcer activity of amino acids, a series of urea/thiourea derivatives of glutamic acid conjugated benzisothiazole analogue 3a–u with various substituents on aryl ring were synthesized, spectroscopically characterized and evaluated for in vitro H⁺/K⁺-ATPase inhibition. Majority of the compounds possessed potency compared to that of omeprazole, a reference drug. In particular, methoxy derivatives 3p–u were the most active compounds possessing a significant 15-fold increase for para substituent thus, contributing positively to gastric H⁺/K⁺-ATPase inhibition.     

Antiobesity and emetic effects of a short-length peptide YY analog and its PEGylated and alkylated derivatives

Neuropeptide Y2 receptor (Y2R) agonism is an important anorectic signal and a target of antiobesity drug discovery. Recently, we synthesized a short-length Y2R agonist, PYY-1119 (4-imidazolecarbonyl-[d-Hyp²⁴,Iva²⁵,Pya(4)²⁶,Cha^27,36,γMeLeu²⁸,Lys³⁰,Aib³¹]PYY(23–36), 1) as an antiobesity drug candidate. Compound 1 induced marked body weight loss in diet-induced obese (DIO) mice; however, 1 also induced severe vomiting in dogs at a lower dose than the minimum effective dose administered to DIO mice. The rapid absorption of 1 after subcutaneous administration caused the severe vomiting. Polyethylene glycol (PEG)- and alkyl-modified derivatives of 1 were synthesized to develop Y2R agonists with improved pharmacokinetic profiles, i.e., lower maximum plasma concentration (C_max) and longer time at maximum concentration (T_max). Compounds 5 and 10, modified with 20?kDa PEG at the N-terminus and eicosanedioic acid at the Lys³⁰ side chain of 1, respectively, showed high Y2R binding affinity and induced significant body weight reduction upon once-daily administration to DIO mice. Compounds 5 and 10, with their relatively low C_max and long T_max, partially attenuated emesis in dogs compared with 1. These results indicate that optimization of pharmacokinetic properties of Y2R agonists is an effective strategy to alleviate emesis induced by Y2R agonism.     

Chemical semisynthesis of aprotinin homologues and derivatives mutated inp′ positions

An extended concept for the replacement of amino acids in theP' region of aprotinin by chemical semisynthesis is presented. Either fragment condensation with dipeptides protected as tert-butyl ester or stepwise introduction of two single amino acid-tert-butyl esters into a partially esterified aprotinin derivative (with free Lys¹⁵-carboxyl group) lacking the amino acids Ala¹⁶ and Arg¹⁷ leads to aprotinin homologues and derivatives mutated in theP ₁ andP ₂ position. This method may complement the recently reported enzymatic synthesis by enabling access to aprotinin homologues and derivatives, which cannot be prepared enzymatically. The synthesis of [Ala¹⁷]BPTI and [seco-17/18]BPTI is described in detail.     

Differential effects of ruminally protected amino acids on fattening of fallow deer in two culling periods

A well-balanced amino acid profile in the feedstuffs for livestock is essential to support adequate growth. This is well studied for monogastric species but still not well understood for ruminants and especially for the most unconventional species, like cervids. This study investigated the influence of ruminally protected lysine (Lys) and methionine (Met) supplementation during the fattening period, as well as two slaughter seasons (late autumn (LA) v. late winter (LW)), on the growth, carcass traits, body condition and blood plasma metabolites of fallow deer (Dama dama). Forty-five yearlings of fallow deer bucks were allocated into three groups, balanced by weight (40.2 ± 2.7 kg). The deer were pasture-fed and supplemented with barley, free-choice mineral premix, silage during the winter period, and varying levels of ruminally protected Lys and Met: no amino acids (Control), 9 g/day of Lys, and 9 g/day of Lys plus 3 g/day of Met (Lys+Met). Animals were slaughtered in two separate seasons, LA (six animals per group), and LW (nine animals per group). Animals culled in LA had higher average daily weight gain than LW (P = 0.002), due to the reduced growth during winter typical for seasonal cervids in temperate zone, mediated by the photoperiod. Dressing percentage was significantly higher in LW and in the Lys+Met group (P = 0.002). Body condition score (P = 0.024), kidney fat index (KFI) (P = 0.005), and internal fat (P < 0.001) increased significantly with Lys+Met supplementation. During LW, KFI (P = 0.004) and kidney fat (P = 0.001) were also significantly higher than in LA. Blood creatinine concentration increased significantly for deer receiving Lys (P = 0.002) and Lys+Met (P < 0.001). Also, triglycerides level increased in Lys group (P < 0.001). These findings highlight the effects of Lys and Met supplementation on the growth and internal fat storage for winter survival, suggesting a different use of the supplemented resource according to the season. Also, the observed effects on protein and fat metabolism of fallow deer may influence the production of farmed animals, and offer interesting insights about the physiology of the species.     

Methionine Sulfoximine In Vivo Modifies the tRNALys Pool of Developing Rat Brain

Abstract: tRNA was extracted from brains of 3-, 8-, and 18-day-old rats that were injected intracerebrally, 45 min before death, with [³H]methyl methionine or [8-³H]guanosine, and intraperitoneally, 3 h before death, with l -methionine-dl-sulfoximine (MSO), a methylation-activating convulsant agent. Although there was no effect of age or of MSO on the per gram yield of tRNA, its specific radioactivity (dpm/A₂₆₀) was highest at 3 days in both the control and the MSO groups. Age- and MSO-related changes in the tRNA^Lys content of the brain tRNA pool were investigated by means of benzoylated DEAE- cellulose (BDC) and reverse-phase chromatography (RPC). BDC chromatography revealed tRNA^Lys species in the brains of the MSO-treated animals that were absent in control brains. Of particular interest was the finding that differences in RPC-5 chromatographic mobility between control and MSO-tRNA^Lys species were abolished by conversion to lysyl-tRNA, suggesting that the MSO-elicited change(s) in tRNAL^Lys structure involved the binding site(s) for lysine. Two additional findings were made: (a) lysine acceptance by the [³H]methyl-labeled tRNA^Lys purified from brains of the MSO-treated animals was higher than that of controls at 18 days; and (b) omission of the BDC chromatographic step accentuated the differences in mobility on RPC-5 columns between tRNA^Lys species of control and MSO-treated brains. Lastly, we found that some tRNA^Lys species present in the MSO-treated brains contained significantly different proportions of N²-methyl guanine and 1-methyl adenine, relative to controls. These MSO-elicited changes in the methyl base content of tRNA^Lys of immature rat brain are the first evidence of an alteration of brain tRNA structure by a centrally acting excitatory agent.