Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: application to apo calmodulin

Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants. We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on detection of nonexchangeable protons over the full range of pH and temperature and therefore are well suited for pKa determination of individual amino acid side chains. The experiments follow the side-chain 15Nzeta (lysine) and 15Nepsilon or 13Czeta (arginine) chemical shift, which changes due to sizable changes in the heteronuclear electron distribution upon (de)protonation. Since heteronuclear chemical shifts are overwhelmed by the charge state of the amino acid side chain itself, these methods supersede 1H-based NMR in terms of accuracy, sensitivity, and selectivity. Moreover, the 15Nzeta and 15Nepsilon nuclei may be used to probe changes in the local electrostatic environment. Applications to three proteins are described: apo calmodulin, calbindin D9k, and FKBP12. For apo calmodulin, residue-specific pKa values of lysine side chains were determined to fall between 10.7 and 11.2 as a result of the high net negative charge on the protein surface. Ideal two-state titration behavior observed for all lysines indicates the absence of significant direct charge interactions between the basic residues. These results are compared with earlier studies based on chemical modification.     

Characterization of amino acid side chain losses in electron capture dissociation

We have used electrospray ionization (ESI) Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry to characterize amino acid side chain losses observed during electron capture dissociation (ECD) of ten 7- to 14-mer peptides. Side-chain cleavages were observed for arginine, histidine, asparagine or glutamine, methionine, and lysine residues. All peptides containing an arginine, histidine, asparagine or glutamine showed the losses associated with that residue. Methionine side-chain loss was observed for doubly-protonated bombesin. Lysine side-chain loss was observed for triply-protonated dynorphin A fragment 1-13 but not for the doubly-protonated ion. The proximity of arginine to a methoxy C-terminal group significantly enhances the extent of side-chain fragmentation. Fragment ions associated with side-chain losses were comparable in abundance to those resulting from backbone cleavage in all cases. In the ECD spectrum of one peptide, the major product was due to fragmentation within an arginine side chain. Our results suggest that cleavages within side chains should be taken into account in analysis of ECD mass spectral data. Losses from arginine, histidine, and asparigine/glutamine can be used to ascertain their presence, as in the analysis of unknown peptides, particularly those with non-linear structures.     

Effects of cation charge-site identity and position on electron-transfer dissociation of polypeptide cations

The effect of cation charge site on gas-phase ion/ion reactions between multiply protonated model peptides and singly charged anions has been examined. Insights are drawn from the quantitative examination of the product partitioning into competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer followed by dissociation (ETD) versus electron transfer without dissociation (ET, no D), and fragmentation of backbone bonds versus fragmentation of side chains. Peptide cations containing protonated lysine, arginine, and histidine showed similar degrees of electron transfer, which were much higher than the peptide having fixed-charge sites, that is, trimethyl ammonium groups. Among the four types of cation charge sites, protonated histidine showed the highest degree of ET, no D, while no apparent intact electron-transfer products were observed for peptides with protonated lysine or arginine. All cation types showed side chain losses with arginine yielding the greatest fraction and lysine the smallest. The above trends were observed for each electron-transfer reagent. However, proton transfer was consistently higher with 1,3-dinitrobeznene anions, as was the fraction of side-chain losses. The partitioning of products among the various electron-transfer channels provides evidence for several of the mechanisms that have been proposed to account for electron-transfer dissociation and electron-capture dissociation. The simplest picture to account for all of the observations recognizes that several mechanisms can contribute to the observed products. Furthermore, the identity of the anionic reagent and the positions of the charge sites can affect the relative contributions of the competing mechanisms.     

低浓度甲醛对多肽和蛋白化学修饰的质谱研究

采用基质辅助激光解析电离飞行时间质谱( MALDI-TOF MS)和纳升电喷雾四极杆飞行时间串联质谱( Nano-ESI -QTOF MS)技术,以标准肽段和流感病毒基质蛋白酶切肽段为模型,研究了甲醛对蛋白质和多肽主链的修饰作用。采用与实际病毒灭活过程一致的实验条件(4℃,0.025%(V/V)福尔马林(37%(w/w)甲醛溶液)处理72 h),进行甲醛与多肽的化学反应。结果表明,在实验条件下,甲醛能与标准肽段N端的氨基反应生成羟甲基加合物,再发生缩合反应生成亚胺,形成+12 Da的产物。此外,甲醛还能与标准肽段中的精氨酸、赖氨酸的侧链发生反应,生成+12 Da的反应产物。对流感病毒基质蛋白的酶切肽段与甲醛的反应的质谱分析结果显示,多数的肽段都生成了+24 Da的产物,质量的增加来源于肽段N端氨基(+12 Da)和C端精氨酸或赖氨酸的侧链(+12 Da)的贡献。此外,还观察到有一个漏切位点的肽段生成了+36 Da的产物。本研究结果表明,在实验条件下,低浓度甲醛主要与肽段和蛋白的N 端氨基,以及精氨酸和赖氨酸侧链发生反应。本研究为分析低浓度甲醛与蛋白质的反应产物提供了有效的质谱分析方法和解谱依据。     

Rational design of a reversible pH-responsive switch for peptide self-assembly

Peptide TZ1H, based on the heptad sequence of a coiled-coil trimer, undergoes fully reversible, pH-dependent self-assembly into long-aspect-ratio helical fibers. Substitution of isoleucine residues with histidine at the core d-positions of alternate heptads introduces a mechanism by which self-assembly is coupled to the protonation state of the imidazole side chain. Circular dichroism spectroscopy, transmission electron microscopy, and microrheology techniques revealed that the self-assembly of TZ1H coincides with a distinct coil-helix conformational transition that occurs within a narrow pH range near the pKa of the imidazole side chains of the core histidine residues.     

Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed helix-loop-helix motif peptide

A 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle has been designed to catalyze the hydrolysis of phosphodiesters. The active site on the surface of the folded catalyst is composed of two histidine and four arginine residues, with the capacity to provide general acid, general base, and/or nucleophilic catalysis as well as transition state stabilization. Uridine 3'-2,2,2 trichloroethylphosphate (2) is a mimic of RNA with a leaving group pKa of 12.3. Its hydrolysis is energetically less favorable than that of commonly used model substrates with p-nitrophenyl leaving groups and therefore a more realistic model for the design of catalysts capable of cleaving RNA. The second-order rate constant for the hydrolysis of 2 at pH 7.0 by the polypeptide catalyst was 418 x 10(-6) M-1 s-1, and that of the imidazole catalyzed reaction was 1.66 x 10(-6) M-1 s-1. The pH dependence suggested that catalysis is due to the unprotonated form of a residue with a pKa of around 5.3, and the observed kinetic solvent isotope effect of 1.9 showed that there is significant hydrogen bonding in the transition state, consistent with general acid-base catalysis. The rate constant ratio k2(Pep)/k2(Im) of 252 is probably due to a combination of nucleophilic and general acid-base catalysis, as well as transition state stabilization. Substrate binding was weak since no sign of saturation kinetics was observed for substrate concentrations in the range from 5 to 40 mM. The results provide a platform for the further development of catalysts for RNA cleavage with a potential role in the development of drugs.     

The effect of neighboring charges on the helix forming ability of charged amino acids in proteins.

It has been found that the fraction of glutamic acid residues which are helical in proteins is larger than might be expected from the experimentally determined value of the helical stability constants of glutamic acid. In order to understand this difference, the effect of neighboring charged side chains on the glutamic acid residues in proteins of known structure is examined. It is found that a positively charged side chain four residues away from a glutamic acid greatly enhances its probability to be helical. Similar results are obtained for aspartic acid, lysine, arginine, and histidine.     

Effect of Basic Amino Acids on Nickel Ion Reduction at a Mercury Electrode

In a 0.02 M borax solution (pH 8.5), basic amino acids (arginine, lysine, and ornithine) react with Ni²⁺ to form a mono‐ligand complex that is reduced at a mercury electrode at about ?0.85 V vs. Ag|AgCl|KCl (3 M). At a long time scale (staircase voltammetry; scan rate<50 mV s^?1), the complex reduction is a catalytic (EC′) process, the rate‐determining step being the regeneration of the reducible species by the reaction of the amino acid with free Ni²⁺. At a short time scale (differential pulse voltammetry or higher scan rate staircase voltammetry), the reaction rate is controlled by the diffusion of the complex. Although the same kind of complexation occurs with either basic amino acids or glycine, the last one does not induce a similar process. The peculiar effect of basic amino acids is due to the side chain that causes the ligand molecule to adopt a favorable orientation at the electrode surface. The differential pulse voltammetry peak current is proportional to the total amino acid concentration over the concentration range from 2 to 100 μM. Hence a voltammetric method for arginine determination in nutritional supplements was developed and validated using HPLC as reference method.     

The influence of side substituents in α-amino acids on their sorption by a cation-exchange membrane

The isotherms of sorption of ornithine, lysine, arginine, and histidine by an MK-40 membrane were obtained by the method of variable concentrations. The influence of the geometric parameters of side groups in the basic amino acids and pH on the degree of their absorption by the membrane was studied. The formation of doubly charged amino acid cations in the membrane phase when membranes in the H⁺ form were used was substantiated IR spectroscopically. The distribution coefficient was found to depend linearly on the size of amino acid side groups. The dependence of interphase surface tension at the membrane-solution interface on the degree of membrane filling was indicative of the formation of sorbate associates in the membrane phase.     

Effect of basic amino acids on photoreaction of ketoprofen in phosphate buffer solution

Photoreaction of ketoprofen (KP), one of the widely used nonsteroidal anti-inflammatory drugs (NSAIDs), was studied with transient absorption spectroscopy in phosphate buffer solution (pH 7.4) in the presence of basic amino acids of histidine (His), lysine (Lys) and arginine (Arg). Deprotonated form of KP (KP(-)) excited with UV-light irradiation gave rise to carbanion through a decarboxylation reaction. It was found that carbanion abstracted a proton from the side chain of the protonated amino acids to yield 3-ethylbenzophenone ketyl biradical (EBPH); however, no reaction was observed with alanine. The relative yield of EBPH by the proton transfer reaction with His was ca. 40 times larger than that of the other two basic amino acids, suggesting that the proton-donating ability of His (protonated His) should be quite high. The information on the photoreaction mechanism of NSAIDs with basic amino acids was essential to understand primary reaction of excited NSAIDs in vivo causing photosensitization on human skin.     

关于静电作用对酶活性部位残基pKa影响的定量计算

随着基因技术的发展,人们几乎已经可以任意替换蛋白质序列中的特定残基。由于理论上对蛋白质性能的预测工作还远远跟不上实验的发展,只能花费大量的人力、物力利用实验方法筛选突变体。这就迫切需要建立一套能够正确预测蛋白质性质的方法。静电作用在酶促反应中起到了重要作用。基于表面带电残基对酶活性部位残基pK_α的影响,可利用替换表面残基的方法改变酶促反应随pH的变化趋势,是蛋白质工程研究中的一种有效方法。由于表面极性残基处于高介电常数的溶剂(水)与低介电常数的蛋白质的界面上,对此问题尚未有圆满的理论方法进行解决。我们利用Kirkwood理论定量地表述了表面荷电残基的替换对酶活性部位残基pK_α的影响,为研究酶突变体的性质,如突变体的电化学性质、酶催化反应随pH变化趋势的改变,酶专一性的改变等提供了一种简便的方法。     

Potential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain

The issue of ionizable protein side chains interacting with lipid membranes has been the focus of much attention since the proposal of the paddle model of voltage-gated ion channels, which suggested multiple arginine (Arg) side chains may move through the hydrocarbon core of a lipid membrane. Recent cell biology experiments have also been interpreted to suggest that these side chains would face only small free energy penalties to cross membranes, challenging a long-standing view in membrane biophysics. Here, we employ side chain analog and transmembrane helix models to determine the free energy of an Arg side chain, as a function of protonation state, across a membrane. We observe high free energy barriers for both the charged and neutral states that would prohibit lipid-exposed movement. The mechanisms for charged and neutral Arg transport are, however, very different, with the neutral state experiencing simple dehydration, whereas the charged state experiences a complex mechanism involving connections to the bilayer interfaces that deform the local membrane structure. We employ special methods to ensure sampling of these interfacial connections and decompose the free energy to shed light on the mechanisms. These deformations are found to preferentially stabilize the protonated form, such that the Arg side chain remains almost exclusively charged inside the membrane, with a pKa shift of 相似文献   

Alpha-N-Benzoylarginine-2-naphthylamide hydrolase (cathepsin BI?) from rat skin. III. Substrate specificity, modifier characteristics, and transformation of the enzyme at acidic pH.

Some properties of rat skin benzoylarginine-2-naphthylamide hydrolase types I (preparations I and AI) and II (preparations II and NII) were studied. Both types were activated by dithiothreitol and EDTA, but responded differently to 1 mM KCN, when benzoylarginine-2-naphthylamide (BANA) was used as a substrate: type I was inhibited, while type II was activated. When leucine-2-naphthylamide was used as a substrate, both types were activated by KCN. Thiol proteinase inhibiting substances, like heavy metals, iodoacetic acid, 4-chloromercuribenzoic acid, and tosyllysine chloromethylketone, inhibited the enzymes. Diisopropylfluorophosphate, phenylmethylsulfonyfluoride, 4-aminobenzamidine, and high-molecular-weight trypsin inhibitors were without effect. The substrate specificity of rat skin BANA hydrolase resembled that of an amino acid naphthylamidase, naphthylamides of methionine, lysine, arginine, and alanine being hydrolyzed most rapidly. The rate of hydrolysis of BANA was only 11% of that of methionine naphthylamide. Amino acid esters with a free alpha-amino group were also good substrates. The transformation of type II to type I at acidic pH was studied. During the transformation amino acids or peptides were formed and probably some inhibitor present in type II was destroyed proteolytically.     

Specific ionic effect for simple and rapid colorimetric sensing assays of amino acids using gold nanoparticles modified with task-specific ionic liquid

In this study, a novel task-specific ionic liquid functionalized gold nanoparticle (TSIL-GNP) was successfully prepared and applied in the recognition of amino acids. Particularly, the surface of GNP was modified with the ionic liquid containing carbamido and ester group via thiol, which was characterized by Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM). The stability of this material in aqueous solution improves apparently and can remain unchanged for more than three months. The effect of pH was also discussed in this study. Attractive ionic interaction would effectively weaken intensity of the covalent coupling between the metal ion and the functional groups of amino acids. Thus, TSIL-GNP was successfully applied to recognizing serine, aspartic acid, lysine, arginine, and histidine in the presence of Cu²⁺ through distinctive color changes. Suspension would be generated once a spot of cysteine was added into the GNPs solution. Results indicated that it had a good linear relationship between extinction coefficients and concentration of amino acids in a wide range of 10⁻³–10⁻⁶ M. Moreover, the proposed strategy was successfully used to analyze the histidine in urinary samples. In brief, TSIL-GNP is a suitable substrate for discrimination of five amino acids in a rapid and simple way without sophisticated instruments.     

The adsorption of amino acids on the surface of highly dispersed silica

The adsorption of arginine, histidine, lysine, and ornithine on the surface of highly dispersed silica from aqueous solutions was studied as a function of pH. The equilibrium constants of the formation of surface complexes were calculated using the Stern model for the electrical double layer. It was shown that the possibility of adsorption of amino acids on the silica surface is determined by the presence of additional basic groups in their molecules.Translated from Kolloidnyi Zhurnal, Vol. 66, No. 6, 2004, pp. 733–738.Original Russian Text Copyright © 2004 by Vlasova, Golovkova.     

Gas-phase basicities of histidine and lysine and their selected di- and tripeptides

The gas-phase basicities (GB) of histidine, lysine, and di- and triglycyl peptides containing either one histidine or one lysine residue have been determined. In all, 12 compounds were examined in a Fourier transform ion cyclotron resonance mass spectrometer. The GBs of the biomolecules were evaluated by proton transfer reactions employing a range of reference compounds with varying gas-phase basicities. In addition, the GBs were determined by using the kinetic method of collision-induced dissociation on a proton-bound dimer containing the peptide and a reference compound. The GBs of histidine and lysine were both found to be 220.8 kcal/mol via proton transfer reactions. The kinetic method experiments, including dissociation of a proton-bound dimer containing both histidine and lysine, also suggest equivalent GBs for these amino acids. However, the small peptides containing lysine are generally more basic than the corresponding histidine-containing peptides. For the peptides, the data suggest that the protonation site is on the basic side chain functional group of the histidine or lysine residues. The GBs of the di- and tripeptides are dependent upon the location of the basic residue. For example, the GBs of the tripeptides glycylglycyl-l-lysine (GlyGlyLys) and l-lysylglycylglycine (LysGlyGly) were both determined to be 230.7 kcal/mol while a GB of kcal/mol was obtained for glycyl-l-lysylglycine (GlyLysGly). A similar GB trend is seen with the histidine-containing tripeptides. Generally, the GBs obtained by using the kinetic method are slightly higher than those obtained by deprotonation reactions; however, the trends in relative GB values are essentially the same with the two techniques.     

组氨酸激酶HK853酸碱调控机制的NMR研究

双组分信号转导系统是细菌应对外界刺激和调控自身生理活动的重要系统。组氨酸激酶是双组分信号转导系统的重要组成部分,大多数组氨酸激酶具有多功能性,不仅能自身磷酸化并能把磷酸基团传递给应激调节蛋白(Response regulator,RR)使之磷酸化,还能催化RR的去磷酸化。研究发现组氨酸激酶HK853的功能受pH值调控,该文利用选择性同位素标记方法,通过NMR技术研究了参与HK853与RR468相互作用的关键氨基酸位点。发现DHp结构域His260侧链的pKa值与HK853的磷酸酶活性有很好的对应关系,HK853与底物形成复合物后其pKa值降低,使His260侧链更易于去质子化,有助于HK853磷酸酶活性的提高。阐明了HK853行使磷酸酶功能时的酸碱调控机制。     

pH-induced micelle formation of poly(histidine-co-phenylalanine)-block-poly(ethylene glycol) in aqueous media

Poly[(L-histidine)-co-(L-phenylalanine)]-block-poly(ethylene glycol) (HF-b-PEG) diblock copolymers were synthesized to be used for preparation of pH-sensitive polymeric micelles. First, HF block was synthesized by ring opening copolymerization of L-histidine and L-phenylalanine N-carboxyanhydride, and then the resulting copolymer was coupled with PEG. The pKa value of diblock copolymer can be controlled by adjusting the histidine/phenylalanine ratio in HF block. It is observed that the block copolymers form micelles in aqueous media and that the micelles are spherical in shape with a unimodal distribution. The micelle is formed at pH higher than pKa of block copolymer while it is not formed at lower pH. This is because the protonation of histidine residue in the HF block converts the hydrophobic core into hydrophilic one at lower pH. Acid-Base titration profile of HF41(5600)-b-PEG, HF56(5500)-b-PEG, H(5100)-b-PEG and 0.1 N NaCl.     

Analysis of cyclic pyrolysis products formed from amino acid monomer

Amino acid was mixed with silica and tetramethylammonium hydroxide (TMAH) to favor pyrolysis of amino acid monomer. The pyrolysis products formed from amino acid monomer were using GC/MS and GC. 20 amino acids of alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine were analyzed. The pyrolysis products were divided into cyclic and non-cyclic products. Among the 20 amino acids, arginine, asparagine, glutamic acid, glutamine, histidine, lysine, and phenylalanine generated cyclic pyrolysis products of the monomer. New cyclic pyrolysis products were formed by isolation of amino acid monomers. They commonly had polar side functional groups to 5-, 6-, or 7-membered ring structure. Arginine, asparagine, glutamic acid, glutamine, histidine, and phenylalanine generated only 5- or 6-membered ring products. However, lysine generated both 6- and 7-membered ring compounds. Variations of the relative intensities of the cyclic pyrolysis products with the pyrolysis temperature and amino acid concentration were also investigated.     

Sequencing Lys-N Proteolytic Peptides by ESI and MALDI Tandem Mass Spectrometry

In this study, we explored the MS/MS behavior of various synthetic peptides that possess a lysine residue at the N-terminal position. These peptides were designed to mimic peptides produced upon proteolysis by the Lys-N enzyme, a metalloendopeptidase issued from a Japanese fungus Grifola frondosa that was recently investigated in proteomic studies as an alternative to trypsin digestion, as a specific cleavage at the amide X-Lys chain is obtained that provides N-terminal lysine peptide fragments. In contrast to tryptic peptides exhibiting a lysine or arginine residue solely at the C-terminal position, and are thus devoid of such basic amino acids within the sequence, these Lys-N proteolytic peptides can contain the highly basic arginine residue anywhere within the peptide chain. The fragmentation patterns of such sequences with the ESI-QqTOF and MALDI-TOF/TOF mass spectrometers commonly used in proteomic bottom-up experiments were investigated.