Modulation of calcium oxalate crystallization by linear aspartic acid-rich peptides

Calcium oxalate monohydrate (COM) kidney stone formation is prevented in most humans by urinary crystallization inhibitors. Urinary osteopontin (OPN) is a prototype of the aspartic acid-rich proteins (AARP) that modulate biomineralization. Synthetic poly(aspartic acids) that resemble functional domains of AARPs provide surrogate molecules for exploring the role of AARPs in biomineralization. Effects of linear aspartic acid-rich peptides on COM growth kinetics and morphology were evaluated by the combination of constant composition (CC) analysis and atomic force microscopy (AFM). A spacer amino acid (either glycine or serine) was incorporated during synthesis after each group of 3 aspartic acids (DDD) in the 27-mer peptide sequences. Kinetic CC studies revealed that the DDD peptide with serine spacers (DDDS) was more than 30 times more effective in inhibiting COM crystal growth than the DDD peptide with glycine spacers (DDDG). AFM revealed changes in morphology on (010) and (-101) COM faces that were generally similar to those previously described for OPN and citrate, respectively. At comparable peptide levels, the effects of step pinning and reduced growth rate caused by DDDS were remarkably greater. In CC nucleation studies, DDDS caused a greater prolongation of induction periods than DDDG. Thus, nucleation studies link changes in interfacial energy caused by peptide adsorption to COM to the CC growth and AFM results. These studies indicate that, in addition to the number of acidic residues, the contributions of other amino acids to the conformation of DDD peptides are also important determinants of the inhibition of COM nucleation and growth.     

Control of calcium oxalate crystal growth by face-specific adsorption of an osteopontin phosphopeptide

Mineral-associated proteins have been proposed to regulate many aspects of biomineralization, including the location, type, orientation, shape, and texture of crystals. To understand how proteins achieve this exquisite level of control, we are studying the interaction between the phosphoprotein osteopontin (OPN) and the biomineral calcium oxalate monohydrate (COM). In the present study, we have synthesized peptides corresponding to amino acids 220-235 of rat bone OPN (pSHEpSTEQSDAIDpSAEK), one of several highly phosphorylated, aspartic-, and glutamic acid-rich sequences found in the protein. To investigate the role of phosphorylation in interaction with crystals, peptides containing no (P0), one (P1), or all three (P3) phosphates were prepared. Using a novel combination of confocal microscopy and scanning electron microscopy, we show that these peptides adsorb preferentially to {100} faces of COM and inhibit growth of these faces in a phosphorylation-dependent manner. To characterize the mechanism of adsorption of OPN peptides to COM, we have performed the first atomic-scale molecular-dynamics simulation of a protein-crystal interaction. P3 adsorbs to the {100} face much more rapidly than P1, which in turn adsorbs more rapidly than P0. In all cases, aspartic and glutamic acid, not phosphoserine, are the amino acids in closest contact with the crystal surface. These studies have identified a COM face-specific adsorption motif in OPN and delineated separate roles for carboxylate and phosphate groups in inhibition of crystal growth by mineral-associated phosphoproteins. We propose that the formation of close-range, stable, and face-specific interactions is a key factor in the ability of phosphoproteins to regulate biomineralization processes.     

Probing crystallization of calcium oxalate monohydrate and the role of macromolecule additives with in situ atomic force microscopy

Kidney stones are crystal aggregates, most commonly containing calcium oxalate monohydrate (COM) microcrystals as the primary constituent. Macromolecules, specifically proteins rich with anionic side chains, are thought to play an important role in the regulation of COM growth, aggregation, and attachment to cells, all key processes in kidney stone formation. The microscopic events associated with crystal growth on the [010], [121], and [100] faces have been examined with in situ atomic force microscopy (AFM). Lattice images of each face reveal two-dimensional unit cells consistent with the COM crystal structure. Each face exhibits hillocks with step sites that can be assigned to specific crystal planes, enabling direct determination of growth rates along specific crystallographic directions. The rates of growth are found to depend on the degree of supersaturation of calcium oxalate in the growth medium, and the growth rates are very sensitive to the manner in which the growth solutions are prepared and introduced to the AFM cell. The addition of macromolecules with anionic side chains, specifically poly(acrylic acid), poly(aspartic acid), and poly(glutamic acid), results in inhibition of growth on the hillock step planes. The magnitude of this effect depends on the macromolecule structure, macromolecule concentration, and the identity of the step site. Poly(acrylic acid) was the most effective inhibitor of growth. Whereas poly(aspartic acid) inhibited growth on the (021) step planes of the (100) hillocks more than poly(glutamic acid), the opposite was found for the same step planes on the (010) hillocks. This suggests that growth inhibition is due to macromolecule binding to both planes of the step site or pinning of the steps due to binding to the (100) and (010) faces alone. The different profiles observed for these three macromolecules argue that local binding of anionic side chains to crystal surface sites governs growth inhibition rather than any secondary polymer structure. Growth inhibition by cationic macromolecules is negligible, further supporting an important role for proteins rich in anionic side chains in the regulation of kidney stone formation.     

Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite

The formation of biogenic materials requires the interaction of organic molecules with the mineral phase. In forming enamel, the amelogenin proteins contribute to the mineralization of hydroxyapatite (HAp). Leucine-rich amelogenin protein (LRAP) is a naturally occurring splice variant of amelogenin that comprises amelogenin's predicted HAp binding domains. We determined the partial structure of phosphorylated and non-phosphorylated LRAP variants bound to HAp using combined solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. New ssNMR measurements in the N-terminus indicate a largely extended structure for both variants, though some measurements are consistent with a partially helical N-terminal segment. The N-terminus of the phosphorylated variant is found to be consistently closer to the HAp surface than the non-phosphorylated variant. Structure prediction was biased using 21 ssNMR measurements in the N- and C-terminus at five HAp crystal faces. The predicted fold of LRAP is similar at all HAp faces studied, regardless of phosphorylation. Largely consistent with experimental observations, LRAP's predicted structure is relatively extended with a helix-turn-helix motif in the N-terminal domain and some helix in the C-terminal domain, and the N-terminal domain of the phosphorylated variant binds HAp more closely than the N-terminal domain of the non-phosphorylated variant. Predictions for both variants show some potential binding specificity for the {010} HAp crystal face, providing further support that amelogenins block crystal growth on the a and b faces to allow elongated crystals in the c-axis.     

Mimicking the biomolecular control of calcium oxalate monohydrate crystal growth: effect of contiguous glutamic acids

Scanning confocal interference microscopy (SCIM) and molecular dynamics (MD) simulations were used to investigate the adsorption of the synthetic polypeptide poly(l-glutamic acid) (poly-glu) to calcium oxalate monohydrate (COM) crystals and its effect on COM formation. At low concentrations (1 μg/mL), poly-glu inhibits growth most effectively in ?001? directions, indicating strong interactions of the polypeptide with {121} crystal faces. Growth in ?010? directions was inhibited only marginally by 1 μg/mL poly-glu, while growth in ?100? directions did not appear to be affected. This suggests that, at low concentrations, poly-glu inhibits lattice-ion addition to the faces of COM in the order {121} > {010} ≥ {100}. At high concentrations (6 μg/mL), poly-glu resulted in the formation of dumbbell-shaped crystals featuring concave troughs on the {100} faces. The effects on crystal growth indicate that, at high concentrations, poly-glu interacts with the faces of COM in the order {100} > {121} > {010}. This mirrors MD simulations, which predicted that poly-glu will adsorb to a {100} terrace plane (most calcium-rich) in preference to a {121} (oblique) riser plane but will adsorb to {121} riser plane in preference to an {010} terrace plane (least calcium-rich). The effects of different poly-glu concentration on COM growth (1-6 μg/mL) may be due to variations between the faces in terms of growth mechanism and/or (nano)roughness, which can affect surface energy. In addition, 1 μg/mL might not be adequate to reach the critical concentration for poly-glu to significantly pin step movement on {100} and {010} faces. Understanding the mechanisms involved in these processes is essential for the development of agents to reduce recurrence of kidney stone disease.     

Rigorous determination of the stoichiometry of protein phosphorylation using mass spectrometry

Quantification of the stoichiometry of phosphorylation is usually achieved using a mixture of phosphatase treatment and differential isotopic labeling. Here, we introduce a new approach to the concomitant determination of absolute protein concentration and the stoichiometry of phosphorylation at predefined sites. The method exploits QconCAT to quantify levels of phosphorylated and nonphosphorylated peptide sequences in a phosphoprotein. The nonphosphorylated sequence is used to determine the absolute protein quantity and serves as a reference to calculate the extent of phosphorylation at the second peptide. Thus, the stoichiometry of phosphorylation and the absolute protein concentration can be determined accurately in a single experiment.     

玉米须提取液对尿液中草酸钙晶体形成的影响

本文采用X射线衍射(XRD)、红外光谱(FTIR)、扫描电子显微镜(SEM)等方法分析了玉米须提取液对正常人尿液中草酸钙晶体形成的影响,通过电导率法研究了草酸钙晶体生长的动力学过程,以及从生物矿化的角度对玉米须提取液影响尿液中草酸钙晶体的可能机理进行了探讨。由于玉米须提取液中有机酸或多糖的羟基、羰基等通过配位作用与Ca²⁺结合形成可溶性配位化合物,减少了Ca²⁺与Oxa^2-的结合能力,从而抑制了CaOxa的成核和生长。同时,可能由于玉米须提取液中有效成分与二水草酸钙(COD)的吸附点键合,增强了COD晶体在溶液中的热力学稳定性,进而抑制了COD晶体向热力学更稳定态的一水草酸钙(COM)晶体转变。结果显示,这种抑制作用随玉米须浓度增大而增大,且COD晶体尺寸随着玉米须浓度的增大而减小。玉米须抑制COD晶体向COM晶体转变的作用为开发预防和治疗尿结石的药物提供了启示。     

HKC细胞损伤前后对草酸钙晶体吞噬能力的差异

采用人类肾脏近端小管上皮细胞系(HKC)建立氧化性损伤模型,研究损伤前后HKC调控草酸钙(CaOxa)结晶的差异。采用CCK-8法检测HKC的细胞活性;利用激光共聚焦显微镜观察HKC损伤后表达的晶体粘附分子骨桥蛋白(OPN);采用倒置显微镜观察HKC的形态变化;采用扫描电子显微镜(SEM)观察HKC微结构及其诱导的晶体;采用X射线衍射分析(XRD)表征晶体的组分。在CaOxa过饱和溶液中,正常HKC主要诱导形成二水草酸钙(COD)晶体,而损伤HKC则同时诱导了COD和一水草酸钙(COM)晶体。正常HKC对COD晶体有较强的吞噬能力,而损伤HKC的这种能力较弱;HKC损伤后表达OPN,促进CaOxa晶体的成核和聚集,从而增加了肾结石形成的危险性。     

粘液素对草酸钙晶体生长的影响

泌尿系结石是一种常见疾病。在70％以上的结石中,草酸钙(CaOxa)单独或和其它钙盐共同为主要成分。一般认为正常人不形成尿石是其尿液中存在的抑制剂抑制了CaOxa晶体的成核、生长、聚集或固相转化。     

Molecular recognition and fluorescence sensing of monophosphorylated peptides in aqueous solution by bis(zinc(II)-dipicolylamine)-based artificial receptors

The phosphorylation of proteins represents a ubiquitous mechanism for the cellular signal control of many different processes, and thus selective recognition and sensing of phosphorylated peptides and proteins in aqueous solution should be regarded as important targets in the research field of molecular recognition. We now describe the design of fluorescent chemosensors bearing two zinc ions coordinated to distinct dipicolylamine (Dpa) sites. Fluorescence titration experiments show the selective and strong binding toward phosphate derivatives in aqueous solution. On the basis of (1)H NMR and (31)P NMR studies, and the single-crystal X-ray structural analysis, it is clear that two Zn(Dpa) units of the binuclear receptors cooperatively act to bind a phosphate site of these derivatives. Good agreement of the binding affinity estimated by isothermal titration calorimetry with fluorescence titration measurements revealed that these two receptors can fluorometrically sense several phosphorylated peptides that have consensus sequences modified with natural kinases. These chemosensors display the following significant features: (i) clear distinction between phosphorylated and nonphosphorylated peptides, (ii) sequence-dependent recognition, and (iii) strong binding to a negatively charged phosphorylated peptide, all of which can be mainly ascribed to coordination chemistry and electrostatic interactions between the receptors and the corresponding peptides. Detailed titration experiments clarified that the phosphate anion-assisted coordination of the second Zn(II) to the binuclear receptors is crucial for the fluorescence intensification upon binding to the phosphorylated derivatives. In addition, it is demonstrated that the binuclear receptors can be useful for the convenient fluorescent detection of a natural phosphatase (PTP1B) catalyzed dephosphorylation.     

Analysis of effect of casein phosphopeptides on zinc binding using mass spectrometry

Phosphorylation is one of the key events in signal transduction and zinc plays an important catalytic and/or structural role in many biological systems. The binding of Zn to a phosphopeptide will alter the physiological functions of a peptide. The binding of casein phosphopeptides (CPPs) to Zn has been analyzed using nanospray mass spectrometry. Electrospray ionization (ESI) spectra of peptides produced by tryptic digestion of alpha-casein incubated with Zn show both free and Zn-bound phosphopeptides. The interaction of CPPs and the corresponding dephosphorylated peptides with zinc is compared. This study demonstrates that the phosphorylation state of a peptide dramatically affects Zn binding, with the decrease in Zn-bound forms of peptide paralleling the decrease in phosphorylation as casein is chemically dephosphorylated, although, in some cases, a small amount of residual Zn-binding capacity remains in the completely dephosphorylated peptide. The observed fragmentation patterns of the Zn-bound CPPs support the thesis that nonphosphorylated residues are involved in the metal binding.     

Designed high affinity Cu2+-binding alpha-helical foldamer

The design, synthesis, and characterization of a folded high-affinity metal-binding peptide is described. Based on the previously described folded peptide NTH-18, in which an alpha-helix was constrained through two disulfide bonds to a C-terminal extension of noncanonical secondary structure, a peptide (1) was designed to contain two histidine residues in positions 3 and 7. Air oxidation of 1 led to the formation of peptide 2, which contained two intramolecular disulfide bonds. The presence of the two histidines significantly destabilized the alpha-helical structure of 2 when compared to NTH-18. However, CD spectroscopy revealed that the addition of certain transition metal ions allowed the reformation of a stable alpha-helix. CD, NMR, and EPR spectroscopy as well as MALDI-TOF mass spectrometry indicated that 2 bound to Cu2+ to form a 1:1 complex via the imidazoles of the two histidine side chains. A glycine displacement assay revealed a dissociation constant for this complex of 5 nM at pH 8, which is the lowest reported value for a designed Cu2+-binding peptide. This peptide displayed more than 100-fold selectivity for Cu2+ over Zn2+, Ni2+, and Co2+. The 1.05 A crystal structure of the Cu(II)-complex of 2 revealed a square-pyramidal coordination geometry and confirmed that 2 bound to copper in an alpha-helical conformation via its two histidine side chains. The high affinity metal binding of peptide 2 demonstrates that metals can be used for the selective nucleation of alpha-helices.     

Random Re-entry Theory of Polymer Melt Crystallization

Consideration of crystallization kinetics in high molecular weight polymers shows that adjacent re-entry is unlikely in melt crystallization and that sections of individual chains will crystallize concurrently at several sites. Surface nucleation controlled growth models can be set up which do not require adjacent re-entry but are in agreement with observations on growth rates and crystal thicknesses. The predominant process in crystallization with random re-entry is the incorporation into the crystal of a loop of chain which has both ends attached to the crystal surface. This leads to predictions of the crystallinity of quenched, spherulitic polymers. Radii of gyration of chains in the crystalline state can be calculated and are in agreement with neutron scattering results.     

极性晶体结晶习性的形成机理

将负离子配位多面体生长基元模型应用于对极性晶体结晶习性的研究。从结晶化学角度探讨了晶体中负离子配位多面体的结晶方位与晶体各族晶面显露规律，提出负离子配位多面体在晶体各族晶面上联结的稳定性决定了晶面的生长速率。在不同的生长温度和溶液碱浓度下，负离子配住多面体相互联结构成不同维度的生长基元，而不同维度的生长基元往晶体各族晶面上叠合的速率比例是在变化的，这是导致晶体结晶形态多变性的主要原因。同时提出：如果把PBC模型中的化学键链设定为配位多面体相联结的键链，使得极性晶体结晶习性中难以解释的问题就会迎刃而解，从而使PBC理论模型的应用会得到更进一步的拓宽。     

Truncation,modification, and optimization of MIG6segment 2 peptide to target lung cancer-related EGFR

Human epidermal growth factor receptor (EGFR) plays a central role in the pathological progression and metastasis of lung cancer; the development and clinical application of therapeutic agents that target the receptor provide important insights for new lung cancer therapies. The tumor-suppressor protein MIG6 is a negative regulator of EGFR, which can bind at the activation interface of asymmetric dimer of EGFR kinase domains to disrupt dimerization and then inactivate the kinase (Zhang X. et al. Nature 2007, 450: 741–744). The protein adopts two separated segments, i.e. MIG6^{segment 1} and MIG6^{segment 2}, to directly interact with EGFR. Here, computational modeling and analysis of the intermolecular interaction between EGFR kinase domain and MIG6^{segment 2} peptide revealed that the peptide is folded into a two-stranded β-sheet composed of β-strand 1 and β-strand 2; only the β-strand 2 can directly interact with EGFR activation loop, while leaving β-strand 1 apart from the kinase. A C-terminal island within the β-strand 2 is primarily responsible for peptide binding, which was truncated from the MIG6^{segment 2} and exhibited weak affinity to EGFR kinase domain. Structural and energetic analysis suggested that phosphorylation at residues Tyr394 and Tyr395 of truncated peptide can considerably improve EGFR affinity, and mutation of other residues can further optimize the peptide binding capability. Subsequently, three derivative versions of the truncated peptide, including phosphorylated and dephosphorylated peptides as well as a double-point mutant were synthesized and purified, and their affinities to the recombinant protein of human EGFR kinase domain were determined by fluorescence anisotropy titration. As expected theoretically, the dephosphorylated peptide has no observable binding to the kinase, and phosphorylation and mutation can confer low and moderate affinities to the peptide, respectively, suggesting a good consistence between the computational analysis and experimental assay.     

海藻硫酸多糖抑制草酸钙结石形成的化学模拟

用体外模拟方法研究了从海藻异枝麒麟菜中提取的硫酸多糖(ESPS)对尿结石患者尿液中草酸钙晶体生长的影响. ESPS不但诱导与尿路细胞膜粘附力较弱的二水草酸钙晶体形成, 而且抑制一水草酸钙的生长和聚集, 归因于一水草酸钙的富钙(101)晶面与聚阴离子ESPS之间的静电相互作用. 上述结果表明, ESPS是一种抑制草酸钙结石的潜在绿色药物.     

Mass-based classification (MBC) of peptides: Highly accurate precursor ion mass values can be used to directly recognize peptide phosphorylation

Accurate mass values as obtainable by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) were employed in a theoretical study to differentiate between nonmodified and phosphorylated peptides. It was found that for peptide masses up to 1,000 u more than 98% of all theoretical monophosphorylated peptides (all possible combinations of proteinogenic amino acids having one phosphorylation on S, T, or Y) can be distinguished from nonphosphorylated peptides directly by their mass, if mass values are determined with an accuracy of better than +/-0.1 ppm. At a peptide mass of 1,500 u still 70% of all possible monophosphorylated peptides are distinguishable from nonmodified peptides by their accurate mass alone. In contrast to established techniques of data-dependent multidimensional mass spectrometry, only the mass of the precursor ion is necessary to decide upon subsequent fragment ion analysis of a peptide for sequence analysis in an LC-MS/MS investigation of a complex sample, when using a precalculated mass distribution table of theoretical peptides. A mass distribution table of nonphosphorylated and monophosphorylated peptides with a bin width of 0.1 mu was made available via the open web site www.peptidecomposer.com.     

Dynamic identification of phosphopeptides using immobilized metal ion affinity chromatography enrichment, subsequent partial beta-elimination/chemical tagging and matrix-assisted laser desorption/ionization mass spectrometric analysis

The enrichment of phosphopeptides using immobilized metal ion affinity chromatography (IMAC) and subsequent mass spectrometric analysis is a powerful protocol for detecting phosphopeptides and analyzing their phosphorylation state. However, nonspecific binding peptides, such as acidic, nonphosphorylated peptides, often coelute and make analyses of mass spectra difficult. This study used a partial chemical tagging reaction of a phosphopeptide mixture, enriched by IMAC and contaminated with nonspecific binding peptides, following a modified beta-elimination/Michael addition method, and dynamic mass analysis of the resulting peptide pool. Mercaptoethanol was used as a chemical tag and nitrilotriacetic acid (NTA) immobilized on Sepharose beads was used for IMAC enrichment. The time-dependent dynamic mass analysis of the partially tagged reaction mixture detected intact phosphopeptides and their mercaptoethanol-tagged derivatives simultaneously by their mass difference (-20 Da for each phosphorylation site). The number of new peaks appearing with the mass shift gave the number of multiply phosphorylated sites in a phosphopeptide. Therefore, this partial chemical tagging/dynamic mass analysis method can be a powerful tool for rapid and efficient phosphopeptide identification and analysis of the phosphorylation state concurrently using only MS analysis data.     

Simulation of calcium oxalate stone <Emphasis Type="Italic">in vitro</Emphasis>

Crystallization of calcium oxalate is studied mainly in the diluted healthy urine using scanning electron microscopy (SEM), and is compared with the crystallization in the diluted pathological urine. It suggests that the average sizes of calcium oxalate crystals are not in direct proportion to the concentrations of Ca²⁺ and Ox^2- ions. Only in the concentration range of 0.60-0.90 mmol/L can larger size of CaOx crystals appear. When the concentrations of Ca²⁺ and Ox^2- ions are 1.20, 0.80, 0.60, 0.30 and 0.15 mmol/L in the healthy urine, the average sizes of calcium oxalate crystallites are 9.5 X 6.5, 20.0 X 13.5 and 15.0 jj,m X 10.0 jj,m, respectively, for the former three samples after 6 d crystallization. No crystal appears even after 30 d crystallization for the samples of concentrations of 0.30 and 0.15 mmol/L due to their low supersaturations. The results theoretically explain why the probability of stone forming is clinically not in direct proportion to the concentrations of Ca²⁺ and Ox^2- ions. Laser scattering technology also confirms this point. The reason why healthy human has no risk of urinary stone but stone-formers have is that there are more urinary macromolecules in healthy human urines than that in stone-forming urines. These macromolecules may control the transformation in CaOx crystal structure from monohydrate cal-cium oxalate (COM) to dihydrate calcium oxalate (COD). COD has a weaker affinity for renal tubule cell membranes than COM. No remarkable effect of the crystallization time is observed on the crystal morphology of CaOx. All the crystals are obtuse hexagon. However, the sizes and the number of CaOx crystals can be affected by the crystallization time. In the early stage of crystalli-zation (1-6 d), the sizes of CaOx crystals increase and the number of crystal particles changes little as increasing the crystallization time due to growth control. In the middle and late stages (6-30 d), the number of crystals increases markedly while the growth rate changes little due to the nucleation control.