Serine Molecules Research Articles

Alkali Metal-Cationized Serine Clusters Studied by Sonic Spray Ionization Tandem Mass Spectrometry

Serine solutions containing salts of alkali metals yield magic number clusters of the type (Ser(4)+C)(+), (Ser(8)+C)(+), (Ser(12)+C)(+), and (Ser(17)+2C)(+2) (where C = Li(+), Na(+), K(+), Rb(+), or Cs(+)), in relative abundances which are strongly dependent on the cation size. Strong selectivity for homochirality is involved in the formation of serine tetramers cationized by K(+), Rb(+), and Cs(+). This is also the case for the octamers cationized by the smaller alkalis but there is a strong preference for heterochirality in the octamers cationized by the larger alkali cations. Tandem mass spectrometry shows that the octamers and dodecamers cationized by K(+), Rb(+), and Cs(+) dissociate mainly by the loss of Ser(4) units, suggesting that the neutral tetramers are the stable building blocks of the observed larger aggregates, (Ser(8)+C)(+) and (Ser(12)+C)(+). Remarkably, although the Ser(4) units are formed with a strong preference for homochirality, they aggregate further regardless of their handedness and, therefore, with a preference for the nominally racemic 4D:4L structure and an overall strong heterochiral preference. The octamers cationized by K(+), Rb(+), or Cs(+) therefore represent a new type of cluster ion that is homochiral in its internal subunits, which then assemble in a random fashion to form octamers. We tentatively interpret the homochirality of these tetramers as a consequence of assembly of the serine molecules around a central metal ion. The data provide additional evidence that the neutral serine octamer is homochiral and is readily cationized by smaller ions.

Contribution of Platelets and Erythrocytes to Thrombin Generation in Patients with β-Thalassemia.

Patients with β-thalassemia show an abnormally high proportion of red blood cells (RBCs) with exposed phosphatidyl serine (PS) molecules on the RBC membrane, which may contribute to thrombophilia in these patients (1). We have reported previously (2) that thromboxane A2 and free-arachidonate—substances released from activated platelets—induce PS exposure in a subpopulation of normal RBCs. The aims of the present study were first, to evaluate the presence of activated circulating platelets in patients with β-thalassemia, and second, to determine tissue factor (TF)-initiated thrombin generation in plasma and the influence of RBCs, platelets and their cooperation on this process in normal subjects and patients with β-thalassemia. Thrombin generation was assessed according to Hemker et al. (3) in 12 patients with β-thalassemia diagnosed by molecular biology, age 5–33 years and in 18 normal subjects. Two patients had thalassemia major (T-M) requiring blood transfusion every 3 weeks and the analysis were performed just prior transfusion. Two had thalassemia intermedia (T-I) with esplenectomy without transfusion requirements and eight had thalassemia minor (T-m). Thrombin generation was evaluated in platelet-poor plasma (PP), platelet-rich plasma (PRP), RBCs in the plasma (P-RBC) and in the presence of both cell types (PRP+RBC). The presence of activated platelets in circulation was evaluated in whole blood by flow cytometry. We monitored P-selectin (CD-62) and the activated αIIbβ3 receptor, defined as PAC-1 binding. The percentage of platelets exposing activation markers CD-62 (mean± SEM, 0.72± 0.17 vs. 4.03± 1.39) and PAC-1(0.75± 0.14 vs. 12.26± 6.47) were significantly higher in patients than in control subjects (P < 0.05). In normal subjects, the presence of erythrocytes in plasma (P-RBC) triggered a quicker thrombin generation and a significant elevation in the thrombin peak (32 ± 5 nM in PP vs. 86 ± 16 nM in P-RBC; P < 0.05), in the absence of cell lysis. These effects of RBCs were markedly higher in the patients with β-thalassemia, who had 2.5-fold higher thrombin generation at 3 min and higher peak thrombin levels (86 ± 16 nM in controls vs. 130 ± 15 nM in patients; P < 0.05). Thrombin generation in PRP was also higher in the patients with thalassemia at early times (3 min; 19 ± 3 nM in controls vs. 43 ± 8 nM in patients; P < 0.05). Importantly, the rate and peak of thrombin generation were significantly amplified by the presence of both cell types (PRP+RBCs), suggesting a biochemical cooperation between activated platelets and RBCs for thrombin generation. This was enhanced in patients with β-thalassemia, particularly those with T-I. In conclusion, chronic platelet activation in patients with β-thalassemia may influence TF-induced thrombin generation in platelets and erythrocytes. Thrombin generation appears to be a novel mode of platelet-erythrocyte cooperation in thrombogenesis.

High-pressure neutron diffraction study of L-serine-I and L-serine-II, and the structure of L-serine-III at 8.1 GPa

The hydrostatic compression of L-serine-d(7) has been studied to 8.1 GPa by neutron powder diffraction. Over the course of this pressure range the compound undergoes two phase transitions, the first between 4.6 and 5.2 GPa, yielding L-serine-II, and the second between 7.3 and 8.1 GPa, yielding L-serine-III. All three polymorphs are orthorhombic, P2(1)2(1)2(1), and feature chains of serine molecules connected via head-to-tail ND...O hydrogen bonds formed between ammonium and carboxylate groups. The chains are linked into a ribbon by a second set of ND...O hydrogen bonds. The hydroxyl moieties are distributed along the outer edges of the ribbon and in phase I they connect the ribbons into a layer by chains of OD...OD hydrogen bonds. The layers are connected together by a third set of ND...O hydrogen bonds, forming R;3_4(14) rings with substantial voids at their centres. In the transition from phase I to II these voids begin to close up, but at the cost of breaking the OD...OD chains. The OD...OD hydrogen bonds are replaced by shorter OD...O hydrogen bonds to carboxylate groups. At 7.3 GPa the O...O distance in the OD...O hydrogen bonds measures only 2.516 (17) A, which is short, and we propose that the phase transition to phase III that occurs between 7.3 and 8.1 GPa relieves the strain that has built up in this region of the structure. The hydroxyl D atom now bifurcates between the OD...O contact that had been present in phase II and a new OD...O contact formed to a carboxylate in another layer. Hirshfeld surface fingerprint plots show that D...D interactions become more numerous, while hydrogen bonds actually begin to lengthen in the transition from phase II to III.

Determination of the crystal structure of EntA, a 2,3-dihydro-2,3-dihydroxybenzoic acid dehydrogenase fromEscherichia coli

The Escherichia coli enterobactin synthetic cluster is composed of six proteins, EntA-EntF, that form the enterobactin molecule from three serine molecules and three molecules of 2,3-dihydroxybenzoic acid (DHB). EntC, EntB and EntA catalyze the three-step synthesis of DHB from chorismate. EntA is a member of the short-chain oxidoreductase (SCOR) family of proteins and catalyzes the final step in DHB synthesis, the NAD+-dependent oxidation of 2,3-dihydro-2,3-dihydroxybenzoic acid to DHB. The structure of EntA has been determined by multi-wavelength anomalous dispersion methods. Here, the 2.0 A crystal structure of EntA in the unliganded form is presented. Analysis of the structure in light of recent structural and bioinformatic analysis of other members of the SCOR family provides insight into the residues involved in cofactor and substrate binding.

Vibrational Spectroscopic Studies of the Interaction of Water with Serine

The vibrational dynamics of water around serine was investigated by using Raman spectroscopy and inelastic incoherent neutron scattering. Experiments with serine in deuterium oxide were performed to assist the assignment. The study shows that for the serine, the exchange of protons-deuterons on the active -NH3+ and -OH groups were relatively easy, whereas there were hardly any exchanged on the -CH or -CH2- groups. The main features of the spectra for hydrated samples (versus the dry samples) were altered considerably; new sharp peaks in the measured spectra appeared, indicating that the hydrogen bonding between water and serine had disturbed the structure of the serine molecule.

Study of the hydrogen bonding interaction of 1:1 complexes of serine with formamide using density functional theory

The hydrogen bonding of 1:1 complexes formed between formamide and serine molecules has been completely investigated in the present study using density functional theory (DFT) method at varied basis set levels from 6-31G to 6-311++G(d,p). Fifteen reasonable geometries on the potential energy hypersurface of formamide and serine system are considered with the global minimum, 13 of them are cyclic double-hydrogen bonded structures and the other two are one-hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

AbstractThe hydrogen bonding of 1:1 complexes formed between serine and water molecules were completely investigated in the present study employing ab initio and Density Functional Theory (DFT) methods at varied basis set levels from 6‐31g to 6‐311++g (2d,2p). For comparison, we also used the second‐order Moller–Plesset Perturbation (MP2) method at the 6‐31+g(d) level. Twelve reasonable geometries on the potential energy hypersurface of serine and water system were considered with the global minimum, 10 of which are cyclic double‐hydrogen bonded structures and the other two are one‐hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels were estimated. The infrared spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the serine–water complexes were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐311++g(d,p) level. The results indicate that the polarity of the solvent played an important role in the structures and relative stabilities of different isomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Crystal structure of L-serine phosphate

The crystal structure of L-serine phosphate (C3O3NH7 · H3PO4) is determined by single-crystal X-ray diffraction. The unit cell parameters are as follows: a = 9.134(5) A, b = 9.489(5) A, c = 4.615(5) A, γ = 99.54(5)°, space group P21, and Z = 2. The amino group of serine is protonated by a hydrogen atom of the phosphoric acid. The H2PO 4 1− ions are linked by hydrogen bonds into infinite ribbons aligned along the twofold screw axes. The ribbons form layers alternating with layers of serine molecules, which are directly linked by hydrogen bonds.

Amino acid chemistry in solution: structural properties and vibrational dynamics of serine using density functional theory and a continuum solvent model

A structural and vibrational study of amino acid serine in aqueous solution has been carried out using Fourier transform spectroscopies and quantum mechanical calculations. FT-IR and FT-Raman spectra of serine in H2O and D2O solutions were recorded and a general assignment of the observed bands was proposed on the basis of a zwitterionic structure for serine. Main criteria were the observed wavenumber shifts upon deuteration and previous assignments for other amino acids. A quadratic force field was computed using ab initio methodology at the 6-31+G** level and the hybrid functional B3LYP. The solvent effect was simulated by placing the serine molecule into an ellipsoidal cavity surrounded by a continuum solvent characterized by its dielectric constant. The solute–solvent electrostatic interaction was evaluated by means a multipolar moment expansion introduced in the Hamiltonian. The ab initio force field was obtained from the analytical second derivatives of the molecular geometry evaluated in a point of minimal energy, which was reached under the same calculation methodology. The optimized structural parameters were compared to those reported for l-serine crystal, which confirmed the zwitterionic structure for this molecule in aqueous solution. Ab initio force constants in cartesian coordinates were transformed into a set of locally symmetrized internal coordinates, thus allowing for a scaling procedure using two generic factors. Normal mode description was obtained as the potential energy distribution. The scaled wavenumbers were compared with those experimental in order to check the previous assignments. It also allowed us to add new data to the sets of experimental wavenumbers. Infrared intensities were calculated for both, H2O and D2O solutions, and compared to the experimental intensities.

Bacterial chemotaxis

Bacterial chemotaxis

Confinement of (S)-serine in tetra-p-sulfonatocalix[4]arene bilayers

Supramolecular complexes of tetra-p-sulfonatocalix[4]arene and (S)-serine have been isolated in the solid state and their molecular structures elucidated by X-ray diffraction studies. Chiral pairs of (S)-serine molecules are confined in ‘capsules’ of tetra-p-sulfonatocalix[4]arene in an overall bilayer arrangement. Complexes containing differing amounts of sodium and caesium cations are reported.

Cofactor Binding to Escherichia colid-3-Phosphoglycerate Dehydrogenase Induces Multiple Conformations Which Alter Effector Binding

The inhibition of Escherichia coli d-3-phosphoglycerate dehydrogenase by l-serine is positively cooperative with a Hill coefficient of approximately 2, whereas the binding of the inhibitor, l-serine, to the apoenzyme displays positive cooperativity in the binding of the first two serine molecules and negative cooperativity in the binding of the last two serine molecules. An earlier report demonstrated that the presence of phosphate appeared to lessen the degree of both the positive and negative cooperativity, but the cause of this effect was unknown. This study demonstrates that the presence of intrinsically bound NADH was responsible to a substantial degree for this effect. In addition, this study also provides evidence for negative cooperativity in NADH binding and for at least two NADH-induced conformational forms of the enzyme that bind the inhibitor in the physiological range. Successive binding of NADH to the enzyme resulted in an increase in the affinity for the first inhibitor ligand bound and a lessening of both the positive and negative cooperativity of inhibitor binding as compared with that seen in the absence of NADH. This effect was specific for NADH and was not observed in the presence of NAD+ or the substrate alpha-ketoglutarate. Conversely, the binding of l-serine did not have a significant effect on the stoichiometry of NADH binding, consistent with it being a V-type allosteric system. Thus, cofactor-related conditions were found in equilibrium binding experiments that significantly altered the cooperativity of inhibitor binding. Since the result of inhibitor binding is a reduction in the catalytic activity, the binding of inhibitor to these NADH-induced conformers must also induce additional conformations that lead to differential inhibition of catalytic activity.

Chiroselective self-directed octamerization of serine: implications for homochirogenesis.

Serine undergoes chiroselective self-directed oligomerization to form a singly protonated octamer under positive ion electrospray conditions, as identified by ion trap tandem mass spectrometry. The experiments also show a series of higher-order clusters (metaclusters) corresponding to [(Ser8H)n]n+, n = 1, 2, 3. There is a magic number effect favoring formation of the protonated octamer over its homologues and also a strong preference for octamer formation from homochiral serine molecules. Collision-induced dissociation suggests that the protonated octamer is composed of four hydrogen-bonded dimers, stabilized by further extensive hydrogen bonding. Density functional calculations support this model and show that the protonated homochiral octamer is energetically stabilized relative to its possible fragments (dimer plus protonated hexamer, etc). The calculations also show that heterochiral octamers are less stable than homochiral octamers (e.g., the protonated 7:1 cluster is 2.1 kcal/mol less stable than the 8:0 analogue). The implications of these results for the origin of homochirality are discussed.

Adsorption of [formula omitted]-Phospho-[formula omitted]-Serine and [formula omitted]-Serine onto Poorly Crystalline Apatite

The adsorption of phosphoserine and serine was studied to determine the effect of amino acid functional groups on the surface reactivity of synthetic poorly crystalline apatite similar to bone mineral. The experimental results for phosphoserine and serine uptake agree respectively with the Langmuir and Freundlich models. Phosphoserine exhibits stronger adsorption capacity and a higher affinity constant for the surface crystals compared to serine molecules. The enhanced adsorption capacity noted for phosphoserine might be related to the presence of phosphate groups in the molecule, which are specific attachment sites. This observation suggests that the strength of phosphate bonds to the solid surface, especially to calcium ions, is higher than that of carboxyl and hydroxyl ones. Spectroscopic observations provide evidence of an adsorption mechanism involving the anionic species of the amino acids and the surface of the crystals. Thus, a change in the position of the band of carboxyl groups occurred for the adsorbed molecules compared to the native amino acids. This revealed that the molecular residues do interact with apatite surface calcium. The shift noted in the frequencies of the bands associated with carboxylate vibrations is more pronounced for phosphoserine, confirming the stronger interaction noted for this molecule. Based on these results, one can conclude that the sorbent and sorbate charged species play an important role in the mechanism of uptake of the amino acids onto crystal surfaces. This may contribute to a better understanding of the mechanism by which phosphoproteins could influence mineralization processes and caries.

Organization of water molecules by adhering to oriented layers of dipalmitoylphosphatidyl serine in the presence of varying concentrations of cholesterol

About seven water molecules adhere to one molecule of dipalmitoylphosphatidyl serine (DPPS) in an oriented surface layer as inferred from the increase of the dichroic ratio R of their OH stretching vibration band (3400 cm −1) from 2 in the random bulk state to about 2.8 when adhering to DPPS. In DPPS–cholesterol mixtures the number of water molecules adhering to the phospholipid molecules and oriented by them increases as cholesterol content increases. This increase is very steep between molar fractions of cholesterol X(chol)=0.2–0.4 and at X(chol)=0.6 about 13 water molecules adhere and are oriented by one DPPS molecule.

Hydration of phosphatidyl serine multilayers and its modulation by conformational change induced by correlated electrostatic interaction

Hydration of the various residues of phospholipids was inferred from the shift in the wave number of their vibration bands, obtained from the amplitudes of their positive and negative peaks in the difference spectra between those of the hydrated and the dry phospholipid multibilayers. The effect of aligned phospholipid layers on the orientation of their hydrating water molecules was inferred from the dichroic ratio of the OH stretching band, measured by polarized attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) with a germanium prism, as a function of the water-to- lipid ratio in the surface film. The results indicate that about seven water molecules are oriented by one phosphatidyl serine molecule in the surface film. About 8 to 11 additional water molecules contribute to the hydration of the polar residues as revealed by the effect on the difference spectra. The hydration appears to be cooperative. A water molecule that initiates hydration of a site facilitates access of additional water molecules, until the hydration of the whole site composed of many different interacting polar residues is completed.

Probing the Regulatory Domain Interface ofd-3-Phosphoglycerate Dehydrogenase with Engineered Tryptophan Residues

D-3-Phosphoglycerate dehydrogenase from Escherichia coli is a homotetrameric enzyme which is allosterically regulated by the end product of its pathway, L-serine. The enzyme binds 4 L-serine molecules at two interfaces formed by the noncovalent association of the regulatory domains. The two domains that comprise each interface are related by an approximately 180 degrees axis of symmetry, and two serine molecules bind at each interface by forming a hydrogen bond network between the domains. A model has been proposed that suggests that serine functions by drawing adjacent domains together and that this in turn translates a conformational change to the active site. A tryptophan residue has been engineered into the helices flanking the regulatory interfaces that displays significant quenching in response to serine binding. Residues on the adjacent subunit appear to be primarily responsible for the tryptophan quenching and thus support the hypothesis that serine binding leads to an increase in the proximity between residues on neighboring subunits. Serine binding studies show that this quenching, as well as inhibition of enzymatic activity, are essentially complete when only two of the four serine binding sites are occupied. The requirement for only one serine per interface is consistent with the notion that the interface is formed by relatively rigid domains and that hydrogen bonding at only a single site is all that is required to substantially close the interface. The fluorescence quenching in response to L-serine binding generally correlates with enzymatic inhibition, but there appears to be a slight lag in inhibition relative to quenching at low serine concentrations. The observed fluorescence quenching of residues in the regulatory domains of D-3-phosphoglycerate dehydrogenase provide the first direct evidence for a conformational change in response to effector binding and provide a means to monitor the first step in the allosteric mechanism.

A model for the regulation of D-3-phosphoglycerate dehydrogenase, a Vmax-type allosteric enzyme.

Escherichia coli D-3-phosphoglycerate dehydrogenase (ePGDH) is a tetramer of identical subunits that is allosterically inhibited by L-serine, the end product of its metabolic pathway. Because serine binding affects the velocity of the reaction and not the binding of substrate or cofactor, the enzyme is classified as of the Vmax type. Inhibition by a variety of amino acids and analogues of L-serine indicate that all three functional groups of serine are required for optimal interaction. Removing or altering any one functional group results in an increase in inhibitory concentration from micromolar to millimolar, and removal or alteration of any two functional groups removes all inhibitory ability. Kinetic studies indicate at least two serine-binding sites, but the crystal structure solved in the presence of bound serine and direct serine-binding studies show that there are a total of four serine-binding sites on the enzyme. However, approximately 85% inhibition is attained when only two sites are occupied. The three-dimensional structure of ePGDH shows that the serine-binding sites reside at the interface between regulatory domains of adjacent subunits. Two serine molecules bind at each of the two regulatory domain interfaces in the enzyme. When all four of the serines are bound, 100% inhibition of activity is seen. However, because the domain contacts are symmetrical, the binding of only one serine at each interface is sufficient to produce approximately 85% inhibition. The tethering of the regulatory domains to each other through multiple hydrogen bonds from serine to each subunit apparently prevents the body of these domains from undergoing the reorientation that must accompany a catalytic cycle. It is suggested that part of the conformational change may involve a hinge formed in the vicinity of the union of two antiparallel beta-sheets in the regulatory domains. The tethering function of serine, in turn, appears to prevent the substrate-binding domain from closing the cleft between it and the nucleotide-binding domain, which may be necessary to form a productive hydrophobic environment for hydride transfer. Thus, the structure provides a plausible model that is consistent with the binding and inhibition data and that suggests that catalysis and inhibition in this rare Vmax-type allosteric enzyme is based on the movement of rigid domains about flexible hinges.

Aqua(1,10-phenanthroline)(L-serinato)copper(II) Nitrate

The unit cell of the title complex, [Cu(C 3 H 6 NO 3 )(C 12 H 8 N 2 )(H 2 O)]NO 3 , contains two nitrate anions and two complex cations, each with two chiral centers, one in the serine molecule and the other at the Cu ion. Each Cu ion displays slightly distorted square-pyramidal coordination, with the water molecule in the apical position and the base defined by the aliphatic N atom and one of the O atoms from the aminocarboxylate ligand and the two N atoms from the phenanthroline molecule. The relative position of the apical water molecule generates the chiral center at the Cu ion. In both molecules, the five-membered chelate ring defined by atoms N1, C12, C11, N2 and Cu is roughly planar, while the ring defined by atoms N3, C13, C14, O1 and Cu has a distorted half-chair conformation.

Structure of pentaaqua(L-serine)holmium(III) trichloride

The crystal structure of a holmium(III) complex with L-serine {[Ho(C 3 H 7 NO 3 )(H 2 O) 5 ]Cl 3 } is reported. As for most cases of lanthanide complexes with amino acids, the coordination number is eight. Each Ho ion is coordinated by two carboxylate O atoms, one hydroxyl O atom of a serine molecule and five other O atoms from water molecules. The Cl anions are not coordinated