X-ray studies on crystalline complexes involving amino acids and peptides: Part XVIII. Crystal structure of a new form of L-arginine D-glutamate and a comparative study of amino acid crystal structures containing molecules of the same and mixed chirality

The new form of L-arginine D-glutamate is monoclinic, P2₁, witha = 9.941(1),b = 4.668(2),c = 17.307(1) Å,β = 95.27(1)°, and Z = 2. In terms of composition, the new form differs from the old form in that the former is a monohydrate whereas the latter is a trihydrate. The structure has been solved by the direct methods and refined to R = 0.085 for 1012 observed reflections. The conformation of the arginine molecule is the same in both the forms whereas that of the glutamate ion is different. The change in the conformation of the glutamate ion is such that it facilitates extensive pseudosymmetry in the crystals. The molecules arrange themselves in double-layers stabilised by head-to-tail sequences involving main chains, in both the forms. However, considerable differences exist between the two forms in the interface, consisting of side chains and water molecules, between double-layers. A comparative study of the relationship between the crystal structures of L and DL amino acids on the one hand and that between the structures of LL and LD amino acid-amino acid complexes on the other, provides interesting insights into amino acid aggregation and the effect of chirality on it. The crystal structures of most hydrophobic amino acids are made up of double-layers and those of most hydrophilic amino acids contain single layers, irrespective of the chiralities of the amino acids involved. In most cases, the molecules tend to appropriately rearrange themselves to preserve the broad features of aggregation patterns when the chirality of half the molecules is reversed as in the structures of DL amino acids. The basic elements of aggregation in the LL and the LD complexes, are similar to those found in the crystals of L and DL amino acids. However, the differences between the LL and the LD complexes in the distribution of these elements are more pronounced than those between the distributions in the structures of L and DL amino acids.     

X-ray studies on crystalline complexes involving amino acids and peptides. Part XX. Crystal structures of DL-arginine acetate monohydrate and DL-lysine acetate and a comparison with the corresponding L-amino acid complexes

Crystals of DL-arginine acetate monohydrate, C6H15N4O2+C2H3O2-.H2O, are monoclinic, P2(1)/c, with a = 13.552(2), b = 5.048(2), c = 18.837(3) A, beta = 101.34(2) degrees and Z = 4, and those of DL-lysine acetate, C6H15N2O2+.C2H3O2- are triclinic, P1, with a = 5.471(2), b = 7.656(2), c = 12.841(2) A, alpha = 94.48(1), beta = 94.59(2), gamma = 98.83(2) degrees and Z = 2. The structures have been solved by direct methods and refined to R = 0.058 and 0.077 for 1522 and 1259 observed reflections respectively. The difference in the number and the nature of proton donors leads to a difference in hydrogen bond density in the two structures. The basic elements of aggregation in both the structures are pairs of amino acid molecules, each pair stabilized by two centrosymmetrically related hydrogen bonds involving alpha-amino and alpha-carboxylate groups, stacked along the shortest dimension to form columns. The pairs are held together in each column by head-to-tail sequences. The columns stack along a crystallographic axis to form layers. Adjacent layers are bridged by acetate ions. The amino acid-acetate interactions are primarily through side chains and involve specific interactions and characteristic interaction patterns. The gross features of molecular aggregation are nearly the same in DL-arginine acetate monohydrate and L-arginine acetate whereas they are substantially different in the lysine complexes. In both cases, one of the two head-to-tail sequences in the L complex is replaced by a hydrogen bonded loop involving alpha-amino and alpha-carboxylate groups, in the DL complex. This may have implications for prebiotic condensation during chemical evolution.     

Variability in ionization state,stoichiometry and aggregation in histidine complexes with formic acid

The crystal structures of the complexes of L and DL histidine with formic acid have been determined as part of an effort to define biologically and evolutionarily important interactions and aggregation patterns. In terms of ionization state and stoichiometry they may be described as L-histidine formate formic acid and DL-histidine formate monohydrate respectively. In the L-histidine complex, amino acid molecules arranged in head-to-tail sequences centred around 2₁ screw axes are interconnected by formic acid molecules and formate ions. Histidine-formate interactions in the structure gives rise to a characteristic interaction pattern involving a linear array of alternating imidazole groups and formate ions. In DL-histidine formale monohydrate, head-to-tail sequences involving glide related molecules are interconnected through main chain-side chain interactions leading to amino acid layers. The layers are held together by formate ions and water molecules arranged in strings along which the ion and the molecule alternate. The patterns of amino acid aggregation in histidine complexes exhibit considerably higher variability than those in complexes involving arginine and lysine do. X-ray studies on crystalline complexes involving amino and peptides Part XXIX.     

X-ray studies on crystalline complexes involving amino acids and peptides. Part XIV: Closed conformation and head-to-tail arrangement in a new crystal form of L-histidine L-aspartate monohydrate

A new form of L-histidine L-aspartate monohydrate crystallizes in space group P2₂ witha = 5.131(1),b = 6.881(1),c= 18.277(2) Å,β= 97.26(1)° and Z = 2. The structure has been solved by the direct methods and refined to anR value of 0.044 for 1377 observed reflections. Both the amino acid molecules in the complex assume the energetically least favourable allowed conformation with the side chains staggered between the α-amino and α-scarboxylate groups. This results in characteristic distortions in some bond angles. The unlike molecules aggregate into alternating double layers with water molecules sandwiched between the two layers in the aspartate double layer. The molecules in each layer are arranged in a head-to-tail fashion. The aggregation pattern in the complex is fundamentally similar to that in other binary complexes involving commonly occurring L amino acids, although the molecules aggregate into single layers in them. The distribution of crystallographic (and local) symmetry elements in the old form of the complex is very different from that in the new form. So is the conformation of half the histidine molecules. Yet, the basic features of molecular aggregation, particularly the nature and the orientation of head-to-tail sequences, remain the same in both the forms. This supports the thesis that the characteristic aggregation patterns observed in crystal structures represent an intrinsic property of amino acid aggregation.     

X-Ray studies on crystalline complexes involving amino acids and peptides. XVII. Chirality and molecular aggregation: The crystal structures of DL-arginine DL-glutamate monohydrate and DL-arginine DL-aspartate

DL -Arginine DL -glutamate monohydrate and DL -arginine DL -aspartate, the first DL -DL amino acid–amino acid complexes to be prepared and x-ray analyzed, crystallize in the space group P1 with a = 5.139(2), b = 10.620(1), c = 14.473(2) Å, α = 101.34(1)°, β = 94.08(2)°, γ = 91.38(2)° and a = 5.402(3), b = 9.933(3), c = 13.881(2) Å, α = 99.24(2)°, β = 99.73(3)°, γ = 97.28(3)°, respectively. The structures were solved using counter data and refined to R values of 0.050 and 0.077 for 1827 and 1739 observed reflections, respectively. The basic element of aggregation in both structures is an infinite chain made up of pairs of molecules. Each pair, consisting of a L - and a D -isomer, is stabilized by two centrosymmetrically or nearly centrosymmetrically related hydrogen bonds involving the α-amino and the α-carboxylate groups. Adjacent pairs in the chain are then connected by specific guanidyl–carboxylate interactions. The infinite chains are interconnected through hydrogen bonds to form molecular sheets. The sheets are then stacked along the shortest cell translation. The interactions between sheets involve two head-to-tail sequences in the glutamate complex and one such sequence in the aspartate complex. However, unlike in the corresponding LL and DL complexes, head-to-tail sequences are not the central feature of molecular aggregation in the DL -DL complexes. Indeed, fundamental differences exist among the aggregation patterns in the LL , the LD , and the DL -DL complexes.     

X-ray studies on crystalline complexes involving amino acids and peptides. X. Head-to-tail sequences in the crystal structure of L-lysine acetate

L-Lysine acetate crystallises in the monoclinic space group P21 with a = 5.411 (1), b = 7.562(1), c = 12.635(2) A and beta = 91.7(1) degrees. The crystal structure was solved by direct methods and refined to an R value of 0.049 using the full matrix least squares method. The conformation and the aggregation of lysine molecules in the structure are similar to those found in the crystal structure of L-lysine L-aspartate. A conspicuous similarity between the crystal structures of L-arginine acetate and L-lysine acetate is that in both cases the strongly basic side chain, although having the largest pK value, interacts with the weakly acidic acetate group leaving the alpha-amino and the alpha-carboxylate groups to take part in head-to-tail sequences. These structures thus indicate that electrostatic effects are strongly modulated by other factors so as to give rise to head-to-tail sequences which have earlier been shown to be an almost universal feature of amino acid aggregation in the solid state.     

X-ray studies on crystalline complexes involving amino acids and peptides. XIX. Effects of change in chirality in the complexes of succinic acid with DL- and L-arginine

Crystals of DL-arginine hemisuccinate dihydrate (I)(monoclinic; P2(1)/c; a = 5.292, b = 16.296. c = 15.203 A; beta = 92.89 degrees; Z = 4) and L-arginine hemisuccinate hemisuccinic acid monohydrate (II) (triclinic; P1; a = 5.099; b = 10.222, c = 14.626 A; alpha = 77.31, beta = 89.46, gamma = 78.42 degrees; Z = 2) were grown under identical conditions from aqueous solutions of the components in molar proportions. The structures were solved by direct methods and refined to R = 0.068 for 2585 observed reflections in the case of (I) and R = 0.036 for 2154 observed reflections in the case of (II). Two of the three crystallographically independent arginine molecules in the complexes have conformations different from those observed so far in the crystal structures containing arginine. The succinic acid molecules and the succinate ions in the structures are centrosymmetric and planar. The crystal structure of (II) is highly pseudosymmetric. Arginine-succinate interactions in both the complexes involve specific guanidyl-carboxylate interactions. The basic elements of aggregation in both the structures are ribbons made up of alternating arginine dimers and succinate ions. However, the ribbons pack in different ways in the two structures. (II) presents an interesting case in which two ionisation states of the same molecule coexist in a crystal. The two complexes provide a good example of the effect of change in chirality on stoichiometry, conformation, aggregation, and ionisation state in the solid state.     

Formation and structure of Cu(II)-poly(L-lysine) complexes in aqueous solution.

Cu(II)-poly(L-lysine) complexes have been studied using potentiometric titrations, optical absorption and circular dichroism spectra. As in the Cu(II)-poly(L-arginine) system studied previously potentiometric and spectral data consistently show that two types of complexes are formed. The first formed below pH 7.6 contains two amine nitrogens and two oxygen from water molecules at the corners of a square in which the metal occupies the center. The second is obtained at pH above 7.6 when the oxygen atoms are replaced by two adjacent peptide nitrogens.     

Infrared linear dichroism investigations of deoxyribonucleic acid complexes with poly(L-arginine) and poly(L-lysine).

Complexes between DNAs from various sources and poly(L-lysine) and poly(L-arginine) were studied by means of infrared linear dichroism. The measurements of dichroic ratios allowed us to determine the orientation of the phosphate group of DNA in the complexes with basic polypeptides. At high relative humidities (higher than 90%, B form), the bisector of the less than OPO in the complexes forms an angle with respect to the helical axis which has a value lower by about 4 degrees than in the corresponding DNA sample. This change of orientation of the phosphate group of DNA indicates a modification of the B form upon binding of polylysine or polyarginine. The structural transitions B leads to A and B leads to C measured as a function of relative humidities were not affected by formation of complexes with both basic polypeptides. Similar results were obtained for complexes prepared by direct mixing or by salt gradient dialysis. The presence of A and C forms was observed in complexes of DNA with poly(L-lysine) and poly(L-arginine) at lower relative humidity. Thus, the conformational flexibility of DNA in complexes with polylysine and polyarginine is not changed despite a substantial increase in the Tm (melting temperature). These results are considered as a model for the understanding of interactions between DNA and histones particularly of the binding of the N-terminal fragment, lysine or arginine rich.     

Electrostatic interaction of poly(L-lysine) with dipalmitoylphosphatidic acid studied by X-ray diffraction

Structure of dipalmitoylphosphatidic acid (DPPA) bilayers in the presence of poly(L-lysine) is proposed from the results of X-ray diffraction obtained by a storage phosphor detector with a high resolution called an imaging plate. The small-angle X-ray diffraction pattern exhibits that DPPA/poly(L-lysine) complex forms a highly ordered multilamellar structure. The electron density profile of the DPPA/poly(L-lysine) complex draws that only one poly(L-lysine) layer is intercalated between the neighboring DPPA bilayers. The wide-angle X-ray diffraction pattern suggests that the presence of poly(L-lysine) hardly affects the nature of hydrocarbon chain packing in the DPPA bilayers. The X-ray reflection from the DPPA/poly(L-lysine) complex indicates that the poly(L-lysine) molecules adopt a beta-sheet conformation on the surface of the DPPA bilayers. The both surface areas occupied by a headgroup of the DPPA and by a lysine residue in poly(L-lysine) are estimated from the observed spacings. The number ratio of lysine residues to DPPA headgroups per unit area is greater than unity. Therefore, one DPPA headgroup interacts with more than one lysine residue electrostatically, i.e., the electric charge distributions in both the surface of a DPPA bilayer and the poly(L-lysine) beta-sheet are incommensurate.     

The induced circular dichroism of bilirubin complexed with the alpha-helix form of poly(L-lysine)

Binding of bilirubin by the alpha-helix conformation of poly(L-lysine) in water induces optical activity. The bisignate circular dichroism spectrum exhibits exciton bands centred at 444 nm, negative, and at 525 nm, positive. The magnitude of the induced circular dichroism depends on the concentration of total bilirubin and total lysine residues, the molar ratio of total lysine residues-to-total bilirubin molecules, the pH and the degree of polymerization of poly(L-lysine). Although bilirubin binds to the random coil conformation of poly(L-lysine), as evidence by the absorption spectrum, the complex is optically inactive. The results suggest that bilirubin binds to the poly(L-lysine) in the form of dimers and oligomers.     

A new antitumor enzyme, L-lysine alpha-oxidase from Trichoderma viride. Purification and enzymological properties

L-Lysine alpha-oxidase from Trichoderma viride Y244-2 has been purified to homogeneity. The enzyme shows absorption maxima at 277, 388, and 466 nm and a shoulder around 490 nm and contains 2 mol of FAD/mol of enzyme. The enzyme has a molecular weight of approximately 116,000 and consists of two subunits identical in molecular weight (about 56,000). In addition to L-lysine, L-ornithine, L-phenylalanine, L-tyrosine, L-arginine, and L-histidine are oxidized by the enzyme to a lesser extent. Several lysine analogs such as delta-hydroxylysine are oxidized efficiently. Balance studies showed that 1 mol of L-lysine is converted to an equimolar amount of alpha-keto-epsilon-aminocaproate, ammonia, and hydrogen peroxide with the consumption of 1 mol of oxygen. alpha-Keto-epsilon-aminocaproate spontaneously is dehydrated intramolecularly into delta 1-piperideine-2-carboxylate in the presence of catalase, and is oxidatively decarboxylated into delta-aminovalerate in the absence of catalase. The Michaelis constants are as follows: 0.04 mM for L-lysine, 0.44 mM for L-ornithine, 14 mM for L-phenylalanine, and 1.6 mM for oxygen with L-lysine.     

Stereospecific abstraction of epsilon-pro-R-hydrogen of L-lysine by L-lysine epsilon-dehydrogenase from Agrobacterium tumefaciens

The stereochemical aspects of the L-lysine epsilon-dehydrogenase reaction were examined with (6R)-L-[6-3H]lysine and (6S)-DL-[6-3H]lysine. When (6S)-DL-[6-3H]lysine was used as a substrate, the tritium was found in the product, delta 1-piperideine-6-carboxylate. In contrast, the radioactivity from (6R)-L-[6-3H]lysine was not retained in the product. Thus, the pro-R hydrogen at the prochiral C-6 carbon of L-lysine is specifically abstracted by the enzyme: the enzyme behaves stereochemically as an amino acid D-dehydrogenase.     

Transport of L-lysine in the fission yeast Schizosaccharomyces pombe

Systems of L-lysine transport in Schizosaccharomyces pombe are not constitutive, as at no phase of growth in a rich medium is lysine taken up. Transport activity appears only after preincubation of harvested cells with glucose or another suitable source of energy. If cycloheximide is added during this preincubation no transport systems are synthesized. After removal of glucose, the activity of the transport system decays with a half-time of 13 min. The transport of L-lysine into S. pombe cells from the stationary phase of growth preincubated for 60 min with 1% D-glucose is mediated by at least two systems, the high-affinity one with a Kt of 26 mumol/l and Jmax of 4.95 nmol/min per mg dry wt., the low-affinity one with a KT of 1.1 mmol/l and Jmax of 11.8 nmol/min per mg dry wt. The transport of lysine mediated by these two systems proceeds uphill. The high-affinity system has a pH optimum at 4.0-4.2, the accumulation ratio is highest at a cell density 2-5 mg dry wt. per ml and decreases with increasing lysine concentrations. Lysine accumulated by this system does not exit from cells. The only potent competitive inhibitors are L-arginine, L-histidine and D-lysine. The other amino acids tested do not behave as competitive inhibitors. Of the various metabolic inhibitors tested, the most potent were proton conductors and antimycin A.     

Effect of L-arginine and L-lysine on lysosomal hydrolases and membrane bound phosphatases in experimentally induced myocardial infarction in rats

The protective effect of L-arginine and L-lysine on lysosomal enzymes and membrane bound ATPases was examined on isoproterenol induced myocardial infarction in rats. Lysosomal enzymes play an important role in the inflammatory process. The rats given isoproterenol (150 mg kg^–1 daily) intraperitoneally for 2 days showed significant changes in the marker enzymes, lysosomal enzymes and membrane bound phosphatases. Histopathological studies also confirmed the induction of myocardial infarction in isoproterenol administered rats. Prior oral treatment with L-arginine (250 mg kg^–1 daily) and L-lysine (5 mg kg^–1 daily) for 5 days significantly prevented these alterations and restored the enzyme activities to near normal. These findings demonstrate the protective effect of L-arginine and L-lysine in combination against isoproterenol induced cardiac damage.     

Crystal structure of valinomycin-monohydrate cage complexes crystallized from dioxane.

Valinomycin, cyclo-[(L-Val-D-Hyv-D-Val-L-Lac)3-], was crystallized from aqueous dioxane solvent as a monohydrate complex in which water molecules were found within the ion-binding cavity of the ionophore: monoclinic P2(1), a = 14.377 (3), b = 41.554 (14), c = 14.080 (3) A, beta = 118.27 (2) degrees, Z = 4. There are two non-equivalent valinomycin-water complexes and three dioxane molecules in the asymmetric unit. The ionophore molecules adopt two similar but non-identical, octahedral, bracelet, cage conformations that are a consequence of two distinct ways in which the complexed water molecules can deform the normal octahedral coordinate geometry of the metal binding site. In the first complex the water molecule forms hydrogen donor bonds to the carbonyl oxygens of two L-valine residues on one facial side of the cavity, while in the second complex the water molecule is trigonal-planar coordinate and binds to two L-valine residues on one entrant face of the cavity plus a third D-valine residue from the opposite side of the cavity.     

The preparation and crystal structure analysis of a 2:1 complex between L-lysine and copper(II) chloride

The crystal structure of bis(L-lysine)Cu(II) chloride dihydrate has been determined by X-ray analysis. The complex crystallizes in the monoclinic space group P2₁, with cell dimensions a = 5.189(1), b = 16.988(3), c = 11.482(2) Å, β = 93.57(1)°. The position of the Cu atom was found from a Patterson synthesis, the remaining atoms were located with DIRDIF. The structure was refined by least-squares to R = 0.060 and R_w = 0.065 for 2637 observed reflections. The copper(II) atom has an essentially square planar coordination with the two lysine molecules chelated via the carboxy oxygen and the α-amino nitrogen. However the two chlorine atoms form weak interactions with the metal to complete a strongly tetragonally elongated six-fold coordination. The two aliphatic chains have rather different geometries and are extended in a zig-zag mode. Extensive hydrogen bonding links the complex and the water molecules together.     

Activation of L-lysine epsilon-dehydrogenase from Agrobacterium tumefaciens by several amino acids and monocarboxylates

The activation of lysine epsilon-dehydrogenase [EC 1.4.1.] by L-lysine was dependent on lysine concentration and was accompanied by association of the dimeric enzymes to a tetramer. The lysine concentration required for the half-maximal activation was 0.28 mM, which was lower than the Km value for L-lysine. In addition to L-lysine, several compounds, which were neither substrates nor inhibitors, activated the enzyme. The compounds which activated the enzyme have common structural characteristics: they have both a carboxyl group and a hydrophobic side chain. These activators also induced the association of the enzyme. The activation of the enzyme occurred well over the pH range 5.0 to 7.5, and the maximal activation was obtained by preincubation for 5 min at 30 degrees C and pH 7.4, when 5 mM L-lysine or 6-aminocaproate was used as an activator. NADH binding experiments indicated that about 2 mol of NADH bind to 1 mol of the tetrameric enzyme: the dimeric enzyme has one catalytic site. Binding experiments with n-[1-14C]heptanoate and L-[U-14C]lysine showed that approximately 2 mol of ligands bind to 1 mol of the dimeric enzyme and L-lysine could not bind to the catalytic site of the enzyme in the absence of NAD+. These results indicate the presence of one catalytic site and two activator binding binding sites in the dimeric enzyme.     

X-Ray Studies on Crystalline Complexes Involving Amino Acids and Peptides XXXI. Effect of Chirality on Ionization State,Stoichiometry and Aggregation in the Complexes of Oxalic Acid with L-and DL-histidine

Abstract

Crystals of the oxalic acid complex of L-histidine (orthorhombic P2₁2₁2₁; a=5.535(4), b=6.809(4), c=26.878(3) Å) R= 3.6% for 1188 observed reflections) contain histidine molecules and semi-oxalate ions in the 1:1 ratio, while the ratio is 1:2 in the crystals of the DL-histidine complex (monoclinic P2₁ lc; a=6.750(7), b=10.139(2), c=19.352(2) Å, β= 90.8°; R= 3.7% for 3176 observed reflections). The histidine molecule in the latter has an unusual ionization state with positively charged amino and imidazole groups and a neutral carboxyl group. The molecule has the sterically least favourable allowed conformation with the side chain imidazole ring staggered between the α-amino and the α- carboxyl (carboxylate) groups, in both the structures. The unlike molecules aggregate into separate alternating layers in both of them. There are elements of similarity in the aggregation patterns in the semi-oxalate layers in the two complexes, but the patterns in the amino acid layers are entirely different. Interestingly, the crystal structure of L-histidine semi-oxalate has broad similarities with that of DL-histidine glycolate, demonstrating how broad features of aggregation could be retained inspite of changes in chirality and composition. The unusual ionization state of the amino acid molecule in the DL-histidine complex is reflected in a hitherto unobserved aggregation pattern in its crystal structure.     

X-ray Studies on Crystalline Complexes Involving Amino Acids and Peptides. XXVII. Effect of Chirality,Specific Interactions and Characteristic Aggregation Patterns in the Structures of Arginine and its Complexes with Formic Acid

Abstract

The crystal structures of DL- arginine dihydrate, DL-arginine formate dihydrate and L-arginine formate have been determined and refined using X-ray crystallographic techniques. The three structures, along with other related ones, demonstrate the conformational variability of arginine. The amino acid molecules aggregate essentially in a similar manner in DL- arginine dihydrate and in the known structure of L-arginine dihydrate; the effects arising out of the reversal of the chirality of half the amino acid molecules are absorbed by small local adjustments. However, such a reversal leads to profound differences in aggregation in DL- arginine and L- arginine formates, in contrast to the situation in the corresponding acetates. Thus the effect of chirality on biomolecular aggregation cannot be easily predicted or even rationalized. Arginine-carboxylate interactions in the complexes primarily involve the guanidyl groups and contain specific interactions. Indeed the primary mode of arginine-carboxylic acid aggregation is substantially invariant in the arginine complexes of succinic, acetic and formic acids.