Acridine derivatives inhibit lysozyme aggregation

We have screened a library of structurally distinct acridine derivatives (19 compounds) for their ability to inhibit lysozyme amyloid aggregation in vitro. Studied acridines were divided into three structurally different groups depending on the molecule planarity and type of the side chain-planar acridines, spiroacridines and tetrahydroacridines. Thioflavine T fluorescence assay and transmission electron microscopy were used for monitoring the inhibiting activity of acridines. We have found that both the structure of the acridine side chains and molecule planarity influence their antiamyloidogenic activity. The planar acridines inhibited lysozyme aggregation effectively. Spiroacridines and tetrahydroacridines had no significant effect on the prevention of lysozyme fibrillization, probably resulting from the presence of the heterocyclic 5-membered ring and non-planarity of molecule. Moreover, in the presence of some tetrahydroacridines the enhanced extent of aggregation was detected. We identified the most active acridine derivates from studied compound library characterized by low micromolar IC(50) values, which indicate their possible application for therapeutic purpose.     

Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin

The planarity of the polyene chain of the retinal chromophore in bacteriorhodopsin is studied using molecular dynamics simulation techniques and applying different force-field parameters and starting crystal structures. The largest deviations from a planar structure are observed for the C(13)==C(14) and C(15)==N(16) double bonds in the retinal Schiff base structure. The other dihedral angles along the polyene chain of the chromophore, although having lower torsional barriers in some cases, do not significantly deviate from the planar structure. The results of the simulations of different mutants of the pigment show that, among the studied amino acids of the binding pocket, the side chain of Trp-86 has the largest impact on the planarity of retinal, and the mutation of this amino acid to alanine leads to chromophore planarity. Deletion of the methyl C(20), removal of a water molecule hydrogen-bonded to H(15), or mutation of other amino acids to alanine did not show any significant influence on the distortion of the chromophore. The results from the present study suggest the importance of the bulky residue of Trp-86 in the isomerization process, in both ground and excited states of the chromophore, and in fine-tuning of the pK(a) of the retinal protonated Schiff base in bacteriorhodopsin. The dark adaptation of the pigment and the last step of the bacteriorhodopsin photocycle imply low barriers against the rotation of the double bonds in the Schiff base region. The twisted double bonds found in the present study are consistent with the proposed mechanism of these ground state isomerization events.     

Structure and conformation of linear peptides. III. Structure of glycyl-glycyl-L-valine

The tripeptide, glycyl-glycyl-L-valine, crystallizes as a dihydrate in the monoclinic space group P2(1), with a = 5.786(1), b = 7.954(2), c = 14.420(3)A, beta = 93.85(2) degrees, Z = 2. The structure was solved by direct methods and refined to an R-value of 0.040 for 876 observed reflections. The molecule exists as a zwitterion in the crystal. The peptide planes show significant deviations from planarity. The chain conformation resembles a reverse turn if the orientation of the carboxyl group is also taken into account. An intramolecular water bridge links the amino and carboxyl ends of the molecule. The crystal packing involves spatial segregation of polar and nonpolar moieties.     

The planar conformation of a strained proline ring: a QM/MM study

QM and QM/MM energy calculations have been carried out on an atomic resolution structure of liganded triosephosphate isomerase (TIM) that has an active site proline (Pro168) in a planar conformation. The origin of the planarity of this proline has been identified. Steric interactions between the atoms of the proline ring and a tyrosine ring (Tyr166) on one side of the proline prevent the ring from adopting the up pucker (chi1 is approximately -30 degrees), while the side chain of a nearby alanine (Ala171) forbids the down pucker (chi1 is approximately +30 degrees). To obtain a proline conformation that is in agreement with the experimentally observed planar state, a quantum system of sufficient size is required and should at least include the nearby side chains of Tyr166, Ala171, and Glu129 to provide enough stabilization. It is argued that the current force fields for structure optimization do not describe strained protein fragments correctly. The proline is part of a catalytic loop that closes upon ligand binding. Comparison of the proline conformation in different TIM X-ray structures, indicates that in the closed conformation of TIM the proline is planar or nearly planar, while in the open conformation it is down puckered. This suggests that the planarity possibly plays a role in the overall catalytic cycle of TIM, presumable acting as a reservoir of energy that becomes available upon loop opening.     

Design and synthesis of novel hydroxyalkylaminomethylchromones for their IL-5 inhibitory activity

A series of hydroxyalkylaminomethylchromone analogs 3 were prepared and evaluated as inhibitors of interleukin-5. The most active analog 3d inhibited interleukin-5 activity with an IC₅₀ of 17.5 μM. The structural requirements of chromone analogs possessing the inhibitory activity against IL-5 could be summarized as: (i) the cyclohexylmethoxy group at 5th position of the A ring, (ii) the planarity of chromone ring, (iii) hydrophobic unit around the B ring with hydroxyl functional group, (iv) the hydrophobic unit which does not have to be a planar and (v) the length of carbon units between amino and hydroxyl group is limited to two.     

On interpretation of protein X‐ray structures: Planarity of the peptide unit

Pauling's mastery of peptide stereochemistry—based on small molecule crystal structures and the theory of chemical bonding—led to his realization that the peptide unit is planar and then to the Pauling–Corey–Branson model of the α‐helix. Similarly, contemporary protein structure refinement is based on experimentally determined diffraction data together with stereochemical restraints. However, even an X‐ray structure at ultra‐high resolution is still an under‐determined model in which the linkage among refinement parameters is complex. Consequently, restrictions imposed on any given parameter can affect the entire structure. Here, we examine recent studies of high resolution protein X‐ray structures, where substantial distortions of the peptide plane are found to be commonplace. Planarity is assessed by the ω‐angle, a dihedral angle determined by the peptide bond (C? N) and its flanking covalent neighbors; for an ideally planar trans peptide, ω = 180°. By using a freely available refinement package, Phenix [Afonine et al. (2012) Acta Cryst. D, 68:352–367], we demonstrate that tightening default restrictions on the ω‐angle can significantly reduce apparent deviations from peptide unit planarity without consequent reduction in reported evaluation metrics (e.g., R‐factors). To be clear, our result does not show that substantial non‐planarity is absent, only that an equivalent alternative model is possible. Resolving this disparity will ultimately require improved understanding of the deformation energy. Meanwhile, we urge inclusion of ω‐angle statistics in new structure reports in order to focus critical attention on the usual practice of assigning default values to ω‐angle constraints during structure refinement. Proteins 2015; 83:1687–1692. © 2015 Wiley Periodicals, Inc.     

The Crystal and Molecular Structure of the Complex of 2′3′-Didehydro-2′3′-Dideoxyguanosine with Pyridine

Abstract

The structure of 2′,3′-didehydro-2′,3′-dideoxyguanosine was determined by X-ray crystallographic analysis of the complex with pyridine. The two independent nucleoside molecules have similar, commonly observed glycosyl link (x = -102.3° and -94.2°) and 5′-hydroxyl (y = 54.0° and 47.6°) conformations. The five-membered rings are very planar with r.m.s. deviations from planarity of less than 0.015 A. 2′,3′-Didehydro-2′,3′-dideoxyadenosine has a similar glycosyl link conformation but a different 5′-hydroxyl group orientation and a slightly less planar 5-membered ring.     

Structure and conformation of linear peptides. XIII. Structure of L-phenylalanyl-glycyl-glycine

The crystal structure of a tripeptide, L-phenylalanyl-glycyl-glycine (C13H17N3O4), molecular weight = 279.3, has been determined. The crystals are orthorhombic, space group P2(1)2(1)2(1), with a = 5.462(1) A, b = 15.285(5), c = 16.056(4), Z = 4, and P (calc) = 1.384 g.cm-3. The final R-index is 0.052 for 866 reflections with sin theta/lambda less than or equal to 0.55 A-1 and I greater than 1 sigma. The molecule exists as a zwitterion, with the N-terminus protonated and the C-terminus in an ionized form. Both the peptide units are in the trans configuration and planar, though one of them shows significant deviations from planarity ([delta w[ = 5.1 degrees). The peptide backbone is folded, with the torsion angles of: psi 1 = 116.2(5) degrees, omega 1 = 178.8(4), phi 2 = -89.7(5). psi 2 = -28.9(6), omega 2 = -174.9(4), phi 3 = 134.9(5), psi 31 = 7.8(6), psi 32 = -172.6(4). The terminal glycine adopts a "D-residue" conformation. For the sidechain of phenylalanine, chi 1 = 175.5(4), chi 2 = -127.0(6).     

Structure and conformation of linear peptides. V. Structure of L-prolyl-glycyl-glycine

The tripeptide, L-prolyl-glycyl-glycine, crystallizes in the trigonal space group P3(2), with a = b = 8.682(2) A, c = 12.008(2) and Z = 3. The structure was solved by direct methods and refined to an R-value of 0.07 for 727 reflections (I greater than 1.0 sigma). The molecule exists as a zwitterion in the crystal. The peptide units are trans and show significant deviations from planarity (omega 1 = 169.7 degrees, omega 2 = -170.1 degrees). The peptide backbone adopts a left-handed helical conformation similar to that of polyglycine II and polyproline II.     

Neutron diffraction study of carbonmonoxymyoglobin.

Neutron diffraction data from a crystal of carbonmonoxymyoglobin were refined by PROLSQ, a modern restrained least-squares procedure in reciprocal space, in conjunction with a solvent analysis technique, to a final R-factor of 11.3%. The ligand CO occupies two sites and its binding conformations are distorted from the linear conformation. The N epsilon atom of the distal histidine residue is deprotonated (not deuterated), and a water molecule is bound to the N delta atom of the distal histidine. The side-chain of Lys56 (D6) exists in two alternative charge-binding sites. His24 (B5) and His119 (GH1) share a hydrogen atom. His12 (A10) and His36 (C1) are deprotonated. The deprotonated imidazole ring of His12 (A10) may act as a hydrogen-bond acceptor. The heme group is planar within 0.09 A root-mean-square (r.m.s.) deviation from planarity. The solvent environments for the two propionic acid groups are different. The side-chain of Arg45 (CD3) forms hydrogen bonds with the side-chain of Asp60 (E3) and one of the two propionic acid groups. An average N-2H . . . O angle in helical regions is 147 (+/- 11) degrees. Eleven main-chain amide hydrogen atoms from hydrophobic residues do not exchange with deuterium. The overall atomic occupancy factors for the main-chain and side-chain atoms are quite uniform, at 0.97 (+/- 0.07) and 0.93 (+/- 0.10), respectively, as shown by an occupancy analysis made at the end of the refinement procedure.     

X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution

The structure of carbon-monoxy (Fe II) myoglobin at 260 K has been solved at a resolution of 1.5 A by X-ray diffraction and a model refined against the X-ray data by restrained least-squares. The CO ligand is disordered and distorted from the linear conformation seen in model compounds. At least two conformations, with Fe--C--O angles of 140 degrees and 120 degrees, are required to model the system. The heme pocket is significantly larger than in deoxy-myoglobin because the distal residues have relaxed around the ligand; the largest displacement occurs for the distal histidine side-chain, which moves more than 1.4 A on ligand binding. The side-chain of Arg45 (CD3) is disordered and apparently exists in two equally populated conformations. One of these does not block the motion of the distal histidine out of the binding pocket, suggesting a mechanism for ligand entry. The heme group is planar (root-mean-square deviation from planarity is 0.08 A) with no doming of the pyrrole groups. The Fe--N epsilon 2 (His93) bond length is 2.2 A and the Fe--C bond length in the CO complex is 1.9 A. The iron is the least-squares plane of the heme, and this leads to the proximal histidine moving by 0.4 A relative to its position in deoxy-myoglobin. This shift correlates with a global structural change, with the proximal part of the molecule translated towards the heme plane.     

Structure and conformation on linear peptides. VI. Structure of D,L-alanyl-L,D-norvaline

The dipeptide, (DL)-alanyl-(DL)-norvaline, crystallizes in the monoclinic space group P2(1)/c, with a = 12.559(2)A, b = 5.265(1), c = 16.003(3), beta = 103.53(2) degrees, Z = 4. The structure was solved by direct methods and refined to an R-value of 0.054 for 871 reflections with I greater than 2 sigma. The molecule exists as a zwitterion in the crystal. The peptide unit is trans and shows significant deviations from planarity (delta omega = 12.4 degrees). The peptide backbone adopts an extended conformation. The unit cell contains D-Ala-L-norval and its enantiomer. The molecular conformation and packing features show a striking resemblance to those for D-Ala-L-Met (1), and leads to the speculation that norvaline might act as an analog of methionine.     

Crystal and molecular structure of L-cis-3,6-dimethyl-2,5-piperazinedione (L-alanyl-L-alanyl-2,5-diketopiperazine)

The crystal structure of L -cis-3, 6-dimethyl-2,5-piperazinedione (L -alanyl-L -alanyl-2,5-diketopinerazine) has been determined. The unit cell is triclinic with a = 8.05, b = 6.08, c = 5.15 Å, α = 131.7°, β = 82.4°, γ = 106.6°. The space group is P1 with one molecule per unit cell. The six-membered ring is found to be nonplanar with an angle between the two amide group planes of 26°. One amide group deviates slightly from planarity. The experimental molecular model is discussed in terms of its flexibility.     

Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen

Protoporphyrinogen IX oxidase, a monotopic membrane protein, which catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX in the heme/chlorophyll biosynthetic pathway, is distributed widely throughout nature. Here we present the structure of protoporphyrinogen IX oxidase from Myxococcus xanthus, an enzyme with similar catalytic properties to human protoporphyrinogen IX oxidase that also binds the common plant herbicide, acifluorfen. In the native structure, the planar porphyrinogen substrate is mimicked by a Tween 20 molecule, tracing three sides of the macrocycle. In contrast, acifluorfen does not mimic the planarity of the substrate but is accommodated by the shape of the binding pocket and held in place by electrostatic and aromatic interactions. A hydrophobic patch surrounded by positively charged residues suggests the position of the membrane anchor, differing from the one proposed for the tobacco mitochondrial protoporphyrinogen oxidase. Interestingly, there is a discrepancy between the dimerization state of the protein in solution and in the crystal. Conserved structural features are discussed in relation to a number of South African variegate porphyria-causing mutations in the human enzyme.     

On the influence of vessel planarity on local hemodynamics at the human carotid bifurcation

The human carotid artery bifurcation is a complex, three-dimensional structure exhibiting non-planarity and both in- and out-of-plane curvature. The aim of this study was to determine the relative importance of vessel planarity, a potential geometric risk factor for atherogenesis, in determining the local hemodynamics. A combination of computational fluid dynamics and magnetic resonance imaging was used to reconstruct the subject-specific hemodynamics for three subjects. Planar models were then constructed by translating the centroids of the lumen contours onto a plane defined by the centroids of the vessel branches near the bifurcation apex. A novel "patching" technique was used to convert the continuous arterial surfaces into contiguous but discrete patches according to an objective scheme, making it possible to compare the original and planar models without the need for registration and warping. Results suggest that the planarity of the vessel has a relatively minor effect on the spatial distribution of mean and oscillatory wall shear stress. Out-of-plane curvature was, however, found to have a marked influence on the extent and magnitude of these hemodynamic variables. We conclude that vessel curvature - whether in- or out-of-plane - rather than planarity may deserve further scrutiny as a potential geometric risk for atherogenesis.     

Structure-activity investigation of the alteration of the physical state of the skeletal network of proteins in human erythrocyte membranes induced by 9-amino-1,2,3,4-tetrahydroacridine

The oral administration of 9-amino-1,2,3,4-tetrahydroacridine (THA) is purported to increase the mental function of Alzheimer's disease patients (Summers et al. (1986) N. Engl. J. Med. 315, 1241-1245). Numerous erythrocyte membrane proteins are known to be identical or highly similar to neuronal proteins. In a previous study (Butterfield and Palmieri [1990) Free Radical Res. Commun., in press), we showed that THA greatly increased skeletal protein-protein interactions in erythrocyte membranes as monitored by a spin label specifically bound to membrane proteins. In this report, a structure-activity study has been performed to determine which THA structural components are involved in its effect on the physical state of human erythrocyte membrane skeletal proteins. The results imply that both the planarity of the molecule and the amino group at the 9-position of the parent acridine molecule are important in the mechanism of interaction with membrane proteins.     

Enhancement of intermolecular aggregation on solvent-influenced strong hydrogen-bonded single crystal

The intermolecular aggregation between the solvent and organic molecules is covered in the current article. 4,4′-(Buta-1,3-diyne-1,4-diyl)dibenzoic acid (DADBA) was used as an organic molecule and dimethyl sulfoxide (DMSO) as a solvent to create the target compound DADBA-DMSO. The material's hydrogen bonding and intermolecular aggregation were determined by appropriate characterization methods, including single-crystal X-ray diffraction (XRD), Fourier-transform infrared (FTIR), photoluminescence (PL), and cyclic voltammetry (CV) analysis. Each hydrogen of the carboxylic group is coordinated by oxygen from the DMSO molecule in the stiff planar layer packing that makes up the DADBA-DMSO crystal structure.     

Helix-forming tendencies of amino acids depend on the restrictions of side-chain rotamer conformations: crystal structure of the tripeptide GAI in two crystalline forms.

In our attempts to design crystalline alpha-helical peptides, we synthesized and crystallized GAI (C11H21N3O4) in two crystal forms, GAI1 and GAI2. Form 1 (GAI1) Gly-L-Ala-L-Ile (C11H21N3O4.3H2O) crystals are monoclinic, space group P2(1) with a = 8.171(2), b = 6.072(4), c = 16.443(4) A, beta = 101.24(2) degrees, V = 800 A3, Dc = 1.300 g cm-3 and Z = 2, R = 0.081 for 482 reflections. Form 2 (GAI2) Gly-L-Ala-L-Ile (C11H21N3O4.1/2H2O) is triclinic, space group P1 with a = 5.830(1), b = 8.832(2), c = 15.008(2) A, alpha = 102.88(1), beta = 101.16(2), gamma = 70.72(2) degrees, V = 705 A3, Z = 2, Dc = 1.264 g cm-3, R = 0.04 for 2582 reflections. GAI1 is isomorphous with GAV and forms a helix, whereas GAI2 does not. In GAI1, the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH3+ and COO- groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an incipient alpha-helix. GAI2 imitates a cyclic peptide and traps a water molecule. The conformation angles chi 11 and chi 12 for the side chain are (-63.7 degrees, 171.1 degrees) for the helical GAI1, and (-65.1 degrees, 58.6 degrees) and (-65.0 degrees, 58.9 degrees) for the two independent nonhelical molecules in GAI2; in GAI1, both the C gamma atoms point away from the helix, whereas in GAI2 the C gamma atom with the g+ conformation points inward to the helix and causes sterical interaction with atoms in the adjacent peptide plane. From these results, it is clear that the helix-forming tendencies of amino acids correlate with the restrictions of side-chain rotamer conformations. Both the peptide units in GAI1 are trans and show significant deviation from planarity [omega 1 = -168(1) degrees; omega 2 = -171(1) degrees] whereas both the peptide units in both the molecules A and B in GAI2 do not show significant deviation from planarity [omega 1 = 179.3(3) degrees; omega 2 = -179.3(3) degrees for molecule A and omega 1 = 179.5(3) degrees; omega 2 = -179.4(3) degrees for molecule B], indicating that the peptide planes in these incipient alpha-helical peptides are considerably bent.     

Consistent force field calculations on 2,5-diketopiperazine and its 3.6-dimethyl derivatives

The minimum energy conformations are calculated for 2, 5-diketopiperazine (DKP) and its 3,6-dimethyl derivatives (DL-DMDKP and LL-DMDKP), using a consistent force field approach developed previously. The energy function parameters that were not required in earlier calculations on alkanes, amides, mid lactams are fitted to spectral and conformational data on the diketopiperazines. Vibrational assignments are suggested for DKP. Conformational energies are also determined over a range of selected values for ring dihedral angles, and the shape of the potential energy functions is examined over deviations from planarity. DKP and LL-DMDKP are found to have non-planar minimum energy conformations, separated from planar by less than a kcal/mole. DL-DMKP exhibits a nearly flat trough about the planar conformation. Calculations of minimum energies with one dihedral angle coordinate constrainted show a coupling between bond angles and dihedral angles in agreement with recent suggestions of Benedetti.     

Quercetin and DNA in solution: analysis of the dynamics of their interaction with a linear dichroism study

Flow-Linear Dichroism (LD) spectra on quercetin-DNA solutions (buffer-ethanol 30%) showed evidence that the flavonol can intercalate the biopolymer. There is no electrostatic component in the formation of the quercetin-DNA complex. The DNA concentration and the planarity of the chromophore are limiting factors in the interaction. There are no induced LD signals for concentrations of the biopolymer less than 7.8 × 10⁻³M phosphate. The interaction is most probably of a hydrophobic nature between the most hydrophobic segment of the quercetin (benzopyran-4-one) and the intercalation site, which allows the chromophore to penetrate the DNA helix and to arrange its planar structure more or less parallel to the adjacent planes of the nitrogenous bases. A comparison between the planar and hydrophobic flavonol quercetin, and the non-planar and hydrophilic flavanone dihydroquercetin, showed that the interaction of the latter with DNA was strongly limited. The notable biological activity of the quercetin compared to the ‘weaker’ activity of the dihydroquercetin could also be derived from the different planarity (and probably hydrophobicity) of the two flavonoids. The very low concentration of the quercetin-DNA complex was efficiently shown by the high sensitivity of the LD technique, whereas it could not be resolved by isotropic UV-Vis and induced circular dichroism spectra. The hypothesis of a frame shift mutagenicity activity of quercetin (Science 1977; 197: 577–578) is highly improbable. In fact, the affinity of quercetin for DNA, which emerges from this study, is very low compared with that of a typical intercalator agent (Q. Rev. Biophys. I 1992; 25: 51–170)