Crystal structures of the peanut lectin-lactose complex at acidic pH: Retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site

2001 ◽  
Vol 43 (3) ◽  
pp. 260-270 ◽  
Author(s):  
R. Ravishankar ◽  
C.J. Thomas ◽  
K. Suguna ◽  
A. Surolia ◽  
M. Vijayan
Keyword(s):  
Crystal Structures ◽  
Quaternary Structure ◽  
Molecular Mimicry ◽  
Crystal Packing ◽  
Acidic Ph ◽  
Peanut Lectin

Influence of 3-{5-[4-(diethylamino)benzylidene]rhodanine}propionic acid on the conformation of 5-(4-chlorobenzylidene)-2-(4-methylpiperazin-1-yl)-3H-imidazol-4(5H)-one

2018 ◽  
Vol 74 (11) ◽  
pp. 1427-1433 ◽  
Author(s):  
Ewa Żesławska ◽  
Wojciech Nitek ◽  
Waldemar Tejchman ◽  
Jadwiga Handzlik
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Protonated Form ◽  
Acid Form ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Basic Form ◽  
Piperazine Ring ◽  
X Ray ◽  
Intermolecular Contacts

The arylidene–imidazolone derivatives are a group of compounds of great interest in medicinal chemistry due to their various pharmacological actions. In order to study the possible conformations of an arylidene–imidazolone derivative, two new crystal structures were determined by X-ray diffraction, namely (Z)-5-(4-chlorobenzylidene)-2-(4-methylpiperazin-1-yl)-3H-imidazol-5(4H)-one, C15H17ClN4O, (6), and its salt 4-[5-(4-chlorobenzylidene)-5-oxo-4,5-dihydro-3H-imidazol-2-yl]-1-methylpiperazin-1-ium 3-{5-[4-(diethylamino)benzylidene]-4-oxo-2-thioxothiazolidin-3-yl}propionate, C15H18ClN4O+·C17H19N2O3S2 −, (7). Both compounds crystallize in the space group P\overline{1}. The basic form (6) crystallizes with two molecules in the asymmetric unit. In the acid form of (6), the N atom of the piperazine ring is protonated by proton transfer from the carboxyl group of the rhodanine acid derivative. The greatest difference in the conformations of (6) and its protonated form, (6c), is observed in the location of the arylidene–imidazolone substituent at the N atom. In the case of (6c), the position of this substituent is close to axial, while for (6), the corresponding position is intermediate between equatorial and axial. The crystal packing is dominated by a network of N—H...O hydrogen bonds. Furthermore, the crystal structures are stabilized by numerous intermolecular contacts of types C—H...N and C—H...Cl in (6), and C—H...O and C—H...S in (7). The geometry with respect to the location of the substituents at the N atoms of the piperazine ring was compared with other crystal structures possessing an N-methylpiperazine moiety.

Two polymorphs of 2-ethyl-3-hydroxy-6-methylpyridinium hydrogenN-acetyl-L-glutamate from powder diffraction data

2013 ◽  
Vol 69 (12) ◽  
pp. 1549-1552 ◽  
Author(s):  
Vladimir V. Chernyshev ◽  
Sergey Y. Efimov ◽  
Ksenia A. Paseshnichenko ◽  
Andrey A. Shiryaev
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Powder Diffraction Data ◽  
Screw Axis ◽  
Dimensional Network ◽  
Polymorphic Modifications

The title salt, C8H12NO+·C7H10NO5−, crystallizes in two polymorphic modifications,viz.monoclinic (M) and orthorhombic (O). The crystal structures of both polymorphic modifications have been established from laboratory powder diffraction data. The crystal packing motifs in the two polymorphs are different, but the conformations of the anions are generally similar. InM, the anions are linked by pairs of hydrogen bonds of the N—H...O and O—H...O types into chains along theb-axis direction, and neighbouring molecules within the chain are related by the 21screw axis. The cations link these chainsviaO—H...O and N—H...O hydrogen bonds into layers parallel to (001). InO, the anions are linked by O—H...O hydrogen bonds into helices along [001], and neighbouring molecules within the helix are related by the 21screw axis. The neighbouring helical turns are linked by N—H...O hydrogen bonds. The cations link the helicesviaO—H...O and N—H...O hydrogen bonds, thus forming a three-dimensional network.

The lines-of-force landscape of interactions between molecules in crystals; cohesive versus tolerant and `collateral damage' contact

2010 ◽  
Vol 66 (3) ◽  
pp. 396-406 ◽  
Author(s):  
Angelo Gavezzotti
Keyword(s):  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Minimum Energy ◽  
Lattice Energy ◽  
Interaction Force ◽  
Coordination Shell ◽  
Geometrical Parameters ◽  
Interaction Energies ◽  
Organic Salts

A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule–molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in ∼ 9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO2, SO2). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom–atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care.

Coiled-coil deformations in crystal structures: themeasles virusphosphoprotein multimerization domain as an illustrative example

2014 ◽  
Vol 70 (6) ◽  
pp. 1589-1603 ◽  
Author(s):  
David Blocquel ◽  
Johnny Habchi ◽  
Eric Durand ◽  
Marion Sevajol ◽  
François Ferron ◽  
...  
Keyword(s):  
Measles Virus ◽  
Quaternary Structure ◽  
Dynamic Equilibrium ◽  
Crystal Packing ◽  
Coiled Coil ◽  
Terminal Region ◽  
Size Exclusion ◽  
Structural Deformation ◽  
Structural Comparison ◽  
Exclusion Chromatography

The structures of two constructs of themeasles virus(MeV) phosphoprotein (P) multimerization domain (PMD) are reported and are compared with a third structure published recently by another group [Communieet al.(2013),J. Virol.87, 7166–7169]. Although the three structures all have a tetrameric and parallel coiled-coil arrangement, structural comparison unveiled considerable differences in the quaternary structure and unveiled that the three structures suffer from significant structural deformation induced by intermolecular interactions within the crystal. These results show that crystal packing can bias conclusions about function and mechanism based on analysis of a single crystal structure, and they challenge to some extent the assumption according to which coiled-coil structures can be reliably predicted from the amino-acid sequence. Structural comparison also highlighted significant differences in the extent of disorder in the C-terminal region of each monomer. The differential flexibility of the C-terminal region is also supported by size-exclusion chromatography and small-angle X-ray scattering studies, which showed that MeV PMD exists in solution as a dynamic equilibrium between two tetramers of different compaction. Finally, the possible functional implications of the flexibility of the C-terminal region of PMD are discussed.

scholarly journals Crystal structures of 2-aminopyridine citric acid salts: C5H7N2 +·C6H7O7 − and 3C5H7N2 +·C6H5O7 3−

2018 ◽  
Vol 74 (8) ◽  
pp. 1111-1116 ◽  
Author(s):  
Shet M. Prakash ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
Ismail Warad
Keyword(s):  
Hydrogen Bond ◽  
Citric Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Almost All

2-Aminopyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-aminopyridinium citrate salts, viz. C5H7N2 +·C6H7O7 − (I) (systematic name: 2-aminopyridin-1-ium 3-carboxy-2-carboxymethyl-2-hydroxypropanoate), and 3C5H7N2 +·C6H5O7 3− (II) [systematic name: tris(2-aminopyridin-1-ium) 2-hydroxypropane-1,2,3-tricarboxylate]. The supramolecular synthons present are analysed and their effect upon the crystal packing is presented in the context of crystal engineering. Salt I is formed by the protonation of the pyridine N atom and deprotonation of the central carboxylic group of citric acid, while in II all three carboxylic groups of the acid are deprotonated and the charges are compensated for by three 2-aminopyridinium cations. In both structures, a complex supramolecular three-dimensional architecture is formed. In I, the supramolecular aggregation results from Namino—H...Oacid, Oacid...H—Oacid, Oalcohol—H...Oacid, Namino—H...Oalcohol, Npy—H...Oalcohol and Car—H...Oacid interactions. The molecular conformation of the citrate ion (CA3−) in II is stabilized by an intramolecular Oalcohol—H...Oacid hydrogen bond that encloses an S(6) ring motif. The complex three-dimensional structure of II features Namino—H...Oacid, Npy—H...Oacid and several Car—H...Oacid hydrogen bonds. In the crystal of I, the common charge-assisted 2-aminopyridinium–carboxylate heterosynthon exhibited in many 2-aminopyridinium carboxylates is not observed, instead chains of N—H...O hydrogen bonds and hetero O—H...O dimers are formed. In the crystal of II, the 2-aminopyridinium–carboxylate heterosynthon is sustained, while hetero O—H...O dimers are not observed. The crystal structures of both salts display a variety of hydrogen bonds as almost all of the hydrogen-bond donors and acceptors present are involved in hydrogen bonding.

Salts of aromatic carboxylates: the crystal structures of nickel(II) and cobalt(II) 2,6-naphthalenedicarboxylate tetrahydrate

2001 ◽  
Vol 34 (6) ◽  
pp. 710-714 ◽  
Author(s):  
James A. Kaduk ◽  
Jason A. Hanko
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Geometry Optimization ◽  
Metal Cations ◽  
Carboxyl Groups ◽  
Water Molecules ◽  
Triclinic Space Group ◽  
Aromatic Carboxylates ◽  
Monte Carlo Simulated Annealing

The crystal structures of isostructural 2,6-naphthalenedicarboxylate tetrahydrate salts of nickel(II) and cobalt(II) have been determined using Monte Carlo simulated annealing techniques and laboratory X-ray powder diffraction data. These compounds crystallize in the triclinic space groupP\bar{1}, withZ= 2;a= 10.0851 (4),b= 10.9429 (5),c= 6.2639 (3) Å, α = 98.989 (2), β = 87.428 (3), γ = 108.015 (2)°,V= 649.32 (5) Å3for [Ni(C12H6O4)(H2O)4], anda= 10.1855 (6),b= 10.8921 (6),c= 6.2908 (5) Å, α = 98.519 (4), β = 87.563 (4), γ = 108.304 (3)°,V= 655.28 (8) Å3for [Co(C12H6O4)(H2O)4]. The water-molecule H atoms were located by quantum chemical geometry optimization usingCASTEP. The structure consists of alternating hydrocarbon and metal/oxygen layers parallel to theacplane. Each naphthalenedicarboxylate anion bridges two metal cations; each carboxyl group is monodentate. The resulting structure contains infinite chains parallel to [111]. The octahedral coordination sphere of the metal cations containstranscarboxylates and four equatorial water molecules. The carboxyl groups are rotated by 15–20° out of the naphthalene plane. The metal/oxygen layers are characterized by an extensive hydrogen-bonding network. The orientations of the carboxyl groups are determined by the formation of short (O...O = 2.53 Å) hydrogen bonds between the carbonyl O atoms and theciswater molecules. Molecular mechanics energy minimizations suggest that coordination and hydrogen-bonding interactions are most important in determining the crystal packing.

scholarly journals T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure

2016 ◽  
Vol 72 (4) ◽  
pp. 536-550 ◽  
Author(s):  
Jakub Barciszewski ◽  
Janusz Wisniewski ◽  
Robert Kolodziejczyk ◽  
Mariusz Jaskolski ◽  
Dariusz Rakus ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Catalytic Mechanism ◽  
Quaternary Structure ◽  
Homo Sapiens ◽  
Helical Structure ◽  
Smooth Transition ◽  
Muscle Enzyme ◽  
Enzymatic Function ◽  
Fructose 1,6 Bisphosphatase ◽  
Key Enzyme

Fructose-1,6-bisphosphatase (FBPase) catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and is a key enzyme of gluconeogenesis and glyconeogenesis and, more generally, of the control of energy metabolism and glucose homeostasis. Vertebrates, and notablyHomo sapiens, express two FBPase isoforms. The liver isozyme is expressed mainly in gluconeogenic organs, where it functions as a regulator of glucose synthesis. The muscle isoform is expressed in all cells, and recent studies have demonstrated that its role goes far beyond the enzymatic function, as it can interact with various nuclear and mitochondrial proteins. Even in its enzymatic function, the muscle enzyme is different from the liver isoform, as it is 100-fold more susceptible to allosteric inhibition by AMP and this effect can be abrogated by complex formation with aldolase. All FBPases are homotetramers composed of two intimate dimers: the upper dimer and the lower dimer. They oscillate between two conformational states: the inactive T form when in complex with AMP, and the active R form. Parenthetically, it is noted that bacterial FBPases behave somewhat differently, and in the absence of allosteric activators exist in a tetramer–dimer equilibrium even at relatively high concentrations. [Hineset al.(2007),J. Biol. Chem.282, 11696–11704]. The T-to-R transition is correlated with the conformation of the key loop L2, which in the T form becomes `disengaged' and unable to participate in the catalytic mechanism. The T states of both isoforms are very similar, with a small twist of the upper dimer relative to the lower dimer. It is shown that at variance with the well studied R form of the liver enzyme, which is flat, the R form of the muscle enzyme is diametrically different, with a perpendicular orientation of the upper and lower dimers. The crystal structure of the muscle-isozyme R form shows that in this arrangement of the tetramer completely new protein surfaces are exposed that are most likely targets for the interactions with various cellular and enzymatic partners. The cruciform R structure is stabilized by a novel `leucine lock', which prevents the key residue, Asp187, from locking loop L2 in the disengaged conformation. In addition, the crystal structures of muscle FBPase in the T conformation with and without AMP strongly suggest that the T-to-R transition is a discrete jump rather than a shift of an equilibrium smooth transition through multiple intermediate states. Finally, using snapshots from three crystal structures of human muscle FBPase, it is conclusively demonstrated that the AMP-binding event is correlated with a β→α transition at the N-terminus of the protein and with the formation of a new helical structure.

Tetraphenylarsonium iodide, a new determination

2003 ◽  
Vol 59 (11) ◽  
pp. m484-m486 ◽  
Author(s):  
Philip A. W. Dean ◽  
Donald C. Craig ◽  
Marcia L. Scudder ◽  
Ian G. Dance
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Phosphorus Compound ◽  
Linear Chains

The reported crystal structures of Ph4P+·I− and Ph4As+·I− have been re-examined. An apparent instance of substitutional dimorphism could not be reproduced and, contrary to an earlier report, tetraphenylarsonium iodide, [As(C6H5)4]I or Ph4As+·I−, was found to be isostructural with the phosphorus compound. The cation and anion are both located on \overline 4 symmetry sites. The crystal packing involves linear chains of cations in fourfold phenyl embraces.

Crystallization and preliminary analysis of a DNA dodecamer of d(CGCGmo6AATCCGCG) containing 2′-deoxy-N 6-methoxyadenosine: change in crystal packing with different humidity

1999 ◽  
Vol 55 (4) ◽  
pp. 873-876 ◽  
Author(s):  
Toshiyuki Chatake ◽  
Tomoko Sunami ◽  
Akira Ono ◽  
Yoshihito Ueno ◽  
Akira Matsuda ◽  
...  
Keyword(s):  
Phase Transition ◽  
Contact Angle ◽  
Data Collection ◽  
Crystal Structures ◽  
Preliminary Analysis ◽  
Crystal Packing ◽  
Base Pairing ◽  
X Ray ◽  
Dna Dodecamer

The DNA dodecamer of (CGCGmo6AATCCGCG) containing 2′-deoxy-N 6-methoxyadenosine has been crystallized for X-ray analysis in order to investigate the effects of the modified adenosine on base pairing. It has been found that the crystal changes from one form to another during data collection in a manner similar to a phase transition. The two crystal structures show that this phenomenon, ascribed to differences in humidity, is correlated with a change in the contact angle between the two duplexes.

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