Synthesis and crystal structure of a novel phthalocyanine-calixarene conjugate

2011 ◽  
Vol 15 (07n08) ◽  
pp. 686-690 ◽  
Author(s):  
C. Grazia Bezzu ◽  
Madeleine Helliwell ◽  
Benson M. Kariuki ◽  
Neil B. McKeown
Keyword(s):  
Crystal Structure ◽  
Optical Properties ◽  
Binding Site ◽  
Crystal Structures ◽  
Chemical Species ◽  
Synthesis And Crystal Structure ◽  
Molecular Sensor

We report the synthesis and crystal structure of a novel phthalocyanine-calixarene conjugate (Pc-Calix) derived from a calixarene-based phthalonitrile (Pn-Calix). Crystal structures confirm the retention of the full cone configuration of the calixarene unit, which is thus suitable for the binding of appropriate chemical species. This new conjugate may find application as a molecular sensor in which the calixarene acts as the binding site and the perturbations of the optical properties of the phthalocyanine reports the presence of the binding species.

scholarly journals Calixarene-mediated assembly of a small antifungal protein

IUCrJ ◽  
2019 ◽  
Vol 6 (2) ◽  
pp. 238-247 ◽  
Author(s):  
Jimi M. Alex ◽  
Martin L. Rennie ◽  
Sylvain Engilberge ◽  
Gábor Lehoczki ◽  
Hajdu Dorottya ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Antifungal Activity ◽  
High Resolution ◽  
Complex Formation ◽  
Binding Site ◽  
Crystal Structures ◽  
Protein Assembly ◽  
Bidentate Ligand ◽  
Antifungal Protein ◽  
Protein Recognition

Synthetic macrocycles such as calixarenes and cucurbiturils are increasingly applied as mediators of protein assembly and crystallization. The macrocycle can facilitate assembly by providing a surface on which two or more proteins bind simultaneously. This work explores the capacity of the sulfonato-calix[n]arene (sclx n ) series to effect crystallization of PAF, a small, cationic antifungal protein. Co-crystallization with sclx4, sclx6 or sclx8 led to high-resolution crystal structures. In the absence of sclx n , diffraction-quality crystals of PAF were not obtained. Interestingly, all three sclx n were bound to a similar patch on PAF. The largest and most flexible variant, sclx8, yielded a dimer of PAF. Complex formation was evident in solution via NMR and ITC experiments, showing more pronounced effects with increasing macrocycle size. In agreement with the crystal structure, the ITC data suggested that sclx8 acts as a bidentate ligand. The contributions of calixarene size/conformation to protein recognition and assembly are discussed. Finally, it is suggested that the conserved binding site for anionic calixarenes implicates this region of PAF in membrane binding, which is a prerequisite for antifungal activity.

Helicase mechanisms and the coupling of helicases within macromolecular machines Part I: Structures and properties of isolated helicases

2002 ◽  
Vol 35 (4) ◽  
pp. 431-478 ◽  
Author(s):  
Emmanuelle Delagoutte ◽  
Peter H. von Hippel
Keyword(s):  
Crystal Structure ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Site ◽  
Crystal Structures ◽  
Base Pair ◽  
Biochemical Properties ◽  
Functional Coupling ◽  
Hexameric Helicases ◽  
Base Pair Opening

1. Mechanisms of nucleic acid (NA) unwinding by helicases 4322. Helicases may take advantage of ‘breathing’ fluctuations in dsNAs 4342.1 Stability and dynamics of dsNAs 4342.2 dsNAs ‘breathe’ in isolation 4352.3 Thermodynamics of terminal base pairs of dsNA 4382.4 Thermal fluctuations may be responsible for sequential base-pair opening at replication forks 4392.5 Helicases may capture single base-pair opening events sequentially 4403. Biochemical properties of helicases 4433.1 Binding of NAs 4433.2 Binding and hydrolysis of NTP 4453.3 Coordination between NA binding and NTP binding and hydrolysis activities 4464. Helicase structures and mechanistic consequences 4474.1 Amino-acid sequence analysis reveals conserved motifs that constitute the NTP-binding pocket and a portion of the NA-binding site 4474.2 Organization of hepatitis virus C NS3 RNA helicase 4494.2.1 Biochemical properties of HCV NS3 4494.2.2 Crystal structures of HCV NS3 helicase 4504.2.2.1 The apoprotein 4504.2.2.2 The protein–dU8 complex 4504.2.3 A possible unwinding mechanism 4524.2.4 What is the functional oligomeric state of HCV NS3? 4524.3 Organization of the PcrA helicase 4534.3.1 The apoenzyme and ADP–PcrA complex 4544.3.2 The protein–DNA–sulfate complex 4564.3.3 The PcrA–DNA–ADPNP complex 4564.3.4 A closer look at the NTP-binding site in the crystal structure of PcrA–ADPNP–DNA 4574.3.5 Communication between domains A and B 4574.3.6 How might ssDNA stimulate the ATPase activity of PcrA? 4574.3.7 A possible helicase translocation mechanism 4584.3.8 A possible unwinding mechanism 4584.4 Organization of the Rep helicase 4594.4.1 Biochemical properties 4594.4.2 Crystal structure of Rep bound to ssDNA 4624.5 Organization of the RecG helicase 4624.6 Hexameric helicases 4664.6.1 Insights from crystal structures of hexameric helicases 4674.6.2 Possible translocation and unwinding mechanisms 4685. Conclusions 4696. Acknowledgments 4727. References 472Helicases are proteins that harness the chemical free energy of ATP hydrolysis to catalyze the unwinding of double-stranded nucleic acids. These enzymes have been much studied in isolation, and here we review what is known about the mechanisms of the unwinding process. We begin by considering the thermally driven ‘breathing’ of double-stranded nucleic acids by themselves, in order to ask whether helicases might take advantage of some of these breathing modes. We next provide a brief summary of helicase mechanisms that have been elucidated by biochemical, thermodynamic, and kinetic studies, and then review in detail recent structural studies of helicases in isolation, in order to correlate structural findings with biophysical and biochemical results. We conclude that there are certainly common mechanistic themes for helicase function, but that different helicases have devised solutions to the nucleic acid unwinding problem that differ in structural detail. In Part II of this review (to be published in the next issue of this journal) we consider how these mechanisms are further modified to reflect the functional coupling of these proteins into macromolecular machines, and discuss the role of helicases in several central biological processes to illustrate how this coupling actually works in the various processes of gene expression.

Synthesis and crystal structure and optical properties of fluorenic-core oligomers

2002 ◽  
Vol 12 (4) ◽  
pp. 924-933 ◽  
Author(s):  
Silvia Destri ◽  
Mariacecilia Pasini ◽  
Chiara Botta ◽  
William Porzio ◽  
Fabio Bertini ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Optical Properties ◽  
Synthesis And Crystal Structure

Synthese und Kristallstruktur von Dibariumzink-bis(cyclotriborat) Ba2Zn(B3O6)2/Synthesis and Crystal Structure of Di-barium Zinc Bis-cyclotriborate Ba2Zn(B3O6)2

1996 ◽  
Vol 51 (3) ◽  
pp. 309-312 ◽  
Author(s):  
Silke Busche ◽  
Karsten Bluhm
Keyword(s):  
Crystal Structure ◽  
High Temperature ◽  
Single Crystals ◽  
Crystal Structures ◽  
Structure Type ◽  
Lattice Parameters ◽  
Synthesis And Crystal Structure ◽  
Space Group ◽  
X Ray ◽  
Unknown Structure

Abstract Single crystals of the new compound Ba2Zn(B3O6)2 were obtained by using a B2O3 flux technique. They crystallize in an as yet unknown structure type. X-ray investigations led to space group Ci1-P1̄ (Nr.2) with lattice parameters a = 715.5(2), b = 720.5(2), c = 1178.9(4), a = 78.96(2)°, β = 85.45(2)°, γ = 60.12(1)°, Z = 2. The structure is characterized by iso­lated (B3O6)3--rings and contains two ninefold coordinated Ba-sites. Zn2+ is tetrahedrally coordinated by oxygen. The relation to the crystal structures of high-temperature BaB2O4 and Ba2Ca(B3O6)2 is discussed.

Neue Oxopnictate AI3MVO4: Darstellung und Kristallstruktur von A3AsO4 (A = K, Rb, Cs) und K3BiO4 / New Oxopnictates AI3MVO4: Synthesis and Crystal Structure of A3AsO4 (A = K, Rb, Cs) and K3BiO4

2002 ◽  
Vol 57 (6) ◽  
pp. 599-604 ◽  
Author(s):  
Franziska Emmerling ◽  
Mamdouh Idilbi ◽  
Caroline Röhr
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Crystal Structures ◽  
Close Packing ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Trigonal Bipyramidal Geometry ◽  
Trigonal Bipyramidal ◽  
Centrosymmetric Dimers ◽  
Distorted Trigonal Bipyramidal

Abstract The title compounds have been synthesized via oxidation of the elemental pnicogenes (M = As, Bi) with the hyperoxides AO2 (A = K, Rb, Cs) and their crystal structures were determined on the basis of single crystal X-ray data. In K3AsO4 (orthorhombic, Cccm, a = 1060:1(1), b = 1135:2(1), c = 1694:0(2) pm, Z = 16) and Cs3AsO4(orthorhombic, Pnma, a = 1254:3(2), b = 902:9(2), c = 658:5(3) pm, Z = 4) isolated tetrahedra [AsO4]3- with distances As-O between 167.0 and 170.5 pm are present, which are arranged in a nearly cubic close packing. The structure of K3BiO4 (triclinic, P1̄, a = 643:18(6), b = 657:27(6), c = 762:41(7) pm, α = 101:724(2)°, β = 96:472(2)°, γ = 105:465(2)°, Z = 2) contains centrosymmetric dimers [O3BiO2BiO3]6-, in which the Bi(V) atoms are surrounded by five O atoms in a distorted trigonal bipyramidal geometry with distances Bi-O in the range of 199.5 to 233.1 pm.

scholarly journals Mercury Cyanamide / Carbodiimide Networks: Synthesis and Crystal Structures of Hg2(NCN)Cl2 and Hg3(NCN)2Cl2

2002 ◽  
Vol 57 (10) ◽  
pp. 1108-1114 ◽  
Author(s):  
Xiaohui Liu ◽  
Richard Dronskowski
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Determination ◽  
Crystal Structure Determination ◽  
Two Dimensional ◽  
Synthesis And Crystal Structure ◽  
Packing Efficiency ◽  
Inorganic Network

AbstractWe report about the synthesis and crystal structure determination of Hg2(NCN)Cl2 (P21/c (No. 14), Z = 4, a = 806.7(1), b = 907.1(2), c = 788.0(1) pm, β = 106.446(3)°, 1374 independent reflections, 67 variables, R1 = 0.0463) and Hg3(NCN)2Cl2 (Pca21 (No. 29), Z = 4, a = 702.0(2), b = 1078.5(2), c = 1050.3(2) pm, 1977 independent reflections, 71 variables, R1 = 0.0380). Both compounds contain infinite -Hg-NCN-Hg- zigzag chains which are linked by additional Hg atoms to result in two-dimensional frameworks characterized by 20-membered rings sharing edges. The remarkably flexible structural backbone [Hg3(NCN)2]2+ hosts additional Cl! anions and HgCl2 molecules in Hg2(NCN)Cl2 but only Cl- anions in Hg3(NCN)2Cl2, by that reaching a high packing efficiency in both cases.While Hg2(NCN)Cl2 exclusively contains carbodiimide N=C=N2- species, Hg3(NCN)2Cl2 is the first structural example of an inorganic network built up from both carbodiimide N=C=N2- and cyanamide N-C≡N2- groups.

scholarly journals Crystal structure of a 1,1-dibutyl-1H,3H-naphtho[1,8-cd][1,2,6]oxastannaborinin-3-ol

2021 ◽  
Vol 77 (2) ◽  
pp. 180-183
Author(s):  
Kevin Breitwieser ◽  
Peter Chen
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Site Occupancy ◽  
Asymmetric Unit ◽  
Synthesis And Crystal Structure ◽  
Germanium Tin

The title oxastannaborininol compound, [Sn(C4H9)2(C10H7BO2)], has been synthesized and crystallized. While heterocycles containing a C–O–B group are common, heterocycles containing an E–O–B unit, where E is an element of the carbon group except for carbon, are rare. In fact, while heterocycles containing Si–O–B units are occasionally reported (although without crystal structures), there are no reports for the corresponding germanium, tin or lead analogues. Herein, the first synthesis and crystal structure of a heterocycle containing an Sn–O–B unit is described. The asymmetric unit contains one molecule showing a notable disorder of the tin atom and the butyl groups. They occupy two sets of positions with site-occupancy factors of 0.295 (6) and 0.705 (6).

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