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.

Studies via X-ray analysis on intermolecular interactions and energy frameworks based on the effects of substituents of three 4-aryl-2-methyl-1H-imidazoles of different electronic nature and their in vitro antifungal evaluation

2018 ◽  
Vol 74 (11) ◽  
pp. 1447-1458 ◽  
Author(s):  
Mario A. Macías ◽  
Nerith-Rocio Elejalde ◽  
Estefanía Butassi ◽  
Susana Zacchino ◽  
Jaime Portilla
Keyword(s):  
Crystal Structure ◽  
Antifungal Activity ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Acid Base ◽  
Electronic Nature ◽  
Aryl Ring ◽  
X Ray ◽  
Base Properties

The crystal structures of 2-methyl-4-phenyl-1H-imidazole, C10H10N2, (3a), 4-(4-chlorophenyl)-2-methyl-1H-imidazole hemihydrate, C10H9ClN2·0.5H2O, (3b), and 4-(4-methoxyphenyl)-2-methyl-1H-imidazole, C11H12N2O, (3c), have been analyzed. It was found that the electron-donating/withdrawing tendency of the substituent groups in the aryl ring influence the acid–base properties of the 2-methylimidazole nucleus, changing the strength of the intermolecular N—H...N interactions. This behaviour not only influences the crystal structure but also seems to have an important effect on the antifungal activity. Considering the substituent groups, that is, H in (3a), Cl in (3b) and OMe in (3c), the formation of strong N—H...N connections has the probability (3a) > (3b) > (3c), while compound (3c) proves to be more active than (3a) and (3b) at all concentrations against C. neoformans.

scholarly journals High-Resolution Crystal Structure of Arabidopsis FLOWERING LOCUS T Illuminates Its Phospholipid-Binding Site in Flowering

iScience ◽  
2019 ◽  
Vol 21 ◽  
pp. 577-586 ◽  
Author(s):  
Yuki Nakamura ◽  
Ying-Chen Lin ◽  
Satoshi Watanabe ◽  
Yu-chi Liu ◽  
Kentaro Katsuyama ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Binding Site ◽  
Flowering Locus T ◽  
Phospholipid Binding ◽  
Flowering Locus

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 A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A

2003 ◽  
Vol 185 (14) ◽  
pp. 4074-4080 ◽  
Author(s):  
Tina Izard
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Binding Site ◽  
Active Site ◽  
Binding Sites ◽  
Biosynthetic Pathway ◽  
Coenzyme A ◽  
Asymmetric Unit ◽  
Phosphate Moiety ◽  
Reversible Transfer

ABSTRACT Phosphopantetheine adenylyltransferase (PPAT) regulates the key penultimate step in the essential coenzyme A (CoA) biosynthetic pathway. PPAT catalyzes the reversible transfer of an adenylyl group from Mg2+:ATP to 4′-phosphopantetheine to form 3′-dephospho-CoA (dPCoA) and pyrophosphate. The high-resolution crystal structure of PPAT complexed with CoA has been determined. Remarkably, CoA and the product dPCoA bind to the active site in distinct ways. Although the phosphate moiety within the phosphopantetheine arm overlaps, the pantetheine arm binds to the same pocket in two distinct conformations, and the adenylyl moieties of these two ligands have distinct binding sites. Moreover, the PPAT:CoA crystal structure confirms the asymmetry of binding to the two trimers within the hexameric enzyme. Specifically, the pantetheine arm of CoA bound to one protomer within the asymmetric unit displays the dPCoA-like conformation with the adenylyl moiety disordered, whereas CoA binds the twofold-related protomer in an ordered and unique fashion.

scholarly journals High resolution crystal structure of the FAK FERM domain reveals new insights on the Druggability of tyrosine 397 and the Src SH3 binding site

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Timothy Marlowe ◽  
Alexey Dementiev ◽  
Sheila Figel ◽  
Andrew Rivera ◽  
Michael Flavin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Binding Site ◽  
Ferm Domain
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