Ru-Based CO releasing molecules with azole ligands: interaction with proteins and the CO release mechanism disclosed by X-ray crystallography

2017 ◽  
Vol 46 (29) ◽  
pp. 9621-9629 ◽  
Author(s):  
Nicola Pontillo ◽  
Giarita Ferraro ◽  
Luigi Messori ◽  
Gabriella Tamasi ◽  
Antonello Merlino

Structural data on the adducts formed upon reaction of Ru-based CO releasing molecules containing azole ligands with model proteins are reported.

2007 ◽  
Vol 46 (6) ◽  
pp. 2041-2056 ◽  
Author(s):  
Tatiana Kh. Shokhireva ◽  
Andrzej Weichsel ◽  
Kevin M. Smith ◽  
Robert E. Berry ◽  
Nikolai V. Shokhirev ◽  
...  

2016 ◽  
Vol 90 (23) ◽  
pp. 10800-10810 ◽  
Author(s):  
Charles Sabin ◽  
Tibor Füzik ◽  
Karel Škubník ◽  
Lenka Pálková ◽  
A. Michael Lindberg ◽  
...  

ABSTRACTAichi virus 1(AiV-1) is a human pathogen from theKobuvirusgenus of thePicornaviridaefamily. Worldwide, 80 to 95% of adults have antibodies against the virus. AiV-1 infections are associated with nausea, gastroenteritis, and fever. Unlike most picornaviruses, kobuvirus capsids are composed of only three types of subunits: VP0, VP1, and VP3. We present here the structure of the AiV-1 virion determined to a resolution of 2.1 Å using X-ray crystallography. The surface loop puff of VP0 and knob of VP3 in AiV-1 are shorter than those in other picornaviruses. Instead, the 42-residue BC loop of VP0 forms the most prominent surface feature of the AiV-1 virion. We determined the structure of AiV-1 empty particle to a resolution of 4.2 Å using cryo-electron microscopy. The empty capsids are expanded relative to the native virus. The N-terminal arms of capsid proteins VP0, which mediate contacts between the pentamers of capsid protein protomers in the native AiV-1 virion, are disordered in the empty capsid. Nevertheless, the empty particles are stable, at leastin vitro, and do not contain pores that might serve as channels for genome release. Therefore, extensive and probably reversible local reorganization of AiV-1 capsid is required for its genome release.IMPORTANCEAichi virus 1 (AiV-1) is a human pathogen that can cause diarrhea, abdominal pain, nausea, vomiting, and fever. AiV-1 is identified in environmental screening studies with higher frequency and greater abundance than other human enteric viruses. Accordingly, 80 to 95% of adults worldwide have suffered from AiV-1 infections. We determined the structure of the AiV-1 virion. Based on the structure, we show that antiviral compounds that were developed against related enteroviruses are unlikely to be effective against AiV-1. The surface of the AiV-1 virion has a unique topology distinct from other related viruses from thePicornaviridaefamily. We also determined that AiV-1 capsids form compact shells even after genome release. Therefore, AiV-1 genome release requires large localized and probably reversible reorganization of the capsid.


Author(s):  
James H. Thorpe ◽  
Ian D. Wall ◽  
Robert H. Sinnamon ◽  
Amy N. Taylor ◽  
Robert A. Stavenger

Direct soaking of protein crystals with small-molecule fragments grouped into complementary clusters is a useful technique when assessing the potential of a new crystal system to support structure-guided drug discovery. It provides a robustness check prior to any extensive crystal screening, a double check for assay binding cutoffs and structural data for binding pockets that may or may not be picked out in assay measurements. The structural output from this technique for three novel fragment molecules identified to bind to the antibacterial target Acinetobacter baumannii undecaprenyl pyrophosphate synthase are reported, and the different physicochemical requirements of a successful antibiotic are compared with traditional medicines.


2020 ◽  
Vol 21 (18) ◽  
pp. 6779
Author(s):  
Florian Georgescauld ◽  
Yuyu Song ◽  
Alain Dautant

Nucleoside diphosphate kinases (NDPK) are oligomeric proteins involved in the synthesis of nucleoside triphosphates. Their tridimensional structure has been solved by X-ray crystallography and shows that individual subunits present a conserved ferredoxin fold of about 140 residues in prokaryotes, archaea, eukaryotes and viruses. Monomers are functionally independent from each other inside NDPK complexes and the nucleoside kinase catalytic mechanism involves transient phosphorylation of the conserved catalytic histidine. To be active, monomers must assemble into conserved head to tail dimers, which further assemble into hexamers or tetramers. The interfaces between these oligomeric states are very different but, surprisingly, the assembly structure barely affects the catalytic efficiency of the enzyme. While it has been shown that assembly into hexamers induces full formation of the catalytic site and stabilizes the complex, it is unclear why assembly into tetramers is required for function. Several additional activities have been revealed for NDPK, especially in metastasis spreading, cytoskeleton dynamics, DNA binding and membrane remodeling. However, we still lack the high resolution structural data of NDPK in complex with different partners, which is necessary for deciphering the mechanism of these diverse functions. In this review we discuss advances in the structure, folding and stability of NDPKs.


2016 ◽  
Vol 113 (9) ◽  
pp. 2394-2399 ◽  
Author(s):  
Emilia C. Arturo ◽  
Kushol Gupta ◽  
Annie Héroux ◽  
Linda Stith ◽  
Penelope J. Cross ◽  
...  

Improved understanding of the relationship among structure, dynamics, and function for the enzyme phenylalanine hydroxylase (PAH) can lead to needed new therapies for phenylketonuria, the most common inborn error of amino acid metabolism. PAH is a multidomain homo-multimeric protein whose conformation and multimerization properties respond to allosteric activation by the substrate phenylalanine (Phe); the allosteric regulation is necessary to maintain Phe below neurotoxic levels. A recently introduced model for allosteric regulation of PAH involves major domain motions and architecturally distinct PAH tetramers [Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL, Jr (2013) Arch Biochem Biophys 530(2):73–82]. Herein, we present, to our knowledge, the first X-ray crystal structure for a full-length mammalian (rat) PAH in an autoinhibited conformation. Chromatographic isolation of a monodisperse tetrameric PAH, in the absence of Phe, facilitated determination of the 2.9 Å crystal structure. The structure of full-length PAH supersedes a composite homology model that had been used extensively to rationalize phenylketonuria genotype–phenotype relationships. Small-angle X-ray scattering (SAXS) confirms that this tetramer, which dominates in the absence of Phe, is different from a Phe-stabilized allosterically activated PAH tetramer. The lack of structural detail for activated PAH remains a barrier to complete understanding of phenylketonuria genotype–phenotype relationships. Nevertheless, the use of SAXS and X-ray crystallography together to inspect PAH structure provides, to our knowledge, the first complete view of the enzyme in a tetrameric form that was not possible with prior partial crystal structures, and facilitates interpretation of a wealth of biochemical and structural data that was hitherto impossible to evaluate.


2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Ibrahim A. Al-Swaidan ◽  
Adel S. El-Azab ◽  
Amer M. Alanazi ◽  
Alaa A.-M. Abdel-Aziz

The crystal structure of (4R)-(−)-1-(2,4,6-trimethylbenzenesulfonyl)-3-n-butyryl-4-tert-butyl-2-imidazolidinone(3)was determined by single-crystal X-ray diffraction. Compound3crystallizes in triclinic system in space groupP1 (≠1). The crystal data area=10.62165 Å,b=16.5321 Å,c=8.95729 Å,∝=91.1936∘,β=93.8496∘,γ=88.0974∘,V=1568.22 Å3,Z=3,Dcalc=1.253 g/cm3,μCuKα=15.98 cm−1,F000=636.00,T=20.0°C, andR=0.037. The crystal structure confirmed the occurrence of three molecules of3A,3B, and3Cin which then-butyryl moiety adopted thes-transoidconformation. Crystal structure also revealed that the conformation of 2,4,6-trimethylbenzenesulfonyl groups was inanti-position relative totert-butyl group. The crystal packing showed that three molecules of compound3are stacked as a result of intermolecularπ-πinteractions between the phenyl ring of one molecule and the phenyl ring of the other molecule by approaching each other to an interplanar separation of 5.034 Å. Interestingly, these stacked molecules are also connected by intermolecularCH-πinteraction. The conformational analysis of thes-transoid  3A,3B, and3Cwas separately performed by molecular mechanic MM+ force field. Additionally, computational investigation using semiempirical AM1 and PM3 methods was performed to find a correlation between experimental and calculated geometrical parameters. The data obtained suggest that the structural data furnished by the AM1 method is in better agreement with those experimentally determined for the above compound. It has been found that the lowest energetic conformer computed gives approximate correspondence with experimental solid state data.


1977 ◽  
Vol 32 (4) ◽  
pp. 420-425 ◽  
Author(s):  
K. Zeitz ◽  
H. Oberhammer ◽  
G. Häfelinger

The molecular structure of gaseous 4-fluoro-2′,4′,6′-trimethylbiphenyl was determined by electron diffraction. The average of two independend determinations leads to the following parameters for the structure:CC(ring) = 1.398(1),CC(methyl) = 1.522(5), CH(ring) = 1.082(6), CH(methyl) = CH(ring) + 0.015 = 1.097(6), CF = 1.324(7), Cl-Cl′ = 1.488(9) (inter ring bond), ∢(C,C,H) = 109.9(1.8)° (angle of methylgroup tetrahedra), α = 124.9(0.6)° (angle of ortho-methyl-groups towards the inter ring bond), φ = 77.5(2.1)° (angle of torsion between the planes of the two phenyl rings) which are in good agreement with respect to known structural data on biphenylderivatives. A very interesting result is the angle of torsion with 77.5° which is by 6.5° smaller than the value of 84(1)° determined by X-ray crystallography for the corresponding 4-iodo-compound in the crystalline state1. In all determinations known to us til now for comparable derivatives of biphenyl the angle of torsion was found larger in the gaseous state than in the crystalline state.


2021 ◽  
Vol 153 (7) ◽  
Author(s):  
Chiara Stronczek ◽  
Stephan Lange ◽  
Belinda Bullard ◽  
Sebastian Wolniak ◽  
Emma Börgeson ◽  
...  

The N2A segment of titin is a main signaling hub in the sarcomeric I-band that recruits various signaling factors and processing enzymes. It has also been proposed to play a role in force production through its Ca2+-regulated association with actin. However, the molecular basis by which N2A performs these functions selectively within the repetitive and extensive titin chain remains poorly understood. Here, we analyze the structure of N2A components and their association with F-actin. Specifically, we characterized the structure of its Ig domains by elucidating the atomic structure of the I81-I83 tandem using x-ray crystallography and computing a homology model for I80. Structural data revealed these domains to present heterogeneous and divergent Ig folds, where I81 and I83 have unique loop structures. Notably, the I81-I83 tandem has a distinct rotational chain arrangement that confers it a unique multi-domain topography. However, we could not identify specific Ca2+-binding sites in these Ig domains, nor evidence of the association of titin N2A components with F-actin in transfected C2C12 myoblasts or C2C12-derived myotubes. In addition, F-actin cosedimentation assays failed to reveal binding to N2A. We conclude that N2A has a unique architecture that predictably supports its selective recruitment of binding partners in signaling, but that its mechanical role through interaction with F-actin awaits validation.


2021 ◽  
Author(s):  
Ken Ikeuchi ◽  
Nives Ivic ◽  
Jingdong Cheng ◽  
Robert Buschauer ◽  
Yoshitaka Matsuo ◽  
...  

In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by the deubiquitination enzyme Otu2 upon ribosomal subunit recycling. Despite its importance for general efficiency of translation the exact role and structural basis for this specific translational reset are only poorly understood. Here we present biochemical and structural data showing that Otu2 can engage the recycled 40S subunit together with the recycling factors ABCE1 and Tma64 immediately after 60S dissociation for mRNA recycling, and that it dissociates before 48S initiation complex formation. A combined structural analysis of Otu2 and Otu2-40S complexes by X-ray crystallography, AlphaFold2 prediction and cryo-EM revealed how Otu2 can specifically be recruited to the 40S, but not to the 80S ribosome, for removal of the eS7-bound ubiquitin moiety. Here, interactions of the largely helical N-terminal domain of Otu2 to sites that are masked and therefore inaccessible in the 80S ribosome are of crucial importance. Collectively, we provide the structural basis for the Otu2 driven deubiquitination step providing a first mechanistic understanding of this translational reset step during ribosome recycling/(re)initiation.


2009 ◽  
Vol 16 (2) ◽  
pp. 191-204 ◽  
Author(s):  
Sofia Macedo ◽  
Maria Pechlaner ◽  
Walther Schmid ◽  
Martin Weik ◽  
Katsuko Sato ◽  
...  

One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism of a metalloenzyme. Here, UV–Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects. UV–Vis absorption spectra of native crystals, as well as those soaked in 18 different radioprotectants, show dramatic metal reduction occurring in the first 60 s of irradiation with an X-ray beam from a third-generation synchrotron source. Among the tested radioprotectants only potassium hexacyanoferrate(III) seems to be capable of partially mitigating the rate of metal photoreduction at the concentrations used, but not to a sufficient extent that would allow a complete data set to be recorded from a fully oxidized crystal. On the other hand, analysis of the X-ray crystallographic data confirms ascorbate as an efficient protecting agent against radiation damage, other than metal centre reduction, and suggests further testing of HEPES and 2,3-dichloro-1,4-naphtoquinone as potential scavengers.


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