Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins

Rienzo, Francesca De; Gabdoulline, Razif R.; Wade, Rebecca C.; Sola, Marcó; Menziani, Maria Cristina

doi:10.1007/s00018-004-3181-5

Cited by 24 publications

(20 citation statements)

References 175 publications

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“…Tertiary structures of the two proteins, predicted by homology modeling, were very similar to each other, and they also resembled type B ephrin-B2 from mouse (1IKO; Supplementary Figure S3 ). However, it is noteworthy that the ephrin ligand protein was similar to the cupredoxin domain, a protein domain containing copper binding sites and usually responsible for electron-transfer reactions in bacteria (De Rienzo et al, 2004 ). Distinct from cupredox domain proteins, ephrin acts as a signal molecule in animals, with no metal-binding capability (Toth et al, 2001 ).…”

Section: Resultsmentioning

confidence: 99%

Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host

et al. 2016

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The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33T. Its genome had potential sign of ongoing genome erosion and gene exchange with its host. Testosterone degradation and type III secretion system are commonly present in Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, this bacterium could move into coral cells via endocytosis after binding to coral's Eph receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase are possible type III secretion effectors that might help coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under stress conditions. Based on all these findings, we inferred that E. montiporae was a facultative endosymbiont that can recognize, translocate, communicate and modulate its coral host.

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Section: Resultsmentioning

confidence: 99%

Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host

et al. 2016

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“…10,46 Overall, the performance of the AMOEBA-AOM on plastocyanin and azurin is comparable to previously purposed MM models. 10,46,47 …”

Section: Resultsmentioning

confidence: 99%

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

Xiang

Ponder

2013

J. Chem. Theory Comput.

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An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies.

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“…2. 4 The distance from the copper ion to the plane formed by His39 Nd1, His92 Nd1, and Cys89 Sg. The positive value indicates that the copper atom is located toward the Met97 Sd ligand from the NNS plane.…”

Section: A-synucleinmentioning

confidence: 99%

Investigating metal-binding in proteins by nuclear magnetic resonance

Jensen

Hass

Hansen

et al. 2007

Cell. Mol. Life Sci.

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Metal ions play a key role for the function of many proteins. The interaction of the metal ion with the protein and its involvement in the function of the protein vary widely. In some proteins, the metal ion is bound tightly to the ligand residues and may be the key player in the function of the protein, as in the case of blue copper proteins. In other proteins, the metal ion is bound only temporarily and loosely to the protein, as in the case of some metalloenzymes and other proteins where the metal ion acts as a cofactor necessary for the function of the protein. Such proteins are often known as metal ion-activated proteins. The review focuses on recent nuclear magnetic resonance (NMR) studies of a series of metal-dependent proteins and the characterization of the metal-binding sites. In particular, we focus on NMR techniques for studying metal binding to proteins such as chemical shift mapping, paramagnetic NMR and changes in backbone dynamics upon metal binding.

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Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins

Cited by 24 publications

References 175 publications

Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host

Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

Investigating metal-binding in proteins by nuclear magnetic resonance

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