Protonation of the Copper(I) Form of the Blue Copper Proteins Plastocyanin and Amicyanin – A Molecular Dynamics Study

Buning, Christian; Comba, Peter

doi:10.1002/(sici)1099-0682(200006)2000:6<1267::aid-ejic1267>3.3.co;2-k

Cited by 24 publications

(17 citation statements)

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“…It should not be overlooked that all of the loop mutations may have influenced rotational barriers involved in the dissociation and protonation of the C-terminal His ligand which could have a significant effect on the pK a value. 117 The structural features which control the pK a of the C-terminal His ligand at a T1 copper site remain to be identified.…”

Section: The Influence Of Loop Mutations On His Ligand Protonation An...mentioning

confidence: 99%

The role of ligand-containing loops at copper sites in proteins

Dennison

2008

Nat. Prod. Rep.

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Many approaches are being used to engineer metalloproteins, with most of these informed by, and aiming to further elucidate, the basic structural requirements for biological metal centers. Cupredoxins are type 1 (T1) copper-containing electron transfer (ET) proteins with a -barrel fold that is thought to constrain metal site structure. The T1 copper ion is bound by ligands mainly originating from a single active site loop whose length and structure varies. This Highlight article will focus on protein engineering studies which have investigated the role of the metal-binding loop for active site integrity and functionality. Scaffold differences are present within the cupredoxin family and their influence has also been assessed. Given the widespread occurrence of -barrel domains in nature, and the array of metal sites in proteins composed of loop regions, the studies described on this model system have implications for a variety of metalloproteins.

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Section: The Influence Of Loop Mutations On His Ligand Protonation An...mentioning

confidence: 99%

The role of ligand-containing loops at copper sites in proteins

Dennison

2008

Nat. Prod. Rep.

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“…Another relevant descriptor of water-protein system behavior [25] is the structural and dynamical reorganization of the H-bond network that is established, at sufficient hydration level, between the solvent molecules and the surface protein sites and that can influence the network of intramolecular H -bonds, thus affecting the functionality of the protein. An example of the role played by hydration water was reported by Buning and Comba [27], who investigated the acidic structural transition of two cupredoxins, Ami and Pc, performing MD studies. The protonation state of these proteins is pH dependent due to the presence of a partially exposed histidine in the coordination sphere of the Cu atom (downstream histidine in figs 1 and 2).…”

Section: Protein Structure and Solventmentioning

confidence: 99%

“…For Ami, very similar His conformers to Pc were observed. On the basis of these calculations and previous experimental information, Buning and Comba [27] proposed a model mechanism in which the stabilization of the low pH form is preceded by the decomplexation of His, the isomerization of the protein to a solvent accessible His form and protonation of the flipped His. In this picture, where the role of the solvent molecules is fundamental for protonating the flipped His and stabilizing the unbound form, the extent of solvent accessibility to the C-terminal His determines the possibility of the protein to attain a stable protonated state and, therefore, to lose its specific functionality.…”

Section: Protein Structure and Solventmentioning

confidence: 99%

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

Rienzo

Gabdoulline

Wade

et al. 2004

Cellular and Molecular Life Sciences (CMLS)

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Computational techniques are becoming increasingly important in structural and functional biology, in particular as tools to aid the interpretation of experimental results and the design of new systems. This review reports on recent studies employing a variety of computational approaches to unravel the microscopic details of the structure-function relationships in plastocyanin and other proteins belonging to the blue copper superfamily. Aspects covered include protein recognition, electron transfer and protein-solvent interaction properties of the blue copper protein family. The relevance of integrating diverse computational approaches to address the analysis of a complex protein system, such as a cupredoxin metalloprotein, is emphasized.

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“…Provided a force field can be developed, which accurately reproduces the structures, empirical force field calculations would be a powerful tool for the investigation of the structure and dynamics of blue copper proteins and of metalloproteins in general. Force field calculations have been used successfully for the computation of transition metal and bioinorganic compounds,26–35 but so far there is no accurate, generally applicable and carefully validated force field for blue copper proteins. The aim of this study was to develop and test a general force field for the oxidized form of type 1 blue copper proteins.…”

Section: Introductionmentioning

confidence: 99%

A new molecular mechanics force field for the oxidized form of blue copper proteins

Comba

Remenyi

2002

J Comput Chem

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A molecular mechanics force field for blue copper proteins has been developed, based on a rigid potential energy surface scan of the Cu(II)/His/His/Cys/Met chromophore, using DFT (B3LYP) calculations and the AMBER force field for the protein backbone. The strain-energy-minimized structures of the model chromophore alone are in excellent agreement with the DFT-optimized structure, and those of the entire set of cupredoxins (five structures are considered) are, within the experimental error limits, in good agreement with the single crystal structural data. However, the structural variation in the computed structures is much smaller than those in the experimental structures. It is shown that, due to the large error limits in the experimental data, a validation of the force field with experimental structural data is impossible because, within the error limits, all experimental structures considered are virtually identical. A validation on the basis of spectroscopic data and their correlation with experimental and computed structural data is proposed, and, as a first example, the correlation of intensity ratios of the charge transfer transitions with a specific distortion mode is presented. The quality of the correlation, using the computed structures, is higher than that with the X-ray structures, and this indicates that the computed structures are meaningful.

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Protonation of the Copper(I) Form of the Blue Copper Proteins Plastocyanin and Amicyanin – A Molecular Dynamics Study

Cited by 24 publications

References 0 publications

The role of ligand-containing loops at copper sites in proteins

The role of ligand-containing loops at copper sites in proteins

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

A new molecular mechanics force field for the oxidized form of blue copper proteins

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