The axial methionine ligand may control the redox reorganizations in the active site of blue copper proteins

Ando, Koji

doi:doi:10.1063/1.3495983

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Aggregation of amphiphilic polymers in the presence of adhesive small colloidal particles

The interaction of amphiphilic polymers with small colloids, capable to reversibly stick onto the chains, is studied. Adhesive small colloids in solution are able to dynamically bind two polymer segments. This association leads to topological changes in the polymer network configurations, such as looping and cross-linking, although the reversible adhesion permits the colloid to slide along the chain backbone. Previous analyses only consider static topologies in the chain network. We show that t...

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and...

Structural and energetic reorganizations in redox reaction of type 1 copper proteins are studied by density functional and ab initio molecular orbital calculations. Model complexes of the active site with varying number of ligands, from Cu(SCH₃)^0/+ to Cu(SCH₃)(Im)₂(S(CH₃)₂)^0/+, where Im denotes imidazole, are investigated. Following the findings of structural instability in Cu(I)(SCH₃)(Im)₂ and its stabilization by the addition of the axial methionine (Met) ligand model, the structure and energetics are examined as functions of the Cu–S_Met distance in the range of 2.1–3.3 Å. The reorganization energies in both redox states exhibit a minimum at the Cu–S_Met distance of ∼ 2.4 Å, whereas the ionization potential increases monotonically. The changes of reorganization energies correlate well with one of the Cu–N_His distances rather than the Cu–S_Cys distance. The estimated Arrhenius factor for oxidation of plastocyanin by P700⁺ (in photosystem I) changes by an order of magnitude when the Cu–S_Met distance fluctuates between 2.4 and 3.0 Å, whereas the factor for reduction of plastocyanin by cytochrome f is nearly constant. Together with the data from our previous classical molecular dynamics simulation of solvated protein, we argue that the electron transfer rate is affected, and thus may be controlled, by the fluctuation of a weakly bound axial Met ligand. We also present the assessment of various exchange-correlation functionals, including those with the long-range correction, against the CCSD(T) reference and on the basis of a perturbative adiabatic connection model. For Cu(SCH₃) and Cu(SCH₃)(Im), simple correlations have been found between the reorganization energies and the amount of Hartree–Fock exchange.

Article Outline

INTRODUCTION
COMPUTATIONAL DETAILS
RESULTS AND DISCUSSION
1. Cu(Cys)
2. Perturbative adiabatic connection model
3. Cu(Cys)(His)
4. Cu(Cys)(His)₂
5. Cu(Cys)(His)₂(Met)
6. Reorganization control by Met
7. Estimating the Arrhenius factor
CONCLUDING REMARKS

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KEYWORDS and PACS

Keywords

ab initio calculations, charge exchange, coupled cluster calculations, density functional theory, HF calculations, ionisation potential, molecular biophysics, molecular configurations, molecular electronic states, oxidation, proteins, reduction (chemical)

PACS

87.15.kp

Protein-ligand interactions
87.15.hp

Conformational changes
87.14.E-

Proteins
82.39.Jn

Charge (electron, proton) transfer in biological systems
31.15.eg

Exchange-correlation functionals (in current density functional theory)
31.15.ae

Electronic structure and bonding characteristics

ARTICLE DATA

Digital Object Identifier

http://dx.doi.org/10.1063/1.3495983

PUBLICATION DATA

ISSN

0021-9606 (print)

1089-7690 (online)

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$abstract.society.value is a Member of CrossRef

American Institute of Physics

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