Detailed assessment of X-ray induced structural perturbation in a crystalline state protein

Takeda, Kazuki; Kusumoto, Kouji; Hirano, Yu; Miki, Kunio

doi:10.1016/j.jsb.2009.09.012

Cited by 20 publications

(12 citation statements)

References 54 publications

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“…tepidum and purified as reported previously [14,17]. Oxidation of HiPIP was done by adding of 10 mM K 3 [Fe(CN) 6 ] just before use, because the purified sample was in the reduced state.…”

Section: Methodsmentioning

confidence: 99%

“…The oxidized structure was solved by the molecular replacement method with the CNS program [22] using the structure of HiPIP in the reduced state at 100 K (PDB-ID: 3A39 [17]) as an initial model. One HiPIP molecule is contained in the crystallographic asymmetric unit.…”

Section: Methodsmentioning

confidence: 99%

“…We have performed high-resolution crystallographic investigations of HiPIP from a thermophilic purple bacterium Thermochromatium tepidum [14–17]. In addition, we recently succeeded in performing a charge-density analysis of HiPIP in the reduced state at 0.48 Å resolution [18].…”

Section: Introductionmentioning

confidence: 99%

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Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 Å resolution

et al. 2017

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High-potential iron-sulfur protein (HiPIP) is a soluble electron carrier protein of photosynthetic bacteria with an Fe4S4 cluster. Although structural changes accompanying the electron transfer are important for understanding of the functional mechanism, the changes have not been clarified in sufficient detail. We previously reported the high-resolution crystal structures of HiPIP from a thermophilic purple bacterium Thermochromatium tepidum in the reduced state. In order to perform a detailed comparison between the structures in different redox states, the oxidized structure should also be revealed at high resolution. Therefore, in the present study we performed a crystallographic analysis of oxidized HiPIP and a structural comparison with the reduced form at a high resolution of 0.8 Å. The comparison highlighted small but significant contraction in the iron-sulfur cluster. The changes in Fe-S bond lengths were similar to that predicted by theoretical calculation, although some discrepancies were also found. Almost distances between the sulfur atoms of the iron-sulfur cluster and the protein environment are elongated upon the oxidation. Positional changes of hydrogen atoms in the protein environment, such as on the amide-hydrogen of Cys75 in the proximity of the iron-sulfur cluster, were also observed in the accurate analyses. None of the water molecules exhibited significant changes in position or anisotropy of atomic displacement parameter between the two states, while the orientations of some water molecules were different.

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“…tepidum and purified as reported previously [14,17]. Oxidation of HiPIP was done by adding of 10 mM K 3 [Fe(CN) 6 ] just before use, because the purified sample was in the reduced state.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 Å resolution

et al. 2017

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“…All protein crystal structures were obtained from the Protein Data Bank (PDB). [29] Crystal structures of six HiPIP species were utilized: Rhodocyclus tenuis ( Rt ) [1ISU] at 1.50 Å resolution,[30] Rhodoferax fermentans ( Rf ) [1HLQ] at 1.45 Å resolution,[31] Ectothiorhodospira vacuolata ( Ev ) [1HPI] at 1.80 Å resolution,[32] Ectothiorhodospira halophila ( Eh ) [2HIP] at 2.50 Å resolution,[33] Thermochromatium tepidum ( Tt ) [3A39] at 0.72 Å,[34] [1IUA] at 0.80 Å,[35] [2FLA] at 0.95 Å (reduced), and [2AMS] at 1.40 Å resolution, and Chromatium vinosum ( Cv ) [1CKU] at 1.20 Å resolution. [36] For crystal structures containing more than one molecule in the asymmetric unit, the calculated energies were averaged over all structures with the exception of Eh ; chain B from the Eh structures contained unusual FeS bond lengths so it was not utilized.…”

Section: Methodsmentioning

confidence: 99%

Calculating standard reduction potentials of [4Fe–4S] proteins

Perrin¹,

Ichiye²

2012

J Comput Chem

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The oxidation-reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. While the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combination of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results.

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“…2(a), 2(b) and 2(c) demonstrate that all types of interactions that are known to exist in protein molecules also occur in the crystal contacts. We took this one step further and quantified the occurrence of interactions by type in the crystal lattices of two protein molecules: one with experimentally determined positions of H atoms (PDB entry 3a38; Takeda et al, 2010) and another with theoretically predicted positions (PDB entry 1kmt; Mateja et al, 2002). The results are shown in Table 8.…”

Section: Van Der Waals Interactions Dominate In the Formation Of Protmentioning

confidence: 99%

Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase

Dimova

Devedjiev

2018

Int Union Crystallogr J

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Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.

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Detailed assessment of X-ray induced structural perturbation in a crystalline state protein

Cited by 20 publications

References 54 publications

Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 Å resolution

Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 Å resolution

Calculating standard reduction potentials of [4Fe–4S] proteins

Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase

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