Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c

Roberts, Victoria A.; Freeman, H.C.; Olson, Arthur J.; Tainer, John A.; Getzoff, E. D.

doi:10.1016/s0021-9258(18)98858-7

Cited by 111 publications

(86 citation statements)

References 51 publications

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“…The angles θ 1 , θ 2 , and φ are listed in Supporting Information, Table S7. The total Coulombic energies (E), calculated by this simple method, reproduce the main results of the intricate computations by Roberts et al (41). The following two generalizations hold for all the mutants studied: the most stable configuration of the complex with ferrocytochrome c is max ov, and the three configurations of the complex have similar Coulombic energies.…”

Section: Choice Of Mutations Is Guided By Previous Experimentssupporting

confidence: 72%

“…We examined three configurations of the electrostatic complex between ferrocytochrome c from tuna (73) and cupriplastocyanin from poplar (74). These configurations were designated maximumoverlap (max ov); maximum-overlap, rotated (max ov rot); and northern equatorial (n/eq) in the original study (41) and afterward (54,65,66). For the sake of consistency, we retain these designations and abbreviations.…”

Section: Methodsmentioning

confidence: 99%

“…In the max ov configuration, Glu59 interacts with lysines 13, 25, and 27 in cytochrome c, and Glu60 interacts with lysines 25 and 27. In the n/eq configuration, Glu59 interacts with lysines 5, 7, 8, 13, 86, and 87 and Arg59, and Glu60 interacts with lysines 5, 7, 8, and 13 (41). Clearly, the anionic residues 59 and 60 in plastocyanin differ in their interactions with the cationic residues in cytochrome c. The main conclusion from the effects of mutation on the activation parameters is that the residues 59 and 88 lie in the pathway of rearrangement, while the residue 60 does not.…”

Section: Choice Of Mutations Is Guided By Previous Experimentsmentioning

confidence: 99%

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Effects of Single and Double Mutations in Plastocyanin on the Rate Constant and Activation Parameters for the Rearrangement Gating the Electron-Transfer Reaction between the Triplet State of Zinc Cytochromecand Cupriplastocyanin

et al. 1998

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The unimolecular rate constant for the photoinduced electron-transfer reaction 3Zncyt/pc(II) --> Zncyt+/pc(I) within the electrostatic complex of zinc cytochrome c and spinach cupriplastocyanin is kF. We report the effects on kF of the following factors, all at pH 7.0: 12 single mutations on the plastocyanin surface (Leu12Asn, Leu12Glu, Leu12Lys, Asp42Asn, Asp42Lys, Glu43Asn, Glu59Gln, Glu59Lys, Glu60Gln, Glu60Lys, Gln88Glu, and Gln88Lys), the double mutation Glu59Lys/Glu60Gln, temperature (in the range 273.3-302.9 K), and solution viscosity (in the range 1. 00-116.0 cP) at 283.2 and 293.2 K. We also report the effects of the plastocyanin mutations on the association constant (Ka) and the corresponding free energy of association (DeltaGa) with zinc cytochrome c at 298.2 K. Dependence of kF on temperature yielded the activation parameters DeltaH, DeltaS, and DeltaG. Dependence of kF on solution viscosity yielded the protein friction and confirmed the DeltaG values determined from the temperature dependence. The aforementioned intracomplex reaction is not a simple electron-transfer reaction because donor-acceptor electronic coupling (HAB) and reorganizational energy (lambda), obtained by fitting of the temperature dependence of kF to the Marcus equation, deviate from the expectations based on precedents and because kF greatly depends on viscosity. This last dependence and the fact that certain mutations affect Ka but not kF are two lines of evidence against the mechanism in which the electron-transfer step is coupled with the faster, but thermodynamically unfavorable, rearrangement step. The electron-transfer reaction is gated by the slower, and thus rate determining, structural rearrangement of the diprotein complex; the rate constant kF corresponds to this rearrangement. Isokinetic correlation of DeltaH and DeltaS parameters and Coulombic energies of the various configurations of the Zncyt/pc(II) complex consistently show that the rearrangement is a facile configurational fluctuation of the associated proteins, qualitatively the same process regardless of the mutations in plastocyanin. Correlation of kF with the orientation of the cupriplastocyanin dipole moment indicates that the reactive configuration of the diprotein complex involves the area near the residue 59, between the upper acidic cluster and the hydrophobic patch. Kinetic effects and noneffects of plastocyanin mutations show that the rearrangement from the initial (docking) configuration, which involves both acidic clusters, to the reactive configuration does not involve the lower acidic cluster and the hydrophobic patch but involves the upper acidic cluster and the area near the residue 88.

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Section: Choice Of Mutations Is Guided By Previous Experimentssupporting

confidence: 72%

Section: Methodsmentioning

confidence: 99%

Section: Choice Of Mutations Is Guided By Previous Experimentsmentioning

confidence: 99%

See 1 more Smart Citation

Effects of Single and Double Mutations in Plastocyanin on the Rate Constant and Activation Parameters for the Rearrangement Gating the Electron-Transfer Reaction between the Triplet State of Zinc Cytochromecand Cupriplastocyanin

et al. 1998

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“…Notably, as engagement of the DNA ends activates DNA‐PK activity, 126 this provides a key checkpoint to ensure that there are two free DNA ends held in the complex with autophosphorylation in trans resulting in DNA‐PKcs release from DSB ends 82 . Effectively this autophosphorylation provides an electrostatic switch to release DNA‐PKcs from the two DSB ends, 10 analogously to electrostatic control of proteins for electron transfer 127 …”

Section: Xrcc4 Dynamic Interactions and Assemblies Form The Core Nhej Flexible Bridgementioning

confidence: 99%

“… 82 Effectively this autophosphorylation provides an electrostatic switch to release DNA‐PKcs from the two DSB ends, 10 analogously to electrostatic control of proteins for electron transfer. 127 …”

Section: Xrcc4 Dynamic Interactions and Assemblies Form The Core Nhej Flexible Bridgementioning

confidence: 99%

X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology

Hammel

Tainer

2021

Protein Science

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Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.

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Biomolecular Applications of Poisson–Boltzmann Methods

Baker

2005

Reviews in Computational Chemistry

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INTRODUCTION TO BIOMOLECULAR ELECTROSTATICSThroughout the 1990s, biomolecular simulation has become increasingly commonplace in biology and has gained acceptance as an important biophysical method for understanding molecular structure, dynamics, and function. The energetic properties of a biomolecule are determined by a combination of both short-and long-range forces. Short-range forces include several components, such as van der Waals, bonding forces, angular forces, and torsional interactions. Long-range forces, on the other hand, are typically dominated by electrostatic interactions. Because of their slow decay over distance, electrostatics cannot be neglected or truncated in biomolecular modeling; these forces contribute significantly to molecular interactions at all length scales. As such, methods that enable the accurate and efficient modeling of these interactions are of central importance in molecular simulation.The exact behavior of electrostatic interactions in a simulation is generally determined by four factors: molecular charge distributions, solute atomic radii, mobile ionic species, and solvent. Molecular charge distributions are

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Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c

Cited by 111 publications

References 51 publications

Effects of Single and Double Mutations in Plastocyanin on the Rate Constant and Activation Parameters for the Rearrangement Gating the Electron-Transfer Reaction between the Triplet State of Zinc Cytochromecand Cupriplastocyanin

Effects of Single and Double Mutations in Plastocyanin on the Rate Constant and Activation Parameters for the Rearrangement Gating the Electron-Transfer Reaction between the Triplet State of Zinc Cytochromecand Cupriplastocyanin

X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology

Biomolecular Applications of Poisson–Boltzmann Methods

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