Tuna cytochrome c at 2.0 A resolution. I.Ferricytochrome structure analysis.

Swanson, Rosemarie; Trus, Benes L.; Mandel, N.; Mandel, Gretchen S.; Kallai, Olga B.; Dickerson, Richard E.

doi:10.1016/s0021-9258(17)32783-7

Cited by 202 publications

(53 citation statements)

References 22 publications

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“…Crystals of other cytochromes c have been obtained in this space group only twice, but with lattice parameters different from those presented here. They were a=57.68 A, b=84.58 A and c=37.83 A for bonito cytochrome c [5], and a=63.1 A, b=91.4 A and c=36.7 A for the tuna protein [6]. The three-dimensional structure was solved only for the crystals of bonito cytochrome c.…”

Section: Crystallization and Data Collectionmentioning

confidence: 99%

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The low ionic strength crystal structure of horse cytochrome c at 2.1 å resolution and comparison with its high ionic strength counterpart

Sanishvili¹,

Volz

Westbrook

et al. 1995

Structure

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Neither ionic strength nor crystal-packing interactions have much influence on the conformation of horse cytochrome c. Nevertheless, some differences in the side-chain conformations at high and low ionic strengths may be important for understanding how the protein functions. Close examination of the gamma-turn (residues 27-29) conserved in cytochromes c leads us to propose the 'negative classical' gamma-turn to describe this unusual feature.

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Section: Crystallization and Data Collectionmentioning

confidence: 99%

“…The three-dimensional structure of cytochrome c was one of the first protein structures to be solved by X-ray diffraction methods [4]. The structures of the protein from several species are now available, including baker's yeast, rice, tuna, bonito and horse [5][6][7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

The low ionic strength crystal structure of horse cytochrome c at 2.1 å resolution and comparison with its high ionic strength counterpart

Sanishvili¹,

Volz

Westbrook

et al. 1995

Structure

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“…An enzyme that has attracted interest in studies designed to sort out some of these factors is cytochrome c peroxidase (ferrocytochrome ¿¡hydrogen peroxide oxidoreductase; EC 1.11.1.5;CcP).1 It is a 34-kDa, single-subunit native ferriheme enzyme from bakers' yeast that forms a reversible complex with various species of ferrocytochrome c in the process of reducing hydrogen peroxide to water (Yonetani, 1976; Kang et al, 1977Kang et al, , 1978 Kraut, 1981; Bosshard et al, 1991). CcP and cytochromes c from the three species used in this work (horse, tuna, and yeast) are relatively small, water-soluble proteins that have been well characterized by X-ray diffraction methods so that structures are readily available (Poulos et al, 1980;; Swanson et al, 1977; Takano & Dickerson, 1981; Louie et al, 1988; Louie & Brayer, 1990). In addition, both static and dynamic molecular modeling studies (Poulos & Kraut, 1980;Northrup et al, 1988) as well as extensive steady-state and transient kinetic studies (Kang et al, 1977; Kang & Erman, 1982; Erman et al, 1987;Hazzard et al, 1987Hazzard et al, , 1988aLiang et al, 1988;) have been performed on CcP/cytochrome c complexes.…”

mentioning

confidence: 99%

Proton NMR comparison of noncovalent and covalently cross-linked complexes of cytochrome c peroxidase with horse, tuna, and yeast ferricytochromes c

Moench¹,

Chroni²,

Lou³

et al. 1992

Biochemistry

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Proton NMR spectroscopy at 500 and 361 MHz has been used to characterize the noncovalent or electrostatic complexes of yeast cytochrome c peroxidase (CcP) with horse, tuna, yeast isozyme-1, and yeast isozyme-2 ferricytochromes c and the covalently cross-linked complexes of cytochrome c peroxidase with horse and yeast isozyme-1 ferricytochromes c. Under the conditions employed in this work, the stoichiometry of the predominant complex formed in solution (which totaled greater than 90% of complex formed) was found to be 1:1 in all cases. These studies have elucidated significant differences in the proton NMR absorption spectra and the one-dimensional nuclear Overhauser effect difference spectra of the complexes, depending on the specific species of ferricytochrome c incorporated. In particular, the results indicate that the noncovalent complexes formed between CcP and physiological redox partners (yeast isozyme-1 or yeast isozyme-2 ferricytochromes c) are distinctly different from the noncovalent complexes formed between CcP and ferricytochromes c from horse and tuna. Parallel chemical cross-linking studies carried out using mixtures of cytochrome c peroxidase with horse ferricytochrome c, and cytochrome c peroxidase with yeast isozyme-1 ferricytochrome c further emphasize such cytochrome c-dependent differences, with only the covalently cross-linked complex of physiological redox partners (cytochrome c peroxidase/yeast isozyme-1) displaying NMR spectra characteristic of a heterogeneous mixture of different 1:1 complexes. Finally, one-dimensional nuclear Overhauser effect experiments have proven valuable in selectively and efficiently probing the protein-protein interface in these complexes, including the environment around the cytochrome c heme 3-methyl group and Phe-82.

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“…Four main regions are occupied in the Ramachandran diagram: β-sheets (βS), polyproline II (βP ; left-handed helical structure whose angles are characteristic of β-strands); α-helical (αR); and left handed helix (αL). These regions were characterized using a combination of five steric constraints between four atoms defining the Ramachandran tetrahedron ( [22], Fig. 4).…”

Section: Ramachandran Distributionsmentioning

confidence: 99%

“…Four main regions are occupied in the Ramachandran diagram:

β

‐sheets (

italicβS

), polyproline II

true(italicβP

; left‐handed helical structure whose angles are characteristic of

β

‐strands);

α

‐helical (

italicαR

); and left‐handed helix (

italicαL

). These regions were characterized using a combination of five steric constraints between four atoms 25 defining the Ramachandran tetrahedron (Figure 4). (We note in passing that the sixth edge of this tetrahedron, between

O_{i}

and

N_{i + 1}

, was not used in defining the steric constraints, likely due to the fact that this edge corresponds to a valence angle—a constraint stronger than that associated with the other edges.)…”

Section: Introductionmentioning

confidence: 99%

Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions

O’Donnell¹,

Robert

Cazals³

2021

Proteins

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Tripeptide loop closure (TLC) is a standard procedure to reconstruct protein backbone conformations, by solving a zero‐dimensional polynomial system yielding up to 16 solutions. In this work, we first show that multiprecision is required in a TLC solver to guarantee the existence and the accuracy of solutions. We then compare solutions yielded by the TLC solver against tripeptides from the Protein Data Bank. We show that these solutions are geometrically diverse (up to 3normalÅ Root mean square deviation with respect to the data) and sound in terms of potential energy. Finally, we compare Ramachandran distributions of data and reconstructions for the three amino acids. The distribution of reconstructions in the second angular space (),ϕ2ψ2 stands out, with a rather uniform distribution leaving a central void. We anticipate that these insights, coupled to our robust implementation in the Structural Bioinformatics Library ( https://sbl.inria.fr/doc/Tripeptide_loop_closure‐user‐manual.html), will help understanding the properties of TLC reconstructions, with potential applications to the generation of conformations of flexible loops in particular.

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Tuna cytochrome c at 2.0 A resolution. I.Ferricytochrome structure analysis.

Cited by 202 publications

References 22 publications

The low ionic strength crystal structure of horse cytochrome c at 2.1 å resolution and comparison with its high ionic strength counterpart

The low ionic strength crystal structure of horse cytochrome c at 2.1 å resolution and comparison with its high ionic strength counterpart

Proton NMR comparison of noncovalent and covalently cross-linked complexes of cytochrome c peroxidase with horse, tuna, and yeast ferricytochromes c

Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions

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