Structure−Function Relationships inAnabaenaFerredoxin:  Correlations between X-ray Crystal Structures, Reduction Potentials, and Rate Constants of Electron Transfer to Ferredoxin:NADP+Reductase for Site-Specific Ferredoxin Mutants†,‡

Biochemistry ◽  
1997 ◽  
Vol 36 (37) ◽  
pp. 11100-11117 ◽  
Author(s):  
John K. Hurley ◽  
Anne M. Weber-Main ◽  
Marian T. Stankovich ◽  
Matthew M. Benning ◽  
James B. Thoden ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Structure Function ◽  
Crystal Structures ◽  
Rate Constants ◽  
Site Specific ◽  
X Ray ◽  
Reduction Potentials

scholarly journals Rgg protein structure–function and inhibition by cyclic peptide compounds

2015 ◽  
Vol 112 (16) ◽  
pp. 5177-5182 ◽  
Author(s):  
Vijay Parashar ◽  
Chaitanya Aggarwal ◽  
Michael J. Federle ◽  
Matthew B. Neiditch
Keyword(s):  
Dna Binding ◽  
Structure Function ◽  
Cyclosporin A ◽  
Crystal Structures ◽  
Disulfide Bond ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
X Ray ◽  
Peptide Pheromone ◽  
Dimerization Interface

Peptide pheromone cell–cell signaling (quorum sensing) regulates the expression of diverse developmental phenotypes (including virulence) in Firmicutes, which includes common human pathogens, e.g.,Streptococcus pyogenesandStreptococcus pneumoniae. Cytoplasmic transcription factors known as “Rgg proteins” are peptide pheromone receptors ubiquitous in Firmicutes. Here we present X-ray crystal structures of aStreptococcusRgg protein alone and in complex with a tight-binding signaling antagonist, the cyclic undecapeptide cyclosporin A. To our knowledge, these represent the first Rgg protein X-ray crystal structures. Based on the results of extensive structure–function analysis, we reveal the peptide pheromone-binding site and the mechanism by which cyclosporin A inhibits activation of the peptide pheromone receptor. Guided by the Rgg–cyclosporin A complex structure, we predicted that the nonimmunosuppressive cyclosporin A analog valspodar would inhibit Rgg activation. Indeed, we found that, like cyclosporin A, valspodar inhibits peptide pheromone activation of conserved Rgg proteins in medically relevantStreptococcusspecies. Finally, the crystal structures presented here revealed that the Rgg protein DNA-binding domains are covalently linked across their dimerization interface by a disulfide bond formed by a highly conserved cysteine. The DNA-binding domain dimerization interface observed in our structures is essentially identical to the interfaces previously described for other members of the XRE DNA-binding domain family, but the presence of an intermolecular disulfide bond buried in this interface appears to be unique. We hypothesize that this disulfide bond may, under the right conditions, affect Rgg monomer–dimer equilibrium, stabilize Rgg conformation, or serve as a redox-sensitive switch.

Electron transfer kinetics of cobaloxime complexes

1996 ◽  
Vol 74 (5) ◽  
pp. 658-665 ◽  
Author(s):  
Kefei Wang ◽  
R.B. Jordan
Keyword(s):  
Electron Transfer ◽  
Exchange Rate ◽  
Rate Constants ◽  
Ph Dependence ◽  
Outer Sphere ◽  
The Self ◽  
Oxidation Of Co ◽  
Reduction Potentials ◽  
Inner Sphere ◽  
Kinetics Of

The rates of oxidation of CoII(dmgBF2)2(OH2)2 by CoIII(NH3)5X2+ (X = Br−, Cl−, and N3−) have been studied at 25 °C in 0.10 M LiClO4. The rate constants are 50 ± 9, 2.6 ± 0.2, and 5.9 ± 1.0 M−1 s−1 for X = Br−, Cl−, and N3−, respectively, in 0.01 M acetate buffer at pH 4.7. The relative rates are consistent with the inner-sphere bridging mechanism established earlier by Adin and Espenson for the analogous reactions of CoII(dmgH)2(OH2)2. The rate constants with CoII(dmgBF2)2(OH2)2 typically are ~103 times smaller and this is attributed largely to the smaller driving force for the CoII(dmgBF2)2(OH2)2 complex. The outer-sphere oxidations of cobalt(II) sepulchrate by CoIII(dmgH)2(OH2)2+ (pH 4.76–7.35, acetate, MES, and PIPES buffers) and CoIII(dmgBF2)2(OH2)2+ (pH 3.3–7.42, chloroacetate, acetate, MES, and PIPES buffers) have been studied. The pH dependence gives the following rate constants (M−1 s−1) for the species indicated: (1.55 ± 0.09) × 105 (CoIII(dmgBF2)2(OH2)2+); (5.5 ± 0.3) × 103 (CoII(dmgH)2(OH2)2+); (3.1 ± 0.5) × 102 (CoIII(dmgH)2(OH2)(OH)); (2.5 ± 0.3) × 102 (CoIII(dmgBF2)2(OH2)(OH)). The known reduction potentials for cobalt(III) sepulchrate and the diaqua complexes, and the self-exchange rate for cobalt(II/III) sepulchrate, are used to estimate the self-exchange rate constants for the dioximate complexes. Comparisons to other reactions with cobalt sepulchrate indicates best estimates of the self-exchange rate constants are ~2.4 × 10−2 M−1 s−1 for CoII/III(dmgH)2(OH2)2and ~5.7 × 10−3 M−1 s−1 for CoII/III(dmgBF2)2(OH2)2. Key words: electron transfer, cobaloxime, inner sphere, outer sphere, self-exchange.

scholarly journals 3P036 X-ray crystal structures of carbonmonoxy hemoglobin photolysis intermediates(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

2014 ◽  
Vol 54 (supplement1-2) ◽  
pp. S254
Author(s):  
Ayana Tomita ◽  
Tokushi Sato ◽  
Hiroki Noguchi ◽  
Shunsuke Nozawa ◽  
Shin-ya Koshihara ◽  
...  
Keyword(s):  
Protein Structure ◽  
Structure Function ◽  
Crystal Structures ◽  
Annual Meeting ◽  
X Ray ◽  
Biophysical Society

scholarly journals Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure–function studies

2021 ◽  
Vol 77 (3) ◽  
pp. 173-185
Author(s):  
John R. Helliwell
Keyword(s):  
Structure Function ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Protein Crystal ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
Precision And Accuracy ◽  
Electron Microscopes

The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure–function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.

scholarly journals New Approaches to an Old Problem: Original Techniques in [FeFe]-hydrogenase Research

2020 ◽  
Author(s):  
Henrik Land ◽  
Moritz Senger ◽  
Gustav Berggren ◽  
Sven T. Stripp
Keyword(s):  
Carbon Monoxide ◽  
Electron Transfer ◽  
Proton Transfer ◽  
Ftir Spectroscopy ◽  
Crystal Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
New Approaches ◽  
Naturally Occurring ◽  
Biophysical Techniques

Even 20 years after the first crystal structures of [FeFe]-hydrogenase have been published, several aspects of biological hydrogen turnover are heatedly discussed. In this perspective, we give an overview on how the diversity of naturally occurring and artificially prepared, semi-synthetic [FeFe]-hydrogenases deepens our understanding of hydrogenase chemistry. In parallel, we cover new results from biophysical techniques that go beyond the scope of conventional electrochemistry, X-ray diffraction, EPR, and FTIR spectroscopy. Taking into account both proton transfer and electron transfer as well as the notorious sensitivity of [FeFe]-hydrogenases towards carbon monoxide, the discussion further touches upon the molecular proceedings of biological hydrogen turnover.

Interligand Interactions Affecting Site-Specific Metal Bonding. X-ray Crystal Structures of [Rh2(acetato)4(L)2], Where L = 2,4-Diamino-6-methyl-s-triazine, 2,6-Dimethyl-4-aminopyrimidine, and 2,6-Dimethylpyridine

1994 ◽  
Vol 33 (13) ◽  
pp. 3018-3020 ◽  
Author(s):  
Katsuyuki Aoki ◽  
Masamoto Inaba ◽  
Shousuke Teratani ◽  
Hiroshi Yamazaki ◽  
Yoshikatsu Miyashita
Keyword(s):  
Crystal Structures ◽  
Site Specific ◽  
X Ray ◽  
Metal Bonding ◽  
Specific Metal

Electron transfer from cresols to N3, BrO2, ClO2, NO2 and SO−4 radicals: correlation between rate constants and one-electron reduction potentials

1999 ◽  
Vol 55 (5-6) ◽  
pp. 515-519 ◽  
Author(s):  
Magda Roder ◽  
Gábor Földiák ◽  
László Wojnárovits
Keyword(s):  
Electron Transfer ◽  
Rate Constants ◽  
Reduction Potentials ◽  
Electron Reduction
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