scholarly journals Crystal structures of murine angiogenin‐2 and ‐3 – probing ‘structure – function’ relationships amongst angiogenin homologues

FEBS Journal ◽  
2012 ◽  
Vol 280 (1) ◽  
pp. 302-318 ◽  
Author(s):  
Shalini Iyer ◽  
Daniel E. Holloway ◽  
K. Ravi Acharya
Keyword(s):  
Structure Function ◽  
Crystal Structures

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.

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 2P017 Crystal Structures of Simplified BPTIs Solved at 1.0 and 1.4 Å Resolutions(Proteins-structure and structure-function relationship,Poster Presentations)

2007 ◽  
Vol 47 (supplement) ◽  
pp. S117
Author(s):  
Mohammad Monirul Islam ◽  
Shihori Sohya ◽  
Keiichi Noguchi ◽  
Masafumi Yohda ◽  
Yutaka Kuroda
Keyword(s):  
Structure Function ◽  
Crystal Structures ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
Poster Presentations

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.

Cruciform structures and functions

1996 ◽  
Vol 29 (4) ◽  
pp. 279-307 ◽  
Author(s):  
Youri Timsit ◽  
Dino Moras
Keyword(s):  
High Resolution ◽  
Structure Function ◽  
Crystal Structures ◽  
Function Analysis ◽  
Dna Interactions ◽  
Biologically Relevant ◽  
Dna Molecule ◽  
Biological Importance ◽  
Crystal Packings

In this paper, a structure-function analysis of B-DNA self-fitting is reviewed in the light of recent oligonucleotide crystal structures. Their crystal packings provided a high-resolution view of B-DNA helices closely and specifically fitted by groove-backbone interaction, a natural and biologically relevant manner to assemble B-DNA helices. In revealing that new properties of the DNA molecule emerge during condensation, these crystallographic studies have pointed to the biological importance of DNA—DNA interactions.

Structure−Function Relationships and Crystal Structures of the Vitamin D Receptor Bound 2α-Methyl-(20S,23S)- and 2α-Methyl-(20S,23R)-epoxymethano-1α,25-dihydroxyvitamin D3

2010 ◽  
Vol 53 (3) ◽  
pp. 1159-1171 ◽  
Author(s):  
Pierre Antony ◽  
Rita Sigüeiro ◽  
Tiphaine Huet ◽  
Yoshiteru Sato ◽  
Nick Ramalanjaona ◽  
...  
Keyword(s):  
Vitamin D ◽  
Structure Function ◽  
Crystal Structures ◽  
Vitamin D Receptor ◽  
Dihydroxyvitamin D3
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