scholarly journals The susceptibility of disulfide bonds towards radiation damage may be explained by S...O interactions

IUCrJ ◽  
2020 ◽  
Vol 7 (5) ◽  
pp. 825-834
Author(s):  
Rajasri Bhattacharyya ◽  
Jesmita Dhar ◽  
Shubhra Ghosh Dastidar ◽  
Pinak Chakrabarti ◽  
Manfred S. Weiss
Keyword(s):  
Electron Transfer ◽  
Disulfide Bond ◽  
Disulfide Bonds ◽  
Metal Ion ◽  
Structural Information ◽  
Close Contact ◽  
Bond Cleavage ◽  
Protein Structures ◽  
Protein Crystal ◽  
X Ray

Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S—S bonds which engage in a close contact with a carbonyl O atom along the extension of the S—S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S—S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.

scholarly journals Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis

2019 ◽  
Author(s):  
Helena W. Qi ◽  
Heather Kulik
Keyword(s):  
Amino Acids ◽  
High Resolution ◽  
Crystal Structures ◽  
Close Contact ◽  
Protein Structures ◽  
Protein Crystal ◽  
X Ray ◽  
High Quality Protein ◽  
Van Der Waals Radii ◽  
Close Contacts

<div><div><div><p>We investigate unexpectedly short non-covalent distances (< 85% of the sum of van der Waals radii) in atomically resolved X-ray crystal structures of proteins. We curate over 13,000 high quality protein crystal structures and an ultra-high resolution (1.2 Å or better) subset containing > 1,000 structures. Although our non-covalent distance criterion excludes standard hydrogen bonds known to be essential in protein stability, we observe over 82,000 close contacts in the curated protein structures. Analysis of the frequency of amino acids participating in these interactions demonstrates some expected trends (i.e., enrichment of charged Lys, Arg, Asp, and Glu) but also reveals unexpected enhancement of Tyr in such interactions. Nearly all amino acids are observed to form at least one close contact with all other amino acids, and most interactions are preserved in the much smaller ultra high-resolution subset. We quantum-mechanically characterize the interaction energetics of a subset of > 6,000 close contacts with symmetry adapted perturbation theory to enable decomposition of interactions. We observe the majority of close contacts to be favorable. The shortest favorable non-covalent distances are under 2.2 Å and are very repulsive when characterized with classical force fields. This analysis reveals stabilization by a combination of electrostatic and charge transfer effects between hydrophobic (i.e., Val, Ile, Leu) amino acids and charged Asp or Glu. We also observe a unique hydrogen bonding configuration between Tyr and Asn/Gln involving both residues acting simultaneously as hydrogen bond donors and acceptors. This work confirms the importance of first-principles simulation in explaining unexpected geometries in protein crystal structures.</p></div></div></div>

scholarly journals Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis

2019 ◽  
Author(s):  
Helena W. Qi ◽  
Heather Kulik
Keyword(s):  
Amino Acids ◽  
High Resolution ◽  
Crystal Structures ◽  
Close Contact ◽  
Protein Structures ◽  
Protein Crystal ◽  
X Ray ◽  
High Quality Protein ◽  
Van Der Waals Radii ◽  
Close Contacts

<div><div><div><p>We investigate unexpectedly short non-covalent distances (< 85% of the sum of van der Waals radii) in atomically resolved X-ray crystal structures of proteins. We curate over 13,000 high quality protein crystal structures and an ultra-high resolution (1.2 Å or better) subset containing > 1,000 structures. Although our non-covalent distance criterion excludes standard hydrogen bonds known to be essential in protein stability, we observe over 82,000 close contacts in the curated protein structures. Analysis of the frequency of amino acids participating in these interactions demonstrates some expected trends (i.e., enrichment of charged Lys, Arg, Asp, and Glu) but also reveals unexpected enhancement of Tyr in such interactions. Nearly all amino acids are observed to form at least one close contact with all other amino acids, and most interactions are preserved in the much smaller ultra high-resolution subset. We quantum-mechanically characterize the interaction energetics of a subset of > 6,000 close contacts with symmetry adapted perturbation theory to enable decomposition of interactions. We observe the majority of close contacts to be favorable. The shortest favorable non-covalent distances are under 2.2 Å and are very repulsive when characterized with classical force fields. This analysis reveals stabilization by a combination of electrostatic and charge transfer effects between hydrophobic (i.e., Val, Ile, Leu) amino acids and charged Asp or Glu. We also observe a unique hydrogen bonding configuration between Tyr and Asn/Gln involving both residues acting simultaneously as hydrogen bond donors and acceptors. This work confirms the importance of first-principles simulation in explaining unexpected geometries in protein crystal structures.</p></div></div></div>

scholarly journals Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

2013 ◽  
Vol 69 (12) ◽  
pp. 2381-2394 ◽  
Author(s):  
Kristin A. Sutton ◽  
Paul J. Black ◽  
Kermit R. Mercer ◽  
Elspeth F. Garman ◽  
Robin L. Owen ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Disulfide Bond ◽  
Disulfide Bonds ◽  
Bond Cleavage ◽  
Absorbed Dose ◽  
Product Formation ◽  
Visible Absorption ◽  
Structural Investigations ◽  
X Ray ◽  
Uv Visible

Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5–0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.

scholarly journals X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein

2019 ◽  
Vol 75 (9) ◽  
pp. 841-851 ◽  
Author(s):  
Hiromi Yoshida ◽  
Katsuhiro Kojima ◽  
Masaki Shiota ◽  
Keiichi Yoshimatsu ◽  
Tomohiko Yamazaki ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Disulfide Bonds ◽  
Hydrophobic Interactions ◽  
Direct Electron Transfer ◽  
Glucose Dehydrogenase ◽  
Catalytic Subunit ◽  
Effective Electron ◽  
Α Subunit ◽  
X Ray ◽  
Membrane Bound

The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe–4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.

scholarly journals MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models

2018 ◽  
Vol 74 (7) ◽  
pp. 606-620 ◽  
Author(s):  
Jouko J. Virtanen ◽  
Yang Zhang
Keyword(s):  
Protein Structures ◽  
Target Position ◽  
Protein Crystal ◽  
Conformational Search ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Homologous Proteins ◽  
X Ray ◽  
Replica Exchange Monte Carlo ◽  
Protein Models

Molecular replacement (MR) has commonly been employed to derive the phase information in protein crystal X-ray diffraction, but its success rate decreases rapidly when the search model is dissimilar to the target. MR-REX has been developed to perform an MR search by replica-exchange Monte Carlo simulations, which enables cooperative rotation and translation searches and simultaneous clash and occupancy optimization. MR-REX was tested on a set of 1303 protein structures of different accuracies and successfully placed 699 structures at positions that have an r.m.s.d. of below 2 Å to the target position, which is 10% higher than was obtained by Phaser. However, cases studies show that many of the models for which Phaser failed and MR-REX succeeded can be solved by Phaser by pruning them and using nondefault parameters. The factors effecting success and the parts of the methodology which lead to success are studied. The results demonstrate a new avenue for molecular replacement which outperforms (and has results that are complementary to) the state-of-the-art MR methods, in particular for distantly homologous proteins.

scholarly journals X-ray induced disulfide bond cleavage studied with EPR, optical absorption and X-ray diffraction

2013 ◽  
Vol 69 (a1) ◽  
pp. s86-s86
Author(s):  
Edward H. Snell ◽  
Kristi A. Sutton ◽  
Paul Black ◽  
Kermit R. Mercer ◽  
Elspeth F. Garman ◽  
...  
Keyword(s):  
Optical Absorption ◽  
Disulfide Bond ◽  
Bond Cleavage ◽  
X Ray Diffraction ◽  
X Ray

scholarly journals Principles and characteristics of biological assemblies in experimentally determined protein structures

2019 ◽  
Author(s):  
Qifang Xu ◽  
Roland L. Dunbrack
Keyword(s):  
Physical Properties ◽  
Computational Methods ◽  
Structural Information ◽  
Protein Structures ◽  
Sequence Conservation ◽  
Homologous Proteins ◽  
X Ray ◽  
Biologically Relevant ◽  
X Ray Crystallography

AbstractMore than half of all structures in the PDB are assemblies of two or more proteins, including both homooligomers and heterooligomers. Structural information on these assemblies comes from X-ray crystallography, NMR, and cryo-EM spectroscopy. The correct assembly in an X-ray structure is often ambiguous, and computational methods have been developed to identify the most likely biologically relevant assembly based on physical properties of assemblies and sequence conservation in interfaces. Taking advantage of the large number of structures now available, some of the most recent methods have relied on similarity of interfaces and assemblies across structures of homologous proteins.

Disulfide Bond Cleavage: A Redox Reaction Without Electron Transfer

2010 ◽  
Vol 16 (17) ◽  
pp. 5097-5101 ◽  
Author(s):  
Florian Hofbauer ◽  
Irmgard Frank
Keyword(s):  
Electron Transfer ◽  
Disulfide Bond ◽  
Redox Reaction ◽  
Bond Cleavage

scholarly journals Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin

2012 ◽  
Vol 68 (2) ◽  
pp. 119-123 ◽  
Author(s):  
Julian C.-H. Chen ◽  
Zoë Fisher ◽  
Andrey Y. Kovalevsky ◽  
Marat Mustyakimov ◽  
B. Leif Hanson ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Room Temperature ◽  
Protein Structures ◽  
Atomic Displacement ◽  
Protein Crystal ◽  
X Ray Diffraction ◽  
Resolution Time ◽  
X Ray ◽  
Two Temperatures ◽  
Atomic Displacement Parameters

The room-temperature (RT) X-ray structure of H/D-exchanged crambin is reported at 0.85 Å resolution. As one of the very few proteins refined with anisotropic atomic displacement parameters at two temperatures, the dynamics of atoms in the RT and 100 K structures are compared. Neutron diffraction data from an H/D-exchanged crambin crystal collected at the Protein Crystallography Station (PCS) showed diffraction beyond 1.1 Å resolution. This is the highest resolution neutron diffraction reported to date for a protein crystal and will reveal important details of the anisotropic motions of H and D atoms in protein structures.

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