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 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.

The absolute configuration of Λ-[Co(sen)] [(R,R)(+)tart] C1.6H2O and of Δ-[Co(sen)] [(R,R)(+)tart] C1.4. 5H2O (sen is 5-Methyl-5-(4-amino-2-azabutyl)-3,7-diazanonane-1,9-diamine): A comment on the mode of chiral resolutions by (R,R)(+)Tartrate on the antipodal cations of cobalt(III) salts

1984 ◽  
Vol 37 (11) ◽  
pp. 2365 ◽  
Author(s):  
I Bernal ◽  
JD Korp ◽  
II Creaser
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Absolute Configuration ◽  
Close Contact ◽  
Monoclinic Space Group ◽  
Space Group ◽  
X Ray ◽  
Local Block ◽  
Do So ◽  
Close Contacts

The X-ray crystal structures of the Λ and ∆ diastereoisomeric pair of [Co(sen)] [(R,R)(+)tart] ClnH2O (sen is 5-methyl-5-(4-amino-2-azabutyl)-3,7-diazanonane-1,9-diamine, tart is tartrate) have been determined. Crystals of the less soluble Λ isomer, (Λ-(1); n = 6), are othorhombic, space group P212121, with a 10.817(8), b 13.626(8), c 17.724(6) �, while those of the non-preferred Λ isomer, (Λ-(1); n = 4.5), are monoclinic, space group P21, with a 9,469(8), b 12.116(9), c 12.132(7) �, β 95.94(6)�. Both structures were solved by the Patterson method, and refined to R 3.8% (Λ-(1)) and 10.8% (Λ-(1)). In ∆-(1) the waters of hydration are partly disordered in the unit cell. Both crystal structures exhibit extensive hydrogen bonding; however, the mode of contact between the cation and the tartrate dianion in the two compounds is slightly different. In Λ-(1) the three amino hydrogens involved each have only one close contact to a tartrate oxygen, whereas in ∆-(1) each hydrogen has two close contacts. The mode of chiral resolution thus seems to depend on the strength of the hydrogen bonding found in this 'local block', and not simply on its ability to form such a block, since both enantiomers do so.

Crystal Structures of Fragments D and Double-D from Fibrinogen and Fibrin

1999 ◽  
Vol 82 (08) ◽  
pp. 271-276 ◽  
Author(s):  
Glen Spraggon ◽  
Stephen Everse ◽  
Russell Doolittle
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Crystal Structures ◽  
Structure And Function ◽  
X Ray ◽  
Long Period ◽  
And Function

IntroductionAfter a long period of anticipation,1 the last two years have witnessed the first high-resolution x-ray structures of fragments from fibrinogen and fibrin.2-7 The results confirmed many aspects of fibrinogen structure and function that had previously been inferred from electron microscopy and biochemistry and revealed some unexpected features. Several matters have remained stubbornly unsettled, however, and much more work remains to be done. Here, we review several of the most significant findings that have accompanied the new x-ray structures and discuss some of the problems of the fibrinogen-fibrin conversion that remain unresolved. * Abbreviations: GPR—Gly-Pro-Arg-derivatives; GPRPam—Gly-Pro-Arg-Pro-amide; GHRPam—Gly-His-Arg-Pro-amide

scholarly journals Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

2013 ◽  
Vol 6 (1) ◽  
pp. 308 ◽  
Author(s):  
Mikael Elias ◽  
Dorothee Liebschner ◽  
Jurgen Koepke ◽  
Claude Lecomte ◽  
Benoit Guillot ◽  
...  
Keyword(s):  
High Resolution ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Diffraction Structure

The crystal structures of solvent-free alkali-metal squarates from powder diffraction data

2005 ◽  
Vol 220 (11) ◽  
Author(s):  
Robert E. Dinnebier ◽  
Hanne Nuss ◽  
Martin Jansen
Keyword(s):  
High Resolution ◽  
Alkali Metal ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Room Temperature ◽  
Solvent Free ◽  
Crystallographic Data ◽  
Powder Diffraction Data ◽  
X Ray

AbstractThe crystal structures of solvent-free lithium, sodium, rubidium, and cesium squarates have been determined from high resolution synchrotron and X-ray laboratory powder patterns. Crystallographic data at room temperature of Li

scholarly journals Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

2010 ◽  
Vol 114 (40) ◽  
pp. 12811-12824 ◽  
Author(s):  
David S. Cerutti ◽  
Peter L. Freddolino ◽  
Robert E. Duke ◽  
David A. Case
Keyword(s):  
High Resolution ◽  
Force Fields ◽  
Protein Crystal ◽  
X Ray ◽  
Water Models ◽  
Structure Evaluation

Chiral Ferrocene Amines Derived from Amino Acids and Peptides:  Synthesis, Solution and X-ray Crystal Structures and Electrochemical Investigations

2000 ◽  
Vol 39 (24) ◽  
pp. 5437-5443 ◽  
Author(s):  
Alexandra Hess ◽  
Jan Sehnert ◽  
Thomas Weyhermüller ◽  
Nils Metzler-Nolte
Keyword(s):  
Amino Acids ◽  
Crystal Structures ◽  
X Ray ◽  
Peptides Synthesis ◽  
Synthesis Solution

The structures of marialite (Me6) and meionite (Me93) in space groups P42/n and I4/m, and the absence of phase transitions in the scapolite series

2011 ◽  
Vol 26 (2) ◽  
pp. 119-125 ◽  
Author(s):  
Sytle M. Antao ◽  
Ishmael Hassan
Keyword(s):  
Phase Transitions ◽  
High Resolution ◽  
Crystal Structures ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
The Mean

The crystal structures of marialite (Me6) from Badakhshan, Afghanistan and meionite (Me93) from Mt. Vesuvius, Italy were obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements. Their structures were refined in space groups I4/m and P42/n, and similar results were obtained. The Me6 sample has a formula Ca0.24Na3.37K0.24[Al3.16Si8.84O24]Cl0.84(CO3)0.15, and its unit-cell parameters are a=12.047555(7), c=7.563210(6) Å, and V=1097.751(1) Å3. The average ⟨T1-O⟩ distances are 1.599(1) Å in I4/m and 1.600(2) Å in P42/n, indicating that the T1 site contains only Si atoms. In P42/n, the average distances of ⟨T2-O⟩=1.655(2) and ⟨T3-O⟩=1.664(2) Å are distinct and are not equal to each other. However, the mean ⟨T2,3-O⟩=1.659(2) Å in P42/n and is identical to the ⟨T2′-O⟩=1.659(1) Å in I4/m. The ⟨M-O⟩ [7]=2.754(1) Å (M site is coordinated to seven framework O atoms) and M-A=2.914(1) Å; these distances are identical in both space groups. The Me93 sample has a formula of Na0.29Ca3.76[Al5.54Si6.46O24]Cl0.05(SO4)0.02(CO3)0.93, and its unit-cell parameters are a=12.19882(1), c=7.576954(8) Å, and V=1127.535(2) Å3. A similar examination of the Me93 sample also shows that both space groups give similar results; however, the C–O distance is more reasonable in P42/n than in I4/m. Refining the scapolite structure near Me0 or Me100 in I4/m forces the T2 and T3 sites (both with multiplicity 8 in P42/n) to be equivalent and form the T2′ site (with multiplicity 16 in I4/m), but ⟨T2-O⟩ is not equal to ⟨T3-O⟩ in P42/n. Using different space groups for different regions across the series implies phase transitions, which do not occur in the scapolite series.

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