scholarly journals Damaged goods? Evaluating the impact of X-ray damage on conformational heterogeneity in room temperature and cryo-cooled protein crystals

2021 ◽  
Author(s):  
Filip Yabukarski ◽  
Tzanko Doukov ◽  
Daniel A. Mokhtari ◽  
Siyuan Du ◽  
Daniel Herschlag
Keyword(s):  
Protein Function ◽  
Room Temperature ◽  
Proteinase K ◽  
Protein Crystals ◽  
Conformational Ensemble ◽  
Conformational Heterogeneity ◽  
Critical Question ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Impact

X-ray crystallography is a cornerstone of biochemistry. Traditional freezing of protein crystals to cryo-temperatures mitigates X-ray damage and facilitates crystal handling but provides an incomplete window into the ensemble of conformations at the heart of protein function and energetics. Room temperature (RT) X-ray crystallography provides more extensive ensemble information, and recent developments allow conformational heterogeneity, the experimental manifestation of ensembles, to be extracted from single crystal data. However, high sensitivity to X-ray damage at RT raises concerns about data reliability. To systematically address this critical question, we obtained increasingly X-ray-damaged high-resolution datasets (1.02–1.52 Å) from single thaumatin, proteinase K, and lysozyme crystals. Heterogeneity analyses indicated a modest increase in conformational disorder with X-ray damage. Nevertheless, these effects do not alter overall conclusions and can be minimized by limiting the extent of X-ray damage or eliminated by extrapolation to obtain heterogeneity information free from X-ray damage effects. To compare these effects to damage at cryo temperature and to learn more about damage and heterogeneity in cryo-cooled crystals, we carried out an analogous analysis of increasingly damaged proteinase K cryo datasets (0.9–1.16 Å). We found X-ray damage-associated heterogeneity changes that were not observed at RT. This observation and the scarcity of reported X-ray doses and damage extent render it difficult to distinguish real from artifactual conformations, including those occurring as a function of temperature. The ability to aquire reliable heterogeneity information from single crystals at RT provides strong motivation for further development and routine implementation of RT X-ray crystallography to obtain conformational ensemble information.

scholarly journals A Robust Method for Collecting X-ray Diffraction Data from Protein Crystals across Physiological Temperatures

2020 ◽  
Author(s):  
Tzanko Doukov ◽  
Daniel Herschlag ◽  
Filip Yabukarski
Keyword(s):  
Diffraction Data ◽  
Protein Function ◽  
Three Dimensional ◽  
Proteinase K ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
Conformational Ensembles ◽  
X Ray Crystallography ◽  
Lysozyme Crystals

AbstractTraditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Further, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that is directly related to biological function. The next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperatures and was addressed herein. This approach provides complete diffraction datasets with total collection times as short as ~5 sec from single protein crystals, dramatically increasing the amount of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293–363 K for proteinase K, thaumatin, and lysozyme crystals. Our analyses indicate that the diffraction data is of high-quality and do not suffer from excessive dehydration or damage.

scholarly journals Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures

2020 ◽  
Vol 53 (6) ◽  
pp. 1493-1501
Author(s):  
Tzanko Doukov ◽  
Daniel Herschlag ◽  
Filip Yabukarski
Keyword(s):  
Radiation Damage ◽  
Diffraction Data ◽  
Protein Function ◽  
Room Temperature ◽  
Three Dimensional ◽  
Proteinase K ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
Conformational Ensembles

Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure–function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09–1.54 Å resolution data over a temperature range of 293–363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage.

scholarly journals Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Aron Broom ◽  
Rojo V. Rakotoharisoa ◽  
Michael C. Thompson ◽  
Niayesh Zarifi ◽  
Erin Nguyen ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Protein Design ◽  
Active Site ◽  
Room Temperature ◽  
De Novo ◽  
Conformational Ensemble ◽  
Enzyme Design ◽  
X Ray ◽  
Conformational Ensembles ◽  
X Ray Crystallography

Abstract The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M−1s−1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M−1s−1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

scholarly journals Evolution of an enzyme conformational ensemble guides design of an efficient biocatalyst

2020 ◽  
Author(s):  
Aron Broom ◽  
Rojo V. Rakotoharisoa ◽  
Michael C. Thompson ◽  
Niayesh Zarifi ◽  
Erin Nguyen ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Protein Design ◽  
Active Site ◽  
Room Temperature ◽  
De Novo ◽  
Conformational Ensemble ◽  
Enzyme Design ◽  
X Ray ◽  
Conformational Ensembles ◽  
X Ray Crystallography

AbstractThe creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we used room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 160 M−1s−1). We observed that catalytic residues were increasingly rigidified, the active site became better pre-organized, and its entrance was widened. Based on these observations, we engineered HG4, an efficient biocatalyst (kcat/KM 120,000 M−1s−1) containing active-site mutations found during evolution but not distal ones. HG4 structures revealed that its active site was pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

Recrystallization: a method to improve the quality of protein crystals

2015 ◽  
Vol 48 (3) ◽  
pp. 758-762 ◽  
Author(s):  
Hai Hou ◽  
Yue Liu ◽  
Bo Wang ◽  
Fan Jiang ◽  
Hao-Ran Tao ◽  
...  
Keyword(s):  
Crystal Quality ◽  
Proteinase K ◽  
Protein Crystals ◽  
Structural Determination ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Quality Protein ◽  
Before And After

The quality of protein crystals is an important parameter for structural determination with X-ray crystallography. Indeed, a prerequisite for obtaining high-resolution diffraction data is that the crystals be of sufficient quality. However, obtaining high-quality protein crystals is a well known bottleneck to protein structural determination that remains a difficult task. In this paper, it is demonstrated that recrystallization can be an effective method of improving the quality of protein crystals. Five proteins, lysozyme, proteinase K, concanavalin A, thaumatin and catalase, were used for this investigation, and the crystal quality of these proteins was examined using X-ray diffraction before and after recrystallization. Comparisons of the crystals before and after recrystallization verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction.

Synthesis, structural characterization and catalytic activity of chlororuthenium(II) complexes with substituted Schiff base/phosphine ancillary ligands

2020 ◽  
Vol 75 (9-10) ◽  
pp. 851-857
Author(s):  
Chong Chen ◽  
Fule Wu ◽  
Jiao Ji ◽  
Ai-Quan Jia ◽  
Qian-Feng Zhang
Keyword(s):  
Schiff Base ◽  
Catalytic Activity ◽  
Structural Characterization ◽  
Room Temperature ◽  
Molecular Structures ◽  
Cationic Complex ◽  
Neutral Complex ◽  
Ancillary Ligands ◽  
X Ray ◽  
X Ray Crystallography

AbstractTreatment of [(η6-p-cymene)RuCl2]2 with one equivalent of chlorodiphenylphosphine in tetrahydrofuran at reflux afforded a neutral complex [(η6-p-cymene)RuCl2(κ1-P-PPh2OH)] (1). Similarly, the reaction of [Ru(bpy)2Cl2·2H2O] (bpy = 2,2′-bipyridine) and chlorodiphenylphosphine in methanol gave a cationic complex [Ru(bpy)2Cl(κ1-P-PPh2OCH3)](PF6) (2), while treatment of [RuCl2(PPh3)3] with [2-(C5H4N)CH=N(CH2)2N(CH3)2] (L1) in tetrahydrofuran at room temperature afforded a ruthenium(II) complex [Ru(PPh3)Cl2(κ3-N,N,N-L1)] (3). Interaction of the chloro-bridged complex [Ru(CO)2Cl2]n with one equivalent of [Ph2P(o-C6H4)CH=N(CH2)2N(CH3)2] (L2) led to the isolation of [Ru(CO)Cl2(κ3-P,N,N-L2)] (4). The molecular structures of the ruthenium(II) complexes 1–4 have been determined by single-crystal X-ray crystallography. The properties of the ruthenium(II) complex 4 as a hydrogenation catalyst for acetophenone were also tested.

scholarly journals Silylated gallium and indium chalcogenide ring systems as potential precursors to ME (E=O, S) materials

2013 ◽  
Vol 11 (7) ◽  
pp. 1225-1238
Author(s):  
Iliana Medina-Ramírez ◽  
Cynthia Floyd ◽  
Joel Mague ◽  
Mark Fink
Keyword(s):  
Thermal Decomposition ◽  
Room Temperature ◽  
Membered Ring ◽  
Molecular Structures ◽  
Nmr Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Yields ◽  
Vt Nmr ◽  
State 1

AbstractThe reaction of R3M (M=Ga, In) with HESiR′3 (E=O, S; R′3=Ph3, iPr3, Et3, tBuMe2) leads to the formation of (Me2GaOSiPh3)2(1); (Me2GaOSitBuMe2)2(2); (Me2GaOSiEt3)2(3); (Me2InOSiPh3)2(4); (Me2InOSitBuMe2)2(5); (Me2InOSiEt3)2(6); (Me2GaSSiPh3)2(7); (Et2GaSSiPh3)2(8); (Me2GaSSiiPr3)2(9); (Et2GaSSiiPr3)2(10); (Me2InSSiPh3)3(11); (Me2InSSiiPr3)n(12), in high yields at room temperature. The compounds have been characterized by multinuclear NMR and in most cases by X-ray crystallography. The molecular structures of (1), (4), (7) and (8) have been determined. Compounds (3), (6) and (10) are liquids at room temperature. In the solid state, (1), (4), (7) and (9) are dimers with central core of the dimer being composed of a M2E2 four-membered ring. VT-NMR studies of (7) show facile redistribution between four- and six-membered rings in solution. The thermal decomposition of (1)–(12) was examined by TGA and range from 200 to 350°C. Bulk pyrolysis of (1) and (2) led to the formation of Ga2O3; (4) and (5) In metal; (7)–(10) GaS and (11)–(12) InS powders, respectively.

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