Acta Crystallographica
Section D STRUCTURAL BIOLOGY ![results and discussion in research paper sample Journals Logo](https://journals.iucr.org/logos/iucr_journals_logo_spaces.png)
1. Introduction
2. materials and methods, 4. discussion, 5. conclusion and outlook, supporting information.
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Factors affecting macromolecule orientations in thin films formed in cryo-EM
a National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Post, Bellary Road, Bengaluru 560 065, India * Correspondence e-mail: [email protected]
The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air–water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.
Keywords: cryo-EM ; thin films ; preferred macromolecular orientation ; surfactants ; temperature .
EMDB references: CRP pentamer with CTAB, EMD-37864 ; CRP decamer with CTAB, EMD-37865 ; PaaZ with CTAB at 4°C, EMD-37866 ; catalase with SLS, EMD-37952 ; spike with CTAB, EMD-37953 ; catalase at 20°C, EMD-37954 ; catalase at 4°C, EMD-37955 ; catalase with CTAB, EMD-37956 ; β-galactosidase, no tag, EMD-39808 ; β-galactosidase, with tag, EMD-39809
PDB references: CRP pentamer with CTAB, 8wv4 ; CRP decamer with CTAB, 8wv5 ; PaaZ with CTAB at 4°C, 8wv6 ; catalase with SLS, 8wzh ; spike with CTAB, 8wzi ; catalase at 20°C, 8wzj ; catalase at 4°C, 8wzk ; catalase with CTAB, 8wzm
| Examples of anisotropic cryo-EM maps resulting from orientation bias. The upper panel shows the reference-free 2D class averages of ( ) SARS-CoV-2 spike protein and ( ) human erythrocyte catalase. For the spike protein, preferred bottom views are observed. In the case of catalase, a preference for the top/bottom view is evident. In the lower panel, 3D maps with anisotropic features are shown for the preferred and perpendicular views as labelled. The symmetries applied during reconstruction were 1 and 2 for the spike protein and catalase, respectively. |
To achieve this goal, we tested some commonly used surfactants with different properties on a set of five proteins: C-reactive protein (CRP) pentamers, CRP decamers, catalase, PaaZ and spike. In addition, we explored the effect of the presence of the histidine tag for spike and β -galactosidase and of physical factors such as the temperature during the sample-application step for catalase and PaaZ. We also serendipitously observed an effect of the grid hole dimensions of the holey carbon grid on the orientation distribution of catalase and discuss this briefly. Through this analysis, we identified factors that affect and determine the behaviour of the macromolecule on grids before freezing and studied their effects with a focus on the preferred orientation problem. This account highlights the factors that contribute to orientation bias and provides valuable information that can assist in achieving the optimal freezing conditions for any given macromolecule.
2.1. Source of proteins
Human C-reactive protein (catalogue No. C4063) and human erythrocyte catalase (catalogue No. C3556) were obtained from Sigma–Aldrich. The protein samples were either concentrated using an Amicon 100 kDa concentrator or diluted in respective buffers for grid freezing. All detergent stocks were made in ultrapure water and dilutions were made and used on the day of the experiment.
The SARS-CoV-2 S plasmid was a kind gift from the Krammer laboratory at Icahn School of Medicine, Mount Sinai. The spike gene was amplified from the plasmid and subcloned in the BacMam vector with a C-terminal HRV 3C cleavage tag followed by a seven-histidine and twin Strep tag. Bacmid DNA and virus were prepared as described in the Invitrogen Bac-to-Bac manual. After two generations of amplification in Sf9 cells, the V2 virus was used for transfection of HEK293F cells at a density of 2 million per millilitre. Sodium butyrate (4 m M ) was added to enhance the production of protein 8 h post-infection. The medium supernatant containing the secreted spike protein was harvested on day 3 by centrifuging the cells at 150 g for 10 min. The medium was incubated with pre-equilibrated Ni–NTA (Qiagen) beads at room temperature for 1–2 h (1 ml of beads per 200 ml of medium). The Ni–NTA beads were washed with phosphate-buffered saline (PBS) containing 20 m M imidazole, followed by elution with 280 m M imidazole in PBS. The eluted protein was run on SDS–PAGE to assess its purity, further concentrated and injected onto a 24 ml Superdex 200 (Cytiva) size-exclusion column to exchange the buffer to 50 m M Tris pH 8, 200 m M NaCl, 1 m M DTT. To cleave the tag, the eluted fractions from Ni–NTA chromatography were diluted with 50 m M Tris pH 8, 200 m M NaCl, 1 m M DTT and incubated with HRV 3C protease overnight at 4°C, followed by reverse IMAC to obtain the spike protein without tag in the flowthrough. The flowthrough was concentrated using an Amicon 100 kDa concentrator, flash-frozen using liquid nitrogen and stored at −80°C until further use.
2.2. Grid preparation
6.3 µl of the protein was thawed on ice and 0.7 µl of 10× additive (surfactant) stock was added to obtain a final concentration of 1×. This sample was incubated on ice for 2–5 min and then centrifuged at 21 000 g for 20 min. Meanwhile, a Vitrobot Mark IV (Thermo Fisher Scientific) chamber was equilibrated at 20°C (unless stated otherwise) and 100% humidity. Quantifoil 1.2/1.3 or Quantifoil 0.6/1 grids were glow-discharged in a reduced-air environment with a PELCO easiGlow chamber using a standard setting of 25 mA current for 1 min. The grid was mounted on the Vitrobot Mark IV and 3 µl of sample was applied to the grid. A blotting time of 3–4 s, a wait time of 10 s and a blot force of 0 were used to obtain a thin film of the specimen. For data sets where grids were prepared at different temperatures, the protein was incubated on a thermal block at the required temperature for 3–7 min before applying it to the grid. The Vitrobot chamber was maintained at the required temperature and 100% humidity. The blot time, blot force and wait time were kept constant.
2.3. Grid screening and data collection
Summary of the parameters for data sets collected under different conditions | Protein | Condition | Grid type (Quantifoil) | Buffer composition | Protein concentration (mg ml ) | Detector | Box size (pixels) | Pixel size | CRP pentamer and decamer | No additive | 1.2/1.3 | 20 m Tris pH 8, 280 m NaCl, 5 m CaCl , 0.03% NaN | 2.1 | Falcon 3 | 256 | 1.07 | CTAB | 1.2/1.3 | 2.6 | Falcon 3 | 256 | 1.07 | SLS | 1.2/1.3 | 2.6 | K2 | 320 | 1.08 | Tween 20 | 1.2/1.3 | 3.6 | K2 | 320 | 1.08 | Tween 80 | 1.2/1.3 | 6.8 | K2 | 320 | 1.08 | A8-35 | 1.2/1.3 | 3.6 | Falcon 3 | 320 | 1.07 | Catalase | No additive, 20°C | 1.2/1.3 | 50 m Tris pH 8 | 0.625 | Falcon 3 | 256 | 1.07 | CTAB | 1.2/1.3 | 3.4 | K2 | 320 | 1.08 | SLS | 1.2/1.3 | 3.4 | Falcon 3 | 256 | 1.07 | Tween 20 | 1.2/1.3 | 3.4 | K2 | 320 | 1.08 | Tween 80 | 1.2/1.3 | 4.1 | Falcon 3 | 320 | 1.07 | A8-35 | 1.2/1.3 | 3.4 | Falcon 3 | 320 | 1.07 | 4°C | 1.2/1.3 | 0.625 | Falcon 3 | 256 | 1.07 | 37°C | 1.2/1.3 | 0.625 | Falcon 3 | 320 | 1.38 | 4°C | 0.6/1 | 0.625 | Falcon 3 | 320 | 1.07 | 20°C | 0.6/1 | 0.625 | Falcon 3 | 256 | 1.07 | PaaZ | No additive, 4°C | 0.6/1 | 25 m HEPES pH 7.4, 50 m NaCl | 0.8 | Falcon 3 | 320 | 1.07 | No additive, 20°C | 0.6/1 | 0.8 | Falcon 3 | 256 | 1.07 | No additive, 37°C | 0.6/1 | 0.8 | Falcon 3 | — | 1.38 | CTAB, 4°C | 0.6/1 | 0.8 | Falcon 3 | 256 | 1.07 | Spike | With tag, no additive | 0.6/1 | 50 m Tris pH 8, 200 m NaCl, 1 m DTT | 1 | Falcon 3 | 256 | 1.07 | With tag, with CTAB | 0.6/1 | 1.3 | Falcon 3 | 320 | 1.07 | Without tag, no additive | 0.6/1 | 2 | Falcon 3 | 256 | 1.07 | Without tag, with CTAB | 0.6/1 | 2 | Falcon 3 | 256 | 1.07 | β-Galactosidase | With tag, no additive | 0.6/1 | 100 m Tris pH 8, 200 m NaCl, 5 m CaCl 2.5 m MgCl , 2 m β-ME | 5 | Falcon 3 | 320 | 1.07 | Without tag, no additive | 0.6/1 | 5 | Falcon 3 | 320 | 1.07 | | 2.4. Data processing and model refinement3.1. analysis of preferred views of selected macromolecules. | Representative micrographs, with a few selected particles indicated with red circles, and 2D class averages of the test proteins used in this study. ( ) The C-reactive protein (CRP) pentamer adopts a preferred bottom view, which shows the pentameric arrangement of the monomers. ( ) The CRP decamer adopts a preferred side view, which shows the staggered arrangement of two CRP pentamers stacked on top of each other. The same micrograph is used in ( ) and ( ). ( ) Catalase adopts a preferred top view, as seen in the micrograph and 2D class averages. ( ) SARS-CoV-2 spike adopts a preferred bottom view showing the trimeric arrangement. ( ) PaaZ adopts a preferred side view, as seen in the 2D class averages, and the micrograph shows occasional clumping of hexamers on the grids. ( ) β-Galactosidase with an N-terminal polyhistidine tag adopts a preferred side view, as seen in the 2D class averages, and the micrograph shows aggregation on grids. For the above data sets, the catalase and PaaZ grids were prepared at 4°C and all other grids were prepared at 20°C. | 3.2. Surfactants affect macromolecule orientation distributions in a charge-dependent manner Properties of the surfactants used in this study | Additive | Charge | Ionic or non-ionic | CMC | Concentration used | Aggregation number | Molecular weight (Da) | Alkyl-chain length | Saturation in alkyl chain | CTAB | Positive | Ionic | 1 m (0.04%) | 0.054 m (0.002%) | 170 | 364 | 16 | Saturated | SLS | Negative | Ionic | 14.6 m (0.42%) | 1.37 m (0.04%) | — | 293 | 12 | Saturated | Tween 20 | Neutral | Non-ionic | 0.06 m (0.007%) | 0.04 m (0.005%) | 80 | 1228 | 12 | Saturated | Tween 80 | Neutral | Non-ionic | 0.012 m (0.002%) | 0.038 m (0.005%) | 58 | 1310 | 18 | Unsaturated | A8-35 | Negative | Ionic | NA | 0.01% | NA | ∼9000 | NA | NA | | Comparison of parameters for no-additive and surfactant-additive data sets | Protein | Condition | No. of particles | Resolution (Å) (half-map FSC 0.143) | Efficiency of Fourier space coverage | Sphericity | CRP pentamer | No additive | 14601 | 18 | 0.78 | NA | CTAB | 36353 | 3.3 | 0.80 | 0.98 | SLS | 31699 | 4.2 | 0.80 | 0.97 | Tween 20 | 25674 | 3.3 | 0.80 | 0.86 | Tween 80 | 32330 | 7.5 | 0.69 | NA | A8-35 | 26737 | 10 | 0.78 | NA | CRP decamer | No additive | 9419 | 20 | 0.52 | NA | CTAB | 25992 | 3.5 | 0.85 | 0.98 | SLS | 59211 | 3.7 | 0.79 | 0.97 | Tween 20 | 51784 | 4.0 | 0.78 | 0.92 | Tween 80 | 36870 | 4.2 | 0.79 | 0.76 | A8-35 | 104369 | 3.5 | 0.78 | 0.98 | Catalase | No additive | 138000 | 2.7 | 0.72 | 0.96 | CTAB | 153336 | 2.8 | 0.76 | 0.97 | SLS | 33241 | 3.7 | 0.80 | 0.98 | Tween 20 | 88395 | 2.9 | 0.78 | 0.98 | Tween 80 | 92163 | 2.9 | 0.80 | 0.96 | A8-35 | 122000 | 3.1 | 0.77 | 0.98 | PaaZ | No additive | 51393 | 4.0 | 0.76 | 0.80 | CTAB | 89454 | 2.3 | 0.75 | 0.98 | | | Orientation-distribution plots from (Scheres, 2012 ) of proteins upon the addition of surfactants with varying properties to the sample buffer before grid preparation. The reference structures of the respective proteins are generated by creating a surface representation in from models from PDB entries , , and . ( ) Changes in the CRP pentamer orientation distribution upon the addition of surfactants. The distributions are distinct from each other, except for Tween 20 and Tween 80, which have similar distributions. ( ) Changes in the CRP decamer orientation distribution upon addition; all surfactants lead to a similar even orientation distribution. ( ) Changes in the catalase orientation distribution upon the addition of surfactants, where the charged surfactants have distinct distributions (CTAB and SLS) and the neutral surfactants (Tween 20 and Tween 80) and A8-35 show similar distributions. ( ) Changes in PaaZ orientation distributions upon the addition of the cationic CTAB. The effects of SLS and Tween 20 on PaaZ were also tested, but visual inspection of the micrographs ( ) showed no improvement and no data were collected; therefore they are not included (marked by asterisks). The effects of Tween 80 and A8-35 on PaaZ were not tested. | 3.3. The presence of a solvent-exposed polyhistidine tag affects protein orientations in thin films | The effect of a polyhistidine affinity tag on the SARS-CoV-2 spike protein and β-galactosidase orientation distributions. The different parameters that are used to analyse the quality of the maps are shown next to the orientation plots. indicates the number of particles used for reconstruction, indicates the final resolution of the map, indicates the sphericity and indicates the efficiency of Fourier space coverage. ( ) The locations of the tags on the protein models are indicated by black stars. The models used as references are PDB entries and for the spike protein and β-galactosidase, respectively. ( ) The orientation-distribution plots of the spike protein change upon removal of the affinity tag, but the change is not sufficient to obtain an isotropic map. The addition of the cationic CTAB further alters the orientations of the spike protein without tag and leads to a more isotropic map. β-Galactosidase enzyme (bottom panel) orientations change upon removal of the affinity tag and lead to an isotropic high-resolution map without any additive. The unsharpened final combined maps are shown in grey in ( ). | 3.4. The temperature of the incubation chamber during freezing affects protein orientations | The effect of temperature during cryo-EM sample preparation of catalase and PaaZ. Micrographs, maps, orientation-distribution plots and the different parameters that are used to analyse the quality of the maps are shown. indicates the number of particles used for reconstruction, indicates the final resolution of the map, indicates the sphericity and indicates the efficiency of Fourier space coverage. ( ) Catalase orientation distributions change significantly when grids are blotted at different temperatures in the absence of any additive. ( ) PaaZ orientation distributions change slightly when grids are held and blotted at different temperatures in the absence of any additive. In the case of PaaZ, the condition with grids prepared at 4°C with CTAB as an additive is included for comparison as this combination led to a high-resolution isotropic map. | It is evident from these observations that physical factors, such as the grid-preparation temperature, can affect protein behaviour and should be considered as an important screening condition when dealing with orientation bias along with surfactants. 3.5. High-resolution map of E. coli PaaZ in ice | High-resolution cryo-EM map from PaaZ grids prepared at 4°C with CTAB additive. ( ) Comparison of the half-maps and map-versus-model FSCs of the PaaZ data set. ( ) The six coloured individually and in cartoon representation fitted into the cryo-EM map (transparent grey) of PaaZ. ( ) Electrostatic potential surface representation of the domain-swapped PaaZ dimer with waters modelled and shown as cyan spheres. ( ) ResLog plot of PaaZ with the experimental and theoretical numbers of particles required to reach a particular resolution. indicates the number of particles used for reconstruction, is the resolution and indicates the factor, as estimated by post-processing. 3 symmetry was applied for the reconstruction and the ResLog plot indicates the number of particles used, not the number of asymmetric units averaged. | Supplementary Figures and Tables. DOI: https://doi.org/10.1107/S2059798324005229/rr5238sup1.pdf AcknowledgementsWe acknowledge the National Cryo-EM Facility, Bangalore for data collection, which is supported by the Department of Biotechnology (DBT/PR12422/MED/31/287/2014), and the computing facility in the Bangalore Life Science Cluster. We thank Professor Ramaswamy S and all of the laboratory members for critical reading of the manuscript. KRV is part of the EMBO Global Investigator Network. KRV acknowledges the discussion with Drs Pamela Williams and Judith Reeks, Astex, UK on β -galactosidase and the effect of tags. The authors declare no conflicts of interest. Funding informationKRV acknowledges the support of the Department of Atomic Energy, Government of India under Project Identification No. RTI4006. SY acknowledges the graduate fellowship from TIFR/NCBS. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence , which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. Follow Acta Cryst. D | ![](//pechenka.online/777/templates/cheerup1/res/banner1.gif) |
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Table of contents. What not to include in your discussion section. Step 1: Summarize your key findings. Step 2: Give your interpretations. Step 3: Discuss the implications. Step 4: Acknowledge the limitations. Step 5: Share your recommendations. Discussion section example. Other interesting articles.
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The results section of a research paper tells the reader what you found, while the discussion section tells the reader what your findings mean. The results section should present the facts in an academic and unbiased manner, avoiding any attempt at analyzing or interpreting the data. Think of the results section as setting the stage for the ...
The discussion section is one of the final parts of a research paper, in which an author describes, analyzes, and interprets their findings. They explain the significance of those results and tie everything back to the research question(s). In this handout, you will find a description of what a discussion section does, explanations of how to ...
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The discussion section of a research paper is where the author analyzes and explains the importance of the study's results. It presents the conclusions drawn from the study, compares them to previous research, and addresses any potential limitations or weaknesses. The discussion section should also suggest areas for future research.
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2.3. Grid screening and data collection. Grids were screened on a Titan Krios microscope operating at 300 kV using standard low-dose settings, and automated data collection was set up either on a Falcon 3 or Gatan K2 detector in counting mode with the EPU software (Thermo Fisher Scientific). A magnification of 59 000× was only used for the catalase 37°C data set, with a pixel size of 1.38 Å ...