Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample

Direct Comparison of Linear and Macrocyclic Compound Libraries as a Source of Protein Ligands

There has been much discussion of the potential desirability of macrocyclic molecules for the development of tool compounds and drug leads. But there is little experimental data comparing otherwise equivalent macrocyclic and linear compound libraries as a source of protein ligands. In this Letter, we probe this point in the context of peptoid libraries. Bead-displayed libraries of macrocyclic and linear peptoids containing four variable positions and 0–2 fixed residues, to vary the ring size, were screened against streptavidin and the affinity of every hit for the target was measured. The data show that macrocyclization is advantageous, but only when the ring contains 17 atoms, not 20 or 23 atoms. This technology will be useful for conducting direct comparisons between many different types of chemical libraries to determine their relative utility as a source of protein ligands

Sequence Coverage Visualizer: A Web Application for Protein Sequence Coverage 3D Visualization

Protein structure defines protein function and plays an extremely important role in protein characterization. Recently, two groups of researchers from DeepMind and the Baker lab have independently published protein structure prediction tools that can help us obtain predicted protein structures for the whole human proteome. This enabled us to visualize the entire human proteome using predicted 3D structures for the first time. To help other researchers best utilize these protein structure predictions in proteomics experiments, we present the Sequence Coverage Visualizer (SCV), http://scv.lab.gy, a web application for protein sequence coverage 3D visualization. Here we showed a few possible usages of the SCV, including the labeling of post-translational modifications and isotope labeling experiments. These results highlight the usefulness of such 3D visualization for proteomics experiments and how SCV can turn a regular proteomics experiment (identified peptide list) into structural insights. Furthermore, when used together with limited proteolysis, we demonstrated that SCV can help to compare different protein structures from different sources, including predicted ones and existing PDB entries. We hope our tool can provide help in the process of improving protein structure prediction accuracy. Overall, SCV is a convenient and powerful tool for visualizing proteomics results in 3D

Modeling and Detection of Small Electron Polaron: A Comparison between Bond Distortion Method and Occupation Matrix Control Method

When density functional theory (DFT) is used for modeling polaron defects, the delocalized electronic states often appear due to self-interaction errors. Conventionally, the DFT + U method may possibly correct the self-interaction error and thus promote electron localization, but this does not always work. In this paper, based on the GGA + U approach, we have modeled small electron polarons by using bond distortion method (BDM) and occupation matrix control (OMC) method in TiO2. Both of these methods can control the position of the polaron at will. We evaluate the appropriate parameters for constructing stable polarons using the BDM. Meanwhile, the occupation of all orbitals of rutile and only low-energy orbitals of anatase was successfully realized using the OMC method. Calculation results show that the polarons constructed by the BDM are more stable irrespective of the crystal structure for TiO2. Furthermore, whichever method is used, the polarons formed in rutile are more stable. Electronic structure calculations demonstrate that rutile has a larger band gap after successful localization through BDM and OMC methods. On the contrary, the band gap of anatase decreases after localization because of the emergence of a new flat energy level at the Fermi level, generated mainly by localized Ti atoms. In order to better understand the polaron formation, we have studied charge transfer, bonding states, and electrostatic potential distributions around the polaron. In the localized solution, the Ti–O bonds around the polaron are all lengthened, while the stability and covalency of these bonds are reduced. The charge is strongly trapped in a potential well caused by lattice distortion, which leads to a lower electrostatic potential energy at the polaron position. In this work, polaron modeling methods and localized structure in TiO2 contribute to a better understanding of the polaron structure and its related properties

Considering lightness: how the lightness of app icon backgrounds affects consumers’ download intention through risk perception

The number of mobile apps has rapidly increased in recent years, but the distribution of app downloads is uneven. As the first and only visual image of apps before downloading, app icons are vital tools through which app publishers promote their apps. Thus, identifying the elements of app icons that can increase consumers’ download intention is crucial. This research examines how the distribution of the lightness of yellow colour in app icon backgrounds influences consumers’ download intentions as moderated by the aim of the app. The results showed that when choosing an app aiming to resist risk, consumers are more likely to download an app with dark colours on top and light colours on the bottom of the background icon. This effect is mediated by consumers’ risk perceptions of the environment. However, consumers have lower download intentions for apps with the same background when the app does not aim to resist risk. This converse effect is mediated by consumers’ risk perceptions of the services or functions of apps. Our findings not only contribute to the literature concerning symbolic associations, colour inference, and app icon visual design but also provide app developers operational methods to increase consumers’ download intention.</p

Additional file 3 of NKD2 is correlated with the occurrence, progression and prognosis of thyroid carcinoma

Additional file 3. The original results of western blot

The Effect of Dyes with Different π‑Linkers on the Overall Performance of P‑DSSCs: Lessons from Theory

A series of Keggin-type polyoxometalate (POM)-based organic–inorganic complexes (systems 2–8) were designed with different π-linkers on the basis of the molybdate–pyrene hybrid (system 1). UV–vis spectra and charge transfer (CT) parameters of designed systems were systematically analyzed by density functional theory (DFT) and time-dependent DFT (TD-DFT). The results indicate that the absorption spectra are red-shifted and the absorption intensities are enhanced with increasing number of phenylacetylene π-oligomers and introducing benzodifuranone between benzene and ethyne. However, the π-linkers near POMs are “dissolved” in the total system and the excitation occurs in a local region with increasing π-linkers. Systems 3 and 6 possess the maximum CT distance and CT charge among systems 1–5 and systems 6–8, respectively, resulting from the balance point between effectiveness of structures and delocalization. The absorption spectra of systems 6–8 obviously red-shift in comparison to systems 1–5. The present study is a further step toward the optimal absorption and CT properties