The accurate prediction of protein stability upon sequence mutation is an important but unsolved challenge in protein engineering. Large mutational datasets are required to train computational ...predictors, but traditional methods for collecting stability data are either low-throughput or measure protein stability indirectly. Here, we develop an automated method to generate thermodynamic stability data for nearly every single mutant in a small 56-residue protein. Analysis reveals that most single mutants have a neutral effect on stability, mutational sensitivity is largely governed by residue burial, and unexpectedly, hydrophobics are the best tolerated amino acid type. Correlating the output of various stability-prediction algorithms against our data shows that nearly all perform better on boundary and surface positions than for those in the core and are better at predicting large-to-small mutations than small-to-large ones. We show that the most stable variants in the single-mutant landscape are better identified using combinations of 2 prediction algorithms and including more algorithms can provide diminishing returns. In most cases, poor in silico predictions were tied to compositional differences between the data being analyzed and the datasets used to train the algorithm. Finally, we find that strategies to extract stabilities from high-throughput fitness data such as deep mutational scanning are promising and that data produced by these methods may be applicable toward training future stability-prediction tools.
We analyze a photochemical smog episode to understand the oxidative capacity and radical chemistry of the polluted atmosphere in Hong Kong and the Pearl River Delta (PRD) region. A photochemical box ...model based on the Master Chemical Mechanism (MCM v3.2) is constrained by an intensive set of field observations to elucidate the budgets of ROx (ROx = OH+HO2+RO2) and NO3 radicals. Highly abundant radical precursors (i.e. O3, HONO and carbonyls), nitrogen oxides (NOx) and volatile organic compounds (VOCs) facilitate strong production and efficient recycling of ROx radicals. The OH reactivity is dominated by oxygenated VOCs (OVOCs), followed by aromatics, alkenes and alkanes. Photolysis of OVOCs (except for formaldehyde) is the dominant primary source of ROx with average daytime contributions of 34–47 %. HONO photolysis is the largest contributor to OH and the second-most significant source (19–22 %) of ROx. Other considerable ROx sources include O3 photolysis (11–20 %), formaldehyde photolysis (10–16 %), and ozonolysis reactions of unsaturated VOCs (3.9–6.2 %). In one case when solar irradiation was attenuated, possibly by the high aerosol loadings, NO3 became an important oxidant and the NO3-initiated VOC oxidation presented another significant ROx source (6.2 %) even during daytime. This study suggests the possible impacts of daytime NO3 chemistry in the polluted atmospheres under conditions with the co-existence of abundant O3, NO2, VOCs and aerosols, and also provides new insights into the radical chemistry that essentially drives the formation of photochemical smog in the high-NOx environment of Hong Kong and the PRD region.
Nitryl chloride (ClNO2) plays potentially important roles in atmospheric chemistry, but its abundance and effect are not fully understood due to the small number of ambient observations of ClNO2 to ...date. In late autumn 2013, ClNO2 was measured with a chemical ionization mass spectrometer (CIMS) at a mountain top (957 m above sea level) in Hong Kong. During 12 nights with continuous CIMS data, elevated mixing ratios of ClNO2 (>400 parts per trillion by volume) or its precursor N2O5 (>1000 pptv) were observed on six nights, with the highest ever reported ClNO2 (4.7 ppbv, 1 min average) and N2O5 (7.7 ppbv, 1 min average) in one case. Backward particle dispersion calculations driven by winds simulated with a mesoscale meteorological model show that the ClNO2/N2O5‐laden air at the high‐elevation site was due to transport of urban/industrial pollution north of the site. The highest ClNO2/N2O5 case was observed in a later period of the night and was characterized with extensively processed air and with the presence of nonoceanic chloride. A chemical box model with detailed chlorine chemistry was used to assess the possible impact of the ClNO2 in the well‐processed regional plume on next day ozone, as the air mass continued to downwind locations. The results show that the ClNO2 could enhance ozone by 5–16% at the ozone peak or 11–41% daytime ozone production in the following day. This study highlights varying importance of the ClNO2 chemistry in polluted environments and the need to consider this process in photochemical models for prediction of ground‐level ozone and haze.
Key Points
First observation of ClNO2 in the planetary boundary layer of China
Combined high‐resolution meteorological and measurement‐constrained chemical models in data analysis
ClNO2 enhances daytime ozone peak by 5‐16% in well‐processed PRD air
Monocytes are recruited from the blood to sites of inflammation, where they contribute to wound healing and tissue repair. There are at least two subsets of monocytes: classical or proinflammatory ...(CCR2(hi)CX3CR1(low)) and nonclassical, patrolling, or alternative (CCR2(low)CX3CR1(hi)) monocytes. Using spinning-disk confocal intravital microscopy and mice with fluorescent reporters for each of these subsets, we were able to track the dynamic spectrum of monocytes that enter a site of sterile hepatic injury in vivo. We observed that the CCR2(hi)CX3CR1(low) monocytes were recruited early and persisted for at least 48 h, forming a ringlike structure around the injured area. These monocytes transitioned, in situ, from CCR2(hi)Cx3CR1(low) to CX3CR1(hi)CCR2(low) within the ringlike structure and then entered the injury site. This phenotypic conversion was essential for optimal repair. These results demonstrate a local, cytokine driven reprogramming of classic, proinflammatory monocytes into nonclassical or alternative monocytes to facilitate proper wound-healing.
It is challenging to reduce ground-level ozone (O3) pollution at a given locale, due in part to the contributions of both local and distant sources. We present direct evidence that the increasing ...regional effects have negated local control efforts for O3 pollution in Hong Kong over the past decade, by analyzing the daily maximum 8 h average O3 and O x (=O3+NO2) concentrations observed during the high O3 season (September–November) at Air Quality Monitoring Stations. The locally produced O x showed a statistically significant decreasing trend over 2002–2013 in Hong Kong. Analysis by an observation-based model confirms this decline in in situ O x production, which is attributable to a reduction in aromatic hydrocarbons. However, the regional background O x transported into Hong Kong has increased more significantly during the same period, reflecting contributions from southern/eastern China. The combined result is a rise in O3 and a nondecrease in O x . This study highlights the urgent need for close cross-boundary cooperation to mitigate the O3 problem in Hong Kong. China’s air pollution control policy applies primarily to its large cities, with little attention to developing areas elsewhere. The experience of Hong Kong suggests that this control policy does not effectively address secondary pollution, and that a coordinated multiregional program is required.
Hydrogen peroxide (H2O2) and organic peroxides play an important role in atmospheric chemistry, but knowledge of their abundances, sources, and sinks from heterogeneous processes remains incomplete. ...Here we report the measurement results obtained in four seasons during 2011–2012 at a suburban site and a background site in Hong Kong. Organic peroxides were found to be more abundant than H2O2, which is in contrast to most previous observations. Model calculations with a multiphase chemical mechanism suggest important contributions from heterogeneous processes (primarily transition metal ion TMI-HOx reactions) to the H2O2 budget, accounting for about one-third and more than half of total production rate and loss rate, respectively. In comparison, they contribute much less to organic peroxides. The fast removal of H2O2 by these heterogeneous reactions explains the observed high organic peroxide fractions. Sensitivity analysis reveals that the role of heterogeneous processes depends on the abundance of soluble metals in aerosol, serving as a net H2O2 source at low metal concentrations, but as a net sink with high metal loading. The findings of this study suggest the need to consider the chemical processes in the aerosol aqueous phase when examining the chemical budget of gas-phase H2O2.
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining ...sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency.
Many taxis and public buses are powered by liquefied petroleum gas (LPG) in Hong Kong. With more vehicles using LPG, they have become the major contributor to ambient volatile organic compounds ...(VOCs) in Hong Kong. An intervention program which aimed to reduce the emissions of VOCs and nitrogen oxides (NOx) from LPG-fueled vehicles was implemented by the Hong Kong government in September 2013. Long-term real-time measurements indicated that the program was remarkably effective in reducing LPG-related VOCs, NOx and nitric oxide (NO) in the atmosphere. Receptor modeling results further revealed that propane, propene, i-butane, n-butane and NO in LPG-fueled vehicle exhaust emissions decreased by 40.8 ± 0.1, 45.7 ± 0.2, 35.7 ± 0.1, 47.8 ± 0.1 and 88.6 ± 0.7 %, respectively, during the implementation of the program. In contrast, despite the reduction of VOCs and NOx, O3 following the program increased by 0.40 ± 0.03 ppbv (∼ 5.6 %). The LPG-fueled vehicle exhaust was generally destructive to OH and HO2. However, the destruction effect weakened for OH and it even turned to positive contribution to HO2 during the program. These changes led to the increases of OH, HO2 and HO2 ∕ OH ratio, which might explain the positive O3 increment. Analysis of O3–VOCs–NOx sensitivity in ambient air indicated VOC-limited regimes in the O3 formation before and during the program. Moreover, a maximum reduction percentage of NOx (i.e., 69 %) and the lowest reduction ratio of VOCs ∕ NOx (i.e., 1.1) in LPG-fueled vehicle exhaust were determined to give a zero O3 increment. The findings are of great help to future formulation and implementation of control strategies on vehicle emissions in Hong Kong, and could be extended to other regions in China and around the world.
We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to ...describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user‐friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org.
Nitrous acid (HONO) plays important roles in tropospheric chemistry, but its source(s) are not completely understood. Here we analyze measurements of HONO, nitrogen dioxide (NO2), and related ...parameters at a coastal site in Hong Kong during September–December 2012. The nocturnal NO2‐to‐HONO conversion rates were estimated in air masses passing over land and sea surfaces. The conversion rates in the “sea cases” (3.17–3.36 × 10−2 h−1) were significantly higher than those in the “land cases” in our study (1.20–1.30 × 10−2 h−1) and in previous studies by others. These results suggest that air‐sea interactions may be a significant source of atmospheric HONO and need to be considered in chemical transport models.
Key Points
Strong HONO production in sea‐coming air massesAir‐sea interactions may significantly affect atmospheric chemistryChemical transport models may need to consider HONO production on the sea
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