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Scaffolding protein functional sites using deep learning

Karla Montserrat Castro Gilabert, Bruno Emanuel Ferreira De Sousa Correia, Jue Wang, Basile Isidore Martin Wicky, Wei Yang

The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing to prespecify the fold or secondary structure of the scaffold. The first approach, "constrained hallucination," optimizes sequences such that their predicted structures contain the desired functional site. The second approach, "inpainting," starts from the functional site and fills in additional sequence and structure to create a viable protein scaffold in a single forward pass through a specifically trained RoseTTAFold network. We use these two methods to design candidate immunogens, receptor traps, metalloproteins, enzymes, and protein-binding proteins and validate the designs using a combination of in silico and experimental tests.

AMER ASSOC ADVANCEMENT SCIENCE2022

Black carbon and dust in the Third Pole glaciers: revaluated concentrations, mass absorption cross-sections and contributions to glacier ablation

Yang Li, Xinyang Li, Julia Schmale, Wei Yang

In snow and ice, light-absorbing particles (LAPs), such as black carbon (BC) and dust, accelerate the melting of Third Pole glaciers (TPGs). In this study, we revaluated LAP concentrations in the snow pits of TPGs (SP-TPGs), measured LAP mass absorption cross-sections (MACs), and simulated their effects on glacier darkening and melting based on the Spectral Albedo Model for Dirty Snow and a surface energy and mass balance model. The results indicated that because of their short distances to emission sources, the average BC concentrations measured in snow pits in the periphery of Third Pole were much higher than those measured in the inland Tibetan Plateau, and the average dust concentrations generally decreased from north to south. The average MACs of BC in the SP-TPGs varied from 3.1 to 7.7 m2 g−1 at 550 nm, most of the average spectral values were comparable in the visible and near-infrared bands to those calculated by Mie theory, except those in Urumqi Glacier No. 1 (UR), Syek Zapadniy Glacier (SZ), and Laohugou Glacier No.12 (LH), while the average spectral MACs of dust in the SP-TPGs were considerably smaller in magnitude than most of the variations measured in other regions. Compared with the pure snow surfaces, BC and dust played comparable roles in reducing albedo in UR, SZ, LH, and Renlongba Glacier, whereas BC was the most prominent absorber in the other glaciers. The combined effect of BC and dust accelerated melting by 30.4–345.9 mm w.e. (19.7–45.3% of the total mass balance) through surface albedo darkening (0.06–0.17) and increased radiation absorption (25.8–65.7 W m−2) within one month of the ablation season. This study provides a new data set of LAP concentrations and MACs and helps to clarify the roles of these factors in the cryospheric environment of the Third Pole.

2021

Light-absorbing impurities enhance glacier albedo reduction in the southeastern Tibetan plateau

Xinyang Li, Julia Schmale, Wei Yang

Light‐absorbing impurities (LAIs) in snow of the southeastern Tibetan Plateau (TP) and their climatic impacts are of interest not only because this region borders areas affected by the South Asian atmospheric brown clouds but also because the seasonal snow and glacier melt from this region form important headwaters of large rivers. In this study, we collected surface snow and snowpit samples from four glaciers in the southeastern TP in June 2015 to investigate the comprehensive observational data set of LAIs. Results showed that the LAI concentrations were much higher in the aged snow and granular ice than in the fresh snow and snowpits due to postdepositional processes. Impurity concentrations fluctuated across snowpits, with maximum LAI concentrations frequently occurring toward the bottom of snowpits. Based on the SNow ICe Aerosol Radiative model, the albedo simulation indicated that black carbon and dust account for approximately 20% of the albedo reduction relative to clean snow. The radiative forcing caused by black carbon and dust deposition on the glaciers were between 1.0–141 W m−2 and 1.5–120 W m−2, respectively. Black carbon (BC) played a larger role in albedo reduction and radiative forcing than dust in the study area, enhancing approximately 15% of glacier melt. Analysis based on the Fire INventory from NCAR indicated that nonbiomass‐burning sources of BC played an important role in the total BC deposition, especially during the monsoon season. This study suggests that eliminating anthropogenic BC could mitigate glacier melt in the future of the southeastern TP.

2017

Black carbon and dust in the Third Pole glaciers: revaluated concentrations, mass absorption cross-sections and contributions to glacier ablation

Yang Li, Xinyang Li, Julia Schmale, Wei Yang

2021