Lys169 of Human Glucokinase Is a Determinant for Glucose Phosphorylation: Implication for the Atomic Mechanism of Glucokinase Catalysis

Glucokinase (GK), a glucose sensor, maintains plasma glucose homeostasis via phosphorylation of glucose and is a potential therapeutic target for treating maturity-onset diabetes of the young (MODY) and persistent hyperinsulinemic hypoglycemia of infancy (PHHI). To characterize the catalytic mechanism of glucose phosphorylation by GK, we combined molecular modeling, molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations, experimental mutagenesis and enzymatic kinetic analysis on both wild-type and mutated GK. Our three-dimensional (3D) model of the GK-Mg2+-ATP-glucose (GMAG) complex, is in agreement with a large number of mutagenesis data, and elucidates atomic information of the catalytic site in GK for glucose phosphorylation. A 10-ns MD simulation of the GMAG complex revealed that Lys169 plays a dominant role in glucose phosphorylation. This prediction was verified by experimental mutagenesis of GK (K169A) and enzymatic kinetic analyses of glucose phosphorylation. QM/MM calculations were further used to study the role of Lys169 in the catalytic mechanism of the glucose phosphorylation and we found that Lys169 enhances the binding of GK with both ATP and glucose by serving as a bridge between ATP and glucose. More importantly, Lys169 directly participates in the glucose phosphorylation as a general acid catalyst. Our findings provide mechanistic details of glucose phorphorylation catalyzed by GK, and are important for understanding the pathogenic mechanism of MODY

Extensive Crosstalk between O-GlcNAcylation and Phosphorylation Regulates Akt Signaling

O-linked N-acetylglucosamine glycosylations (O-GlcNAc) and O-linked phosphorylations (O-phosphate), as two important types of post-translational modifications, often occur on the same protein and bear a reciprocal relationship. In addition to the well documented phosphorylations that control Akt activity, Akt also undergoes O-GlcNAcylation, but the interplay between these two modifications and the biological significance remain unclear, largely due to the technique challenges. Here, we applied a two-step analytic approach composed of the O-GlcNAc immunoenrichment and subsequent O-phosphate immunodetection. Such an easy method enabled us to visualize endogenous glycosylated and phosphorylated Akt subpopulations in parallel and observed the inhibitory effect of Akt O-GlcNAcylations on its phosphorylation. Further studies utilizing mass spectrometry and mutagenesis approaches showed that O-GlcNAcylations at Thr 305 and Thr 312 inhibited Akt phosphorylation at Thr 308 via disrupting the interaction between Akt and PDK1. The impaired Akt activation in turn resulted in the compromised biological functions of Akt, as evidenced by suppressed cell proliferation and migration capabilities. Together, this study revealed an extensive crosstalk between O-GlcNAcylations and phosphorylations of Akt and demonstrated O-GlcNAcylation as a new regulatory modification for Akt signaling

The dynamic conformational landscape of the protein methyltransferase SETD8

Elucidating the conformational heterogeneity of proteins is essential for understanding protein function and developing exogenous ligands. With the rapid development of experimental and computational methods, it is of great interest to integrate these approaches to illuminate the conformational landscapes of target proteins. SETD8 is a protein lysine methyltransferase (PKMT), which functions in vivo via the methylation of histone and nonhistone targets. Utilizing covalent inhibitors and depleting native ligands to trap hidden conformational states, we obtained diverse X-ray structures of SETD8. These structures were used to seed distributed atomistic molecular dynamics simulations that generated a total of six milliseconds of trajectory data. Markov state models, built via an automated machine learning approach and corroborated experimentally, reveal how slow conformational motions and conformational states are relevant to catalysis. These findings provide molecular insight on enzymatic catalysis and allosteric mechanisms of a PKMT via its detailed conformational landscape

Mechanistic study of plasma damage to porous low-k : process development and dielectric recovery

textLow-k dielectrics with porosity are being introduced to reduce the RC delay of Cu/low-k interconnect. However, during the O2 plasma ashing process, the porous low-k dielectrics tend to degrade due to methyl depletion, moisture uptake, and densification, increasing the dielectric constant and leakage current. This dissertation presents a study of the mechanisms of plasma damage and dielectric recovery. The kinetics of plasma interaction with low-k dielectrics was investigated both experimentally and theoretically. By using a gap structure, the roles of ion, photon, and radical in producing damage on low-k dielectrics were differentiated. Oxidative plasma induced damage was proportional to the oxygen radical density, enhanced by VUV photon, and increased with substrate temperature. Ion bombardment induced surface densification, blocking radical diffusion. Two analytical models were derived to quantify the plasma damage. Based on the radical diffusion, reaction, and recombination inside porous low-k dielectrics, a plasma altered layer model was derived to interpret the chemical effect in the low ion energy region. It predicted that oxidative plasma induced damage can be reduced by decreasing pore radius, substrate temperature, and oxygen radical density and increasing carbon concentration and surface recombination rate inside low-k dielectrics. The model validity was verified by experiments and Monte-Carlo simulations. This model was also extended to the patterned low-k structure. Based on the ion collision cascade process, a sputtering yield model was introduced to interpret the physical effect in the high ion energy region. The model validity was verified by checking the ion angular and energy dependences of sputtering yield using O2/He/Ar plasma, low-k dielectrics with different k values, and a Faraday cage. Low-k dielectrics and plasma process were optimized to reduce plasma damage, including increasing carbon concentration in low-k dielectrics, switching plasma generator from ICP to RIE, increasing hard mask thickness, replacing O2 by CO2 plasma, increasing CO addition in CO/O2 plasma, and increasing N2 addition in CO2/N2 plasma. By combining analytical techniques with the Kramers-Kronig dispersion relation and quantum chemistry calculation, the origin of dielectric loss was ascribed to the physisorbed water molecules. Post-ash CH4 plasma treatment, vapor silylation process, and UV radiation were developed to repair plasma damage.Physic

Applications and advancements of instrumental variable approach in causal inference in environmental epidemiology

In environmental epidemiological research, extensive non-random environmental exposures and complex confounding biases pose significant challenges when attempting causal inference. In recent years, the introduction of causal inference methods into observational studies has provided a broader range of statistical tools for causal inference research in environmental epidemiology. The instrumental variable (IV) approach, as a causal inference technique for effectively controlling unmeasured confounding factors, has gradually found application in the field of environmental epidemiological research. This article reviewed the basic principles of IV and summarized the current research progress and limitations of applying IV for causal inference in environmental epidemiology. IV application in the field of environmental epidemiology is still in the initial stage. Rational use of IV and effective integration with other causal inference methods will become the focus of the development of causal inference in environmental epidemiology. The aim of this paper is to provide a methodological reference and basis for future studies involving causal inference to target population health effects of environmental exposures in China

Frailty Risk in Older Adults Associated With Long-Term Exposure to Ambient PM2.5 in 6 Middle-Income Countries

Background: A series of studies have explored the health effects of long-term exposure to ambient PM2.5 among older adults. However, few studies have investigated the adverse effect of long-term exposure to ambient PM2.5 on frailty, and the results are inconclusive. This study sought to investigate the associations between long-term exposure to ambient PM2.5 and frailty in 6 low- and middle-income countries. Methods: We included an analytical sample of 34 138 individuals aged 50 and older from the Study on global AGEing and adult health Wave 1 (2007/2010). Air pollution estimates were generated using a standard methodology derived from Moderate Resolution Imaging Spectroradiometer observations and Multiangle Imaging Spectroradiometer instruments from the Terra satellite, along with simulations from the GEOS-Chem chemical transport model. A 3-level hierarchical logistic model was used to evaluate the association between frailty index and long-term PM2.5 exposure at 3 levels (individual, province, and country). Results: In rural areas, each 10 μg/m3 increase in ambient PM2.5 was associated with a 30% increase in the odds of frailty (OR = 1.30, 95% CI: 1.21-1.39) after adjusting for various potential confounding factors. The gender-stratified analysis showed that the association seemed to be slightly stronger in men (OR = 1.31, 95% CI: 1.18-1.46) than in women (OR = 1.21, 95% CI: 1.07-1.36) in rural areas. Conclusion: In a large sample of community-based older adults from 6 middle-income countries, we found evidence that long-term PM2.5 exposure was associated with frailty in rural areas

Scalable Fabrication of Natural-Fiber Reinforced Composites with Electromagnetic Interference Shielding Properties by Incorporating Powdered Activated Carbon

This article discusses preparing Kenaf fiber-polyester composites incorporated with powdered activated carbon (PAC) using the vacuum-assisted resin transfer molding(VARTM) process