Emerging atomistic modeling methods for heterogeneous electrocatalysis
Heterogeneous electrocatalysis lies at the center of various technologies that could help
enable a sustainable future. However, its complexity makes it challenging to accurately and …
enable a sustainable future. However, its complexity makes it challenging to accurately and …
Stomatal CO2/bicarbonate sensor consists of two interacting protein kinases, Raf-like HT1 and non-kinase-activity requiring MPK12/MPK4
The continuing rise in the atmospheric carbon dioxide (CO2) concentration causes stomatal
closing, thus critically affecting transpirational water loss, photosynthesis, and plant growth …
closing, thus critically affecting transpirational water loss, photosynthesis, and plant growth …
Accurate calculation of relative binding free energies between ligands with different net charges
In drug discovery programs, modifications that change the net charge of the ligands are
often considered to improve the binding potency and solubility, or to address other …
often considered to improve the binding potency and solubility, or to address other …
Split the charge difference in two! A rule of thumb for adding proper amounts of ions in MD simulations
MR Machado, S Pantano - Journal of Chemical Theory and …, 2020 - ACS Publications
Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD)
simulations, methods or practical rules to set ionic strength are scarce and rarely …
simulations, methods or practical rules to set ionic strength are scarce and rarely …
Intrinsic disorder and conformational coexistence in auxin coreceptors
S Ramans-Harborough, AP Kalverda… - Proceedings of the …, 2023 - National Acad Sciences
AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) transcriptional repressor proteins and the
TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB) proteins to …
TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB) proteins to …
Sequence and Structure-Guided Engineering of Urethanase from Agrobacterium tumefaciens d3 for Improved Catalytic Activity
X Yao, T Kang, Z Pu, T Zhang, J Lin… - Journal of Agricultural …, 2022 - ACS Publications
The amidase from Agrobacterium tumefaciens d3 (AmdA) degrades the carcinogenic ethyl
carbamate (EC) in alcoholic beverages. However, its limited catalytic activity hinders …
carbamate (EC) in alcoholic beverages. However, its limited catalytic activity hinders …
Implicit solvent with explicit ions generalized Born model in molecular dynamics: Application to DNA
ES Kolesnikov, Y Xiong… - Journal of Chemical Theory …, 2024 - ACS Publications
The ion atmosphere surrounding highly charged biomolecules, such as nucleic acids, is
crucial for their dynamics, structure, and interactions. Here, we develop an approach for the …
crucial for their dynamics, structure, and interactions. Here, we develop an approach for the …
Molecular basis of RNA-driven ATP hydrolysis in DExH-box helicases
The spliceosome machinery catalyzes precursor messenger (pre-m) RNA splicing. In each
cycle, the spliceosome experiences massive compositional and conformational remodeling …
cycle, the spliceosome experiences massive compositional and conformational remodeling …
Characterization of cytoskeletal and structural effects of INF2 variants causing glomerulopathy and neuropathy
H Ueda, QTH Tran, LNT Tran, K Higasa, Y Ikeda… - Scientific Reports, 2023 - nature.com
Focal segmental glomerulosclerosis (FSGS) is a common glomerular injury leading to end-
stage renal disease. Monogenic FSGS is primarily ascribed to decreased podocyte integrity …
stage renal disease. Monogenic FSGS is primarily ascribed to decreased podocyte integrity …
Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models
We have compared distributions of sodium and potassium ions around double-stranded
DNA, simulated using fixed charge SPC/E, TIP3P, and OPC water models and the …
DNA, simulated using fixed charge SPC/E, TIP3P, and OPC water models and the …