Four categories of globular proteins, including all-a, all-β, α＋β, and α/β types, are simplified as the off-lattice HNP model involving the secondary-structural information of each protein. The propensity of thr...Four categories of globular proteins, including all-a, all-β, α＋β, and α/β types, are simplified as the off-lattice HNP model involving the secondary-structural information of each protein. The propensity of three types of residues, i.e., H, N, and P to form a secondary structure is investigated based on 146 protein samples. We find that P residues are easy to form a-helices, whereas H residues have a higher tendency to construct β-sheets. The statistical analysis also indicates that the occurrence of P residues is invariably higher than that of H residues, which is independent of protein category. Changes in bond- and non-bonded potential energies of all protein samples under a wide temperature range are presented by coarse-grained molecular dynamics （MD） simulation. The simulation results clearly show a linear relationship between the bond-stretching/bending potential energy and the reduced temperature. The bond-torsional and non-bonded potential energies show distinct transitions with temperature. The bond-torsional energy increases to the maximum and then decreases with the increase of temperature, which is opposite to the change in non-bonded potential energy. The transition temperature of non-bonded potential energy is independent of the protein category, while that of bond-torsional energy is closely related to the protein secondary structure, i.e., α-helix or E-sheet. The quantitatively bonded- and semi- quantitatively non-bonded potential energy of 24 α＋β and 23 α/β protein samples are successfully predicted according to the statistical results obtained from MD simulations.展开更多
Aggregation-induced emission(AIE)is a phenomenon where a molecule that is weakly or non-luminescent in a diluted solution becomes highly emissive when aggregated.AIE luminogens(AIEgens)hold promise in diverse applicat...Aggregation-induced emission(AIE)is a phenomenon where a molecule that is weakly or non-luminescent in a diluted solution becomes highly emissive when aggregated.AIE luminogens(AIEgens)hold promise in diverse applications like bioimaging,chemical sensing,and optoelectronics.Investigation in AIE luminescence is also critical for understanding aggregation kinetics as the aggregation process is an essential component of AIE emission.Experimental investigation of AIEgen aggregation is challenging due to the fast timescale of the aggregation and the amorphous aggregate structures.Computer simulations such as molecular dynamics(MD)simulation provide a valuable approach to complement experiments with atomic-level knowledge to study the fast dynamics of aggregation processes.However,individual simulations still struggle to systematically elucidate heterogeneous kinetics of the formation of amorphous AIEgen aggregates.Kinetic network models(KNMs),constructed from an ensemble of MD simulations,hold great potential in addressing this challenge.In these models,dynamic processes are modeled as a series ofMarkovian transitions occurring among metastable conformational states at discrete time intervals.In this perspective article,we first review previous studies to characterize the AIEgen aggregation kinetics and their limitations.We then introduce KNMs as a promising approach to elucidate the complex kinetics of aggregations to address these limitations.More importantly,we discuss our perspective on linking the output of KNMs to experimental observations of time-resolved AIE luminescence.We expect that this approach can validate the computational predictions and provide great insights into the aggregation kinetics for AIEgen aggregates.These insights will facilitate the rational design of improved AIEgens in their applications in biology and materials sciences.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.21204078,11304282,and 11202201)the Natural Science Foundation of Zhejiang Province,China(Grant No.LY12B04003)
文摘Four categories of globular proteins, including all-a, all-β, α＋β, and α/β types, are simplified as the off-lattice HNP model involving the secondary-structural information of each protein. The propensity of three types of residues, i.e., H, N, and P to form a secondary structure is investigated based on 146 protein samples. We find that P residues are easy to form a-helices, whereas H residues have a higher tendency to construct β-sheets. The statistical analysis also indicates that the occurrence of P residues is invariably higher than that of H residues, which is independent of protein category. Changes in bond- and non-bonded potential energies of all protein samples under a wide temperature range are presented by coarse-grained molecular dynamics （MD） simulation. The simulation results clearly show a linear relationship between the bond-stretching/bending potential energy and the reduced temperature. The bond-torsional and non-bonded potential energies show distinct transitions with temperature. The bond-torsional energy increases to the maximum and then decreases with the increase of temperature, which is opposite to the change in non-bonded potential energy. The transition temperature of non-bonded potential energy is independent of the protein category, while that of bond-torsional energy is closely related to the protein secondary structure, i.e., α-helix or E-sheet. The quantitatively bonded- and semi- quantitatively non-bonded potential energy of 24 α＋β and 23 α/β protein samples are successfully predicted according to the statistical results obtained from MD simulations.
文摘Aggregation-induced emission(AIE)is a phenomenon where a molecule that is weakly or non-luminescent in a diluted solution becomes highly emissive when aggregated.AIE luminogens(AIEgens)hold promise in diverse applications like bioimaging,chemical sensing,and optoelectronics.Investigation in AIE luminescence is also critical for understanding aggregation kinetics as the aggregation process is an essential component of AIE emission.Experimental investigation of AIEgen aggregation is challenging due to the fast timescale of the aggregation and the amorphous aggregate structures.Computer simulations such as molecular dynamics(MD)simulation provide a valuable approach to complement experiments with atomic-level knowledge to study the fast dynamics of aggregation processes.However,individual simulations still struggle to systematically elucidate heterogeneous kinetics of the formation of amorphous AIEgen aggregates.Kinetic network models(KNMs),constructed from an ensemble of MD simulations,hold great potential in addressing this challenge.In these models,dynamic processes are modeled as a series ofMarkovian transitions occurring among metastable conformational states at discrete time intervals.In this perspective article,we first review previous studies to characterize the AIEgen aggregation kinetics and their limitations.We then introduce KNMs as a promising approach to elucidate the complex kinetics of aggregations to address these limitations.More importantly,we discuss our perspective on linking the output of KNMs to experimental observations of time-resolved AIE luminescence.We expect that this approach can validate the computational predictions and provide great insights into the aggregation kinetics for AIEgen aggregates.These insights will facilitate the rational design of improved AIEgens in their applications in biology and materials sciences.
