Interfacial interactions of proteins with cell membranes play important roles in fundamental physiological processes of cells.The binding of proteins to membranes involves interactions between amino acids and membrane...Interfacial interactions of proteins with cell membranes play important roles in fundamental physiological processes of cells.The binding of proteins to membranes involves interactions between amino acids and membranes.However,the mechanism underlying amino acids'membrane behavior remains elusive.Herein,all-atom molecular dynamic simulations were applied to comprehensively investigating the molecular details of interactions between 20 amino acids with DOPC membranes.Our results show that 20 amino acids exhibit distinct membrane insertion activities,which are not simply determined by the side chain properties of amino acids.Aromatic Tyr/Phe/Trp,hydrophobic Val/Ile/Leu/Met,positively-charged Arg and hydrophilic Cys exhibit significantly strong membrane insertion capacities with different characteristic insertion depths and insertion angles.Surprisingly,hydrophobic Ala,positively-charged His/Lys,hydrophilic Asn/Ser/Gln/Thr,negatively-charged Asp/Glu and Pro/Gly have low membrane insertion capabilities.Considering the chemical structures and interaction details of amino acids with membranes,we suggest that the abundance and diversity of interaction sites and types,the synergistic effect of hydrophilic and hydrophobic interactions of amino acids with membranes and the structural flexibility of amino acids are key factors for determining membrane insertion capabilities and characteristics of amino acids.Our study sheds light on the atomic mechanism of interactions between single amino acids and membranes.展开更多
The correct method used in forest soil respiration measurement by Li-6400 is a premise of data quality control. According to the study in a larch plantation, collars should be inserted at 12 hours in advance to effici...The correct method used in forest soil respiration measurement by Li-6400 is a premise of data quality control. According to the study in a larch plantation, collars should be inserted at 12 hours in advance to efficiently reduce the influence of CO2 spring-out.Moreover, collar insertion depth substantially affected soil respiration measurement, i.e. when collar was shallowly inserted into soil,transversal gas diffusion and the CO2 re-spring-out caused by unstable collars in the measurement could lead to overestimating soil respiration rate; however, when collar was deeply inserted into soil, root respiration decline caused by root-cut and the most active respiratory of the surface soil separated by the inserted collars could lead to underestimating soil respiration rate. Furthermore, an error less than 5% could be guaranteed in typical sunny day if the target [CO2] was set to the mean value of ambient [CO2] in most time of the day, but it should be carefully set in early morning and late afternoon according to changing ambient [CO2]. This protocol of measurement is useful in real measurement.展开更多
基金This work was supported by the Open Research Fund of Songshan Lake Materials Laboratory,China(No.2021SLABFK10)the National Natural Science Foundation of China(Nos.12274307,32230063,21774092 and 22303060)+1 种基金the Natural Science Foundation of Guangdong Province,China(No.2023A1515011610)the Open Research Fund of State Key Laboratory of Surface Physics of Fudan University,China(No.KF2023_03).
文摘Interfacial interactions of proteins with cell membranes play important roles in fundamental physiological processes of cells.The binding of proteins to membranes involves interactions between amino acids and membranes.However,the mechanism underlying amino acids'membrane behavior remains elusive.Herein,all-atom molecular dynamic simulations were applied to comprehensively investigating the molecular details of interactions between 20 amino acids with DOPC membranes.Our results show that 20 amino acids exhibit distinct membrane insertion activities,which are not simply determined by the side chain properties of amino acids.Aromatic Tyr/Phe/Trp,hydrophobic Val/Ile/Leu/Met,positively-charged Arg and hydrophilic Cys exhibit significantly strong membrane insertion capacities with different characteristic insertion depths and insertion angles.Surprisingly,hydrophobic Ala,positively-charged His/Lys,hydrophilic Asn/Ser/Gln/Thr,negatively-charged Asp/Glu and Pro/Gly have low membrane insertion capabilities.Considering the chemical structures and interaction details of amino acids with membranes,we suggest that the abundance and diversity of interaction sites and types,the synergistic effect of hydrophilic and hydrophobic interactions of amino acids with membranes and the structural flexibility of amino acids are key factors for determining membrane insertion capabilities and characteristics of amino acids.Our study sheds light on the atomic mechanism of interactions between single amino acids and membranes.
基金National Natural Science Foundation of China (30300271),Program of Key Basic Research from Ministry of Science and Technology (2004CCA02700) and Sina-Japan cooperation project on larch forest study.
文摘The correct method used in forest soil respiration measurement by Li-6400 is a premise of data quality control. According to the study in a larch plantation, collars should be inserted at 12 hours in advance to efficiently reduce the influence of CO2 spring-out.Moreover, collar insertion depth substantially affected soil respiration measurement, i.e. when collar was shallowly inserted into soil,transversal gas diffusion and the CO2 re-spring-out caused by unstable collars in the measurement could lead to overestimating soil respiration rate; however, when collar was deeply inserted into soil, root respiration decline caused by root-cut and the most active respiratory of the surface soil separated by the inserted collars could lead to underestimating soil respiration rate. Furthermore, an error less than 5% could be guaranteed in typical sunny day if the target [CO2] was set to the mean value of ambient [CO2] in most time of the day, but it should be carefully set in early morning and late afternoon according to changing ambient [CO2]. This protocol of measurement is useful in real measurement.
