TAR DNA结合蛋白43(transactive response DNA binding protein 43,TDP-43),一种可变剪切因子,可以特异性地结合富含TG序列的DNA,涉及多种神经退行性疾病.分子动力学模拟方法虽然是研究分子间相互作用强有力的工具,但它非常耗时,且难以...TAR DNA结合蛋白43(transactive response DNA binding protein 43,TDP-43),一种可变剪切因子,可以特异性地结合富含TG序列的DNA,涉及多种神经退行性疾病.分子动力学模拟方法虽然是研究分子间相互作用强有力的工具,但它非常耗时,且难以对有大的构象变化的体系进行充分采样来研究其变构行为.本工作使用粗粒化的基于弹性势的高斯网络模型(Gaussian network model,GNM)研究人TDP-43与靶标DNA间相互作用的动力学.进一步地,利用本课题组之前提出的基于GNM的热力学循环方法识别TDP-43与DNA相互作用的关键残基,其微扰引起了大的结合自由能的变化.DNA结合后,TDP-43上富含正电残基的loop1和loop3片段有较大的柔性损失,这反映了它们在识别和结合中的诱导契合作用.另外发现,基于热力学循环的方法不仅识别到一些与DNA特异性相互作用有关的重要残基,而且识别到一些远离结合界面但在结合引起的分子构象变化中发挥重要作用的残基.本研究有助于理解TDP-43与DNA的特异性相互作用,可为药物设计提供重要信息,另外该方法可以很方便地拓展到其他蛋白质-核酸相互作用动力学的研究.展开更多
The nervous system processes a vast amount of information,performing computations that underlie perception,cognition,and behavior.During development,neuronal guidance genes,which encode extracellular cues,their recept...The nervous system processes a vast amount of information,performing computations that underlie perception,cognition,and behavior.During development,neuronal guidance genes,which encode extracellular cues,their receptors,and downstream signal transducers,organize neural wiring to generate the complex architecture of the nervous system.It is now evident that many of these neuroguidance cues and their receptors are active during development and are also expressed in the adult nervous system.This suggests that neuronal guidance pathways are critical not only for neural wiring but also for ongoing function and maintenance of the mature nervous system.Supporting this view,these pathways continue to regulate synaptic connectivity,plasticity,and remodeling,and overall brain homeostasis throughout adulthood.Genetic and transcriptomic analyses have further revealed many neuronal guidance genes to be associated with a wide range of neurodegenerative and neuropsychiatric disorders.Although the precise mechanisms by which aberrant neuronal guidance signaling drives the pathogenesis of these diseases remain to be clarified,emerging evidence points to several common themes,including dysfunction in neurons,microglia,astrocytes,and endothelial cells,along with dysregulation of neuron-microglia-astrocyte,neuroimmune,and neurovascular interactions.In this review,we explore recent advances in understanding the molecular and cellular mechanisms by which aberrant neuronal guidance signaling contributes to disease pathogenesis through altered cell-cell interactions.For instance,recent studies have unveiled two distinct semaphorin-plexin signaling pathways that affect microglial activation and neuroinflammation.We discuss the challenges ahead,along with the therapeutic potentials of targeting neuronal guidance pathways for treating neurodegenerative diseases.Particular focus is placed on how neuronal guidance mechanisms control neuron-glia and neuroimmune interactions and modulate microglial function under physiological and pathological conditions.Specifically,we examine the crosstalk between neuronal guidance signaling and TREM2,a master regulator of microglial function,in the context of pathogenic protein aggregates.It is well-established that age is a major risk factor for neurodegeneration.Future research should address how aging and neuronal guidance signaling interact to influence an individual’s susceptibility to various late-onset neurological diseases and how the progression of these diseases could be therapeutically blocked by targeting neuronal guidance pathways.展开更多
文摘TAR DNA结合蛋白43(transactive response DNA binding protein 43,TDP-43),一种可变剪切因子,可以特异性地结合富含TG序列的DNA,涉及多种神经退行性疾病.分子动力学模拟方法虽然是研究分子间相互作用强有力的工具,但它非常耗时,且难以对有大的构象变化的体系进行充分采样来研究其变构行为.本工作使用粗粒化的基于弹性势的高斯网络模型(Gaussian network model,GNM)研究人TDP-43与靶标DNA间相互作用的动力学.进一步地,利用本课题组之前提出的基于GNM的热力学循环方法识别TDP-43与DNA相互作用的关键残基,其微扰引起了大的结合自由能的变化.DNA结合后,TDP-43上富含正电残基的loop1和loop3片段有较大的柔性损失,这反映了它们在识别和结合中的诱导契合作用.另外发现,基于热力学循环的方法不仅识别到一些与DNA特异性相互作用有关的重要残基,而且识别到一些远离结合界面但在结合引起的分子构象变化中发挥重要作用的残基.本研究有助于理解TDP-43与DNA的特异性相互作用,可为药物设计提供重要信息,另外该方法可以很方便地拓展到其他蛋白质-核酸相互作用动力学的研究.
基金supported by JSPS(KAKENHI:21K06205,23K06937,24K23419)AMED(to JYK,SaY,TM,SiY,YT,and NH)JYW had long been supported by the NIH.
文摘The nervous system processes a vast amount of information,performing computations that underlie perception,cognition,and behavior.During development,neuronal guidance genes,which encode extracellular cues,their receptors,and downstream signal transducers,organize neural wiring to generate the complex architecture of the nervous system.It is now evident that many of these neuroguidance cues and their receptors are active during development and are also expressed in the adult nervous system.This suggests that neuronal guidance pathways are critical not only for neural wiring but also for ongoing function and maintenance of the mature nervous system.Supporting this view,these pathways continue to regulate synaptic connectivity,plasticity,and remodeling,and overall brain homeostasis throughout adulthood.Genetic and transcriptomic analyses have further revealed many neuronal guidance genes to be associated with a wide range of neurodegenerative and neuropsychiatric disorders.Although the precise mechanisms by which aberrant neuronal guidance signaling drives the pathogenesis of these diseases remain to be clarified,emerging evidence points to several common themes,including dysfunction in neurons,microglia,astrocytes,and endothelial cells,along with dysregulation of neuron-microglia-astrocyte,neuroimmune,and neurovascular interactions.In this review,we explore recent advances in understanding the molecular and cellular mechanisms by which aberrant neuronal guidance signaling contributes to disease pathogenesis through altered cell-cell interactions.For instance,recent studies have unveiled two distinct semaphorin-plexin signaling pathways that affect microglial activation and neuroinflammation.We discuss the challenges ahead,along with the therapeutic potentials of targeting neuronal guidance pathways for treating neurodegenerative diseases.Particular focus is placed on how neuronal guidance mechanisms control neuron-glia and neuroimmune interactions and modulate microglial function under physiological and pathological conditions.Specifically,we examine the crosstalk between neuronal guidance signaling and TREM2,a master regulator of microglial function,in the context of pathogenic protein aggregates.It is well-established that age is a major risk factor for neurodegeneration.Future research should address how aging and neuronal guidance signaling interact to influence an individual’s susceptibility to various late-onset neurological diseases and how the progression of these diseases could be therapeutically blocked by targeting neuronal guidance pathways.
