Multienzyme cascades enable the sequential synthesis of complex chemicals by combining multiple catalytic processes in one pot,offering considerable time and cost savings compared to a series of separate batch reactio...Multienzyme cascades enable the sequential synthesis of complex chemicals by combining multiple catalytic processes in one pot,offering considerable time and cost savings compared to a series of separate batch reactions.However,challenges related to coordination and regulatory interplay among multiple enzymes reduce the catalytic efficiency of such cascades.Herein,we genetically programmed a scaffold framework that selectively and orthogonally recruits enzymes as designed.The system was then used to generate multienzyme complexes of D-allulose 3-epimerase(DAE),ribitol dehydrogenase(RDH),and formate dehydrogenase(FDH)for rare sugar production.This scaffolded multienzymatic assembly achieves a 10.4-fold enhancement in the catalytic performance compared to its unassembled counterparts,obtaining allitol yield of more than 95%.Molecular dynamics simulations revealed that shorter distances between neighboring enzymes in scaffold-mounted complexes facilitated the transfer of reaction intermediates.A dual-module catalytic system incorporating(1)scaffold-bound complexes of DAE,RDH,and FDH and(2)scaffold-bound complexes of alcohol dehydrogenase and NADH oxidase expressed intracellularly in E.coli was used to synthesize D-allulose from D-fructose.This system synthesized 90.6%D-allulose from 300 g L^(−1)D-fructose,with a space-time yield of 13.6 g L^(−1)h^(−1).Our work demonstrates the programmability and versatility of scaffold-based strategies for the advancement of multienzyme cascades.展开更多
Asymmetric cell division is an important mechanism for creating diversity in a cellular population. Stem cells commonly perform asymmetric division to generate both a daughter stem cell for self-renewal and a more dif...Asymmetric cell division is an important mechanism for creating diversity in a cellular population. Stem cells commonly perform asymmetric division to generate both a daughter stem cell for self-renewal and a more differentiated daughter cell to populate the tissue. During asymmetric cell division, protein cell fate determinants asymmetrically localize to the opposite poles of a dividing cell to cause distinct cell fate. However, it remains unclear whether cell fate determination is robust to fluctuations and noise during this spatial allocation process. To answer this question, we engineered Caulobacter, a bacterial model for asymmetric division, to express synthetic scaffolds with modular protein interaction domains. These scaffolds perturbed the spatial distribution of the PleC-DivJ- DivK phospho-signaling network without changing their endogenous expression levels. Surprisingly, enforcing symmetrical distribution of these cell fate de terminants did not result in symmetric daughter fate or any morphological defects. Further computational analysis suggested that PleC and DivJ form a robust phospho-switch that can tolerate high amount of spatial variation. This insight may shed light on the presence of similar phospho-switches in stem cell asymmetric division regulation. Overall, our study demonstrates that synthetic protein scaffolds can provide a useful tool to probe biological systems for better understanding of their operating principles.展开更多
In de novo protein sequencing,we often could only obtain an incomplete protein sequence,namely a scaffold,from top-down and bottom-up tandem mass spectrometry.While most sections of proteins can be inferred from their...In de novo protein sequencing,we often could only obtain an incomplete protein sequence,namely a scaffold,from top-down and bottom-up tandem mass spectrometry.While most sections of proteins can be inferred from their homologous sequences,some specific section of proteins is always missing and it is hard to predict the missing amino acids in the gaps of the scaffolds.Thus,we only focus on predicting the gaps based on a probabilistic algorithm and a machine learning model instead predicting the complete protein sequence using generative AI models in this paper.We study two versions of the protein scaffold filling problem with known gap size and known gap mass,respectively.For the known size gaps version,we develop several machine learning models based on random forest,k-nearest neighbors,decision tree,and fully connected neural network.For the known gap mass problem,we design a probabilistic algorithm to predict the missing amino acids in the gaps.The experimental results on both real and simulation data show that our proposed algorithms show promising results of 100%and close to 100%accuracy,respectively.展开更多
Scaffold proteins play an important role in the promotion of signal transmission and specificity during cell signaling. In cells, signaling proteins that make up a pathway are often physically orgnaized into complexes...Scaffold proteins play an important role in the promotion of signal transmission and specificity during cell signaling. In cells, signaling proteins that make up a pathway are often physically orgnaized into complexes by scaffold proteins [1]. Previous work [2] has shown that spatial localization of scaffold can enhance signaling locally while simultaneously suppressing signaling at a distance, and the membrane confinement of scaffold proteins may result in a precipitous spatial gradient of the active product protein, high close to the membrane and low within the cell. However, cell-fate decisions critically depend on the temporal pattern of product protein close to the nucleus. In this paper, when phosphorylation signals cannot be transfered by diffusion only, two mechanisms have been proposed for long-range signaling within cells： multiple locations of scaffold proteins and dynamical movement of scaffold proteins. Thus, here we have unveiled how the spatial propagation of the phosphorylated product protein within a cell depends on the spatially and temporal localized scaffold proteins. A class of novel and fast numerical methods for solving stiff reaction diffusion equations with complex domains is briefly introduced.展开更多
Recently,a number of studies reported that casein was composed of various multifunctional bioactive peptides such as casein phosphopeptide andβ-casochemotide-1 that bind calcium ions and induce macrophage chemotaxis,...Recently,a number of studies reported that casein was composed of various multifunctional bioactive peptides such as casein phosphopeptide andβ-casochemotide-1 that bind calcium ions and induce macrophage chemotaxis,which is crucial for bone homeostasis and bone fracture repair by cytokines secreted in the process.We hypothesized that the effects of the multifunctional biopeptides in casein would contribute to improving bone regeneration.Thus,we designed a tissue engineering platform that consisted of casein and polyvinyl alcohol,which was a physical-crosslinked scaffold(milk-derived protein;MDP),via simple freeze-thaw cycles and performed surface modification using 3,4-dihydroxy-L-phenylalanine(DOPA),a mussel adhesive protein,for immobilizing adhesive proteins and cytokines for recruiting cells in vivo(MDP-DOPA).Both the MDP and MDP-DOPA groups proved indirectly contribution of macrophages migration as RAW 264.7 cells were highly migrated toward materials by contained bioactive peptides.We implanted MDP and MDP-DOPA in a mouse calvarial defect orthotopic model and evaluated whether MDP-DOPA showed much faster mineral deposition and higher bone density than that of the no-treatment and MDP groups.The MDP-DOPA group showed the accumulation of host M2 macrophages and mesenchymal stem cells(MSCs)around the scaffold,whereas MDP presented mostly M1 macrophages in the early stage.展开更多
In the realm of drug discovery,recent advancements have paved the way for innovative approaches and methodologies.This comprehensive review encapsulates six distinct yet interrelated mini-reviews,each shedding light o...In the realm of drug discovery,recent advancements have paved the way for innovative approaches and methodologies.This comprehensive review encapsulates six distinct yet interrelated mini-reviews,each shedding light on novel strategies in drug development.(a)The resurgence of covalent drugs is highlighted,focusing on the targeted covalent inhibitors(TCIs)and their role in enhancing selectivity and affinity.(b)The potential of the quantum mechanics-based computational aid drug design(CADD)tool,Cov_DOX,is introduced for predicting protein-covalent ligand binding structures and affinities.(c)The scaffolding function of proteins is proposed as a new avenue for drug design,with a focus on modulating protein-protein interactions through small molecules and proteolysis targeting chimeras(PROTACs).(d)The concept of pro-PROTACs is explored as a promising strategy for cancer therapy,combining the principles of prodrugs and PROTACs to enhance specificity and reduce toxicity.(e)The design of prodrugs through carbon-carbon bond cleavage is discussed,offering a new perspective for the activation of drugs with limited modifiable functional groups.(f)The targeting of programmed cell death pathways in cancer therapies with small molecules is reviewed,emphasizing the induction of autophagy-dependent cell death,ferroptosis,and cuproptosis.These insights collectively contribute to a deeper understanding of the dynamic landscape of drug discovery.展开更多
Auxin controls multiple developmental processes and plant responses to environmental stimuli (Adamowski and Friml, 2015). The plasma membrane-localized PIN-FORMED (PIN) auxin efflux transporters govern directional cel...Auxin controls multiple developmental processes and plant responses to environmental stimuli (Adamowski and Friml, 2015). The plasma membrane-localized PIN-FORMED (PIN) auxin efflux transporters govern directional cell-to-cell transport and the gradient distribution of auxin, and these processes are fine-tuned by reversible phosphorylation (Bassukas et al., 2022). The AGCVIII kinases PINOID (PID) and D6 PROTEIN KINASE (D6PK) have been identified for modulating PIN activity through direct phosphorylation in their central, hydrophylic loop (Zourelidou et al., 2014).展开更多
Spinal cord injury results in the loss of motor and sensory pathways and spontaneous regeneration of adult mammalian spinal cord neurons is limited. Chitosan and sodium alginate have good biocompatibility, biodegradab...Spinal cord injury results in the loss of motor and sensory pathways and spontaneous regeneration of adult mammalian spinal cord neurons is limited. Chitosan and sodium alginate have good biocompatibility, biodegradability, and are suitable to assist the recovery of damaged tissues, such as skin, bone and nerve. Chitosan scaffolds, sodium alginate scaffolds and chitosan-sodium alginate scaffolds were separately transplanted into rats with spinal cord hemisection. Basso-Beattie-Bresnahan locomotor rating scale scores and electrophysiological results showed that chitosan scaffolds promoted recovery of locomotor capacity and nerve transduction of the experimental rats.Sixty days after surgery, chitosan scaffolds retained the original shape of the spinal cord. Compared with sodium alginate scaffolds- and chitosan-sodium alginate scaffolds-transplanted rats, more neurofilament-H-immunoreactive cells （regenerating nerve fibers） and less glial fibrillary acidic protein-immunoreactive cells （astrocytic scar tissue） were observed at the injury site of experimental rats in chitosan scaffold-transplanted rats. Due to the fast degradation rate of sodium alginate, sodium alginate scaffolds and composite material scaffolds did not have a supporting and bridging effect on the damaged tissue. Above all, compared with sodium alginate and composite material scaffolds, chitosan had better biocompatibility, could promote the regeneration of nerve fibers and prevent the formation of scar tissue,and as such, is more suitable to help the repair of spinal cord injury.展开更多
DNA double-strand breaks(DSBs)severely impact the integrity of the genome and cell homeostasis.To address DSBs,cells activate sophisticated mechanisms to repair this DNA damage.Non-homologous end joining(NHEJ)is a pre...DNA double-strand breaks(DSBs)severely impact the integrity of the genome and cell homeostasis.To address DSBs,cells activate sophisticated mechanisms to repair this DNA damage.Non-homologous end joining(NHEJ)is a predominant pathway for repairing DSBs.p53 binding protein 1(53BP1)serves as a pivotal regulator in the NHEJ pathway.By locating and forming phase separation at DSB sites,53BP1 acts as a scaffold protein to recruit downstream components and facilitate DSB repair[1].展开更多
文摘Multienzyme cascades enable the sequential synthesis of complex chemicals by combining multiple catalytic processes in one pot,offering considerable time and cost savings compared to a series of separate batch reactions.However,challenges related to coordination and regulatory interplay among multiple enzymes reduce the catalytic efficiency of such cascades.Herein,we genetically programmed a scaffold framework that selectively and orthogonally recruits enzymes as designed.The system was then used to generate multienzyme complexes of D-allulose 3-epimerase(DAE),ribitol dehydrogenase(RDH),and formate dehydrogenase(FDH)for rare sugar production.This scaffolded multienzymatic assembly achieves a 10.4-fold enhancement in the catalytic performance compared to its unassembled counterparts,obtaining allitol yield of more than 95%.Molecular dynamics simulations revealed that shorter distances between neighboring enzymes in scaffold-mounted complexes facilitated the transfer of reaction intermediates.A dual-module catalytic system incorporating(1)scaffold-bound complexes of DAE,RDH,and FDH and(2)scaffold-bound complexes of alcohol dehydrogenase and NADH oxidase expressed intracellularly in E.coli was used to synthesize D-allulose from D-fructose.This system synthesized 90.6%D-allulose from 300 g L^(−1)D-fructose,with a space-time yield of 13.6 g L^(−1)h^(−1).Our work demonstrates the programmability and versatility of scaffold-based strategies for the advancement of multienzyme cascades.
文摘Asymmetric cell division is an important mechanism for creating diversity in a cellular population. Stem cells commonly perform asymmetric division to generate both a daughter stem cell for self-renewal and a more differentiated daughter cell to populate the tissue. During asymmetric cell division, protein cell fate determinants asymmetrically localize to the opposite poles of a dividing cell to cause distinct cell fate. However, it remains unclear whether cell fate determination is robust to fluctuations and noise during this spatial allocation process. To answer this question, we engineered Caulobacter, a bacterial model for asymmetric division, to express synthetic scaffolds with modular protein interaction domains. These scaffolds perturbed the spatial distribution of the PleC-DivJ- DivK phospho-signaling network without changing their endogenous expression levels. Surprisingly, enforcing symmetrical distribution of these cell fate de terminants did not result in symmetric daughter fate or any morphological defects. Further computational analysis suggested that PleC and DivJ form a robust phospho-switch that can tolerate high amount of spatial variation. This insight may shed light on the presence of similar phospho-switches in stem cell asymmetric division regulation. Overall, our study demonstrates that synthetic protein scaffolds can provide a useful tool to probe biological systems for better understanding of their operating principles.
基金supported by the USA National Science Foundation under Grant Nos.2307571,2307572,and 2307573.
文摘In de novo protein sequencing,we often could only obtain an incomplete protein sequence,namely a scaffold,from top-down and bottom-up tandem mass spectrometry.While most sections of proteins can be inferred from their homologous sequences,some specific section of proteins is always missing and it is hard to predict the missing amino acids in the gaps of the scaffolds.Thus,we only focus on predicting the gaps based on a probabilistic algorithm and a machine learning model instead predicting the complete protein sequence using generative AI models in this paper.We study two versions of the protein scaffold filling problem with known gap size and known gap mass,respectively.For the known size gaps version,we develop several machine learning models based on random forest,k-nearest neighbors,decision tree,and fully connected neural network.For the known gap mass problem,we design a probabilistic algorithm to predict the missing amino acids in the gaps.The experimental results on both real and simulation data show that our proposed algorithms show promising results of 100%and close to 100%accuracy,respectively.
基金supported by the NSF/NIH initiative on Mathematical Biologythrough R01GM75309 R01GM67247 from the National Institute of General Medical Sciencesby NIHP50GM76516 and NSF DMS0917492
文摘Scaffold proteins play an important role in the promotion of signal transmission and specificity during cell signaling. In cells, signaling proteins that make up a pathway are often physically orgnaized into complexes by scaffold proteins [1]. Previous work [2] has shown that spatial localization of scaffold can enhance signaling locally while simultaneously suppressing signaling at a distance, and the membrane confinement of scaffold proteins may result in a precipitous spatial gradient of the active product protein, high close to the membrane and low within the cell. However, cell-fate decisions critically depend on the temporal pattern of product protein close to the nucleus. In this paper, when phosphorylation signals cannot be transfered by diffusion only, two mechanisms have been proposed for long-range signaling within cells： multiple locations of scaffold proteins and dynamical movement of scaffold proteins. Thus, here we have unveiled how the spatial propagation of the phosphorylated product protein within a cell depends on the spatially and temporal localized scaffold proteins. A class of novel and fast numerical methods for solving stiff reaction diffusion equations with complex domains is briefly introduced.
基金supported by the Basic Science Research Program through the National Research Foundation of Korea(NRF)funded by the Ministry of Education(2020R1A6A3A01098495,2020R1A6A1A03043283)by the Bio&Medical Technology Development Program of the National Research Foundation(NRF)funded by the Korean government(MSIT)(2018M3A9E2023259)supported by Basic Science Research Capacity Enhancement Project through Korea Basic Science Institute(National research Facilities and Equipment Center)grant funded by the Ministry of Education(2019R1A6C1010033).
文摘Recently,a number of studies reported that casein was composed of various multifunctional bioactive peptides such as casein phosphopeptide andβ-casochemotide-1 that bind calcium ions and induce macrophage chemotaxis,which is crucial for bone homeostasis and bone fracture repair by cytokines secreted in the process.We hypothesized that the effects of the multifunctional biopeptides in casein would contribute to improving bone regeneration.Thus,we designed a tissue engineering platform that consisted of casein and polyvinyl alcohol,which was a physical-crosslinked scaffold(milk-derived protein;MDP),via simple freeze-thaw cycles and performed surface modification using 3,4-dihydroxy-L-phenylalanine(DOPA),a mussel adhesive protein,for immobilizing adhesive proteins and cytokines for recruiting cells in vivo(MDP-DOPA).Both the MDP and MDP-DOPA groups proved indirectly contribution of macrophages migration as RAW 264.7 cells were highly migrated toward materials by contained bioactive peptides.We implanted MDP and MDP-DOPA in a mouse calvarial defect orthotopic model and evaluated whether MDP-DOPA showed much faster mineral deposition and higher bone density than that of the no-treatment and MDP groups.The MDP-DOPA group showed the accumulation of host M2 macrophages and mesenchymal stem cells(MSCs)around the scaffold,whereas MDP presented mostly M1 macrophages in the early stage.
基金supported by grants from the National Natural Science Foundation of China(No.82273770)the Foundation for Innovative Research Groups of the National Natural Science Foundation of Sichuan Province(No.24NSFTD0051).
文摘In the realm of drug discovery,recent advancements have paved the way for innovative approaches and methodologies.This comprehensive review encapsulates six distinct yet interrelated mini-reviews,each shedding light on novel strategies in drug development.(a)The resurgence of covalent drugs is highlighted,focusing on the targeted covalent inhibitors(TCIs)and their role in enhancing selectivity and affinity.(b)The potential of the quantum mechanics-based computational aid drug design(CADD)tool,Cov_DOX,is introduced for predicting protein-covalent ligand binding structures and affinities.(c)The scaffolding function of proteins is proposed as a new avenue for drug design,with a focus on modulating protein-protein interactions through small molecules and proteolysis targeting chimeras(PROTACs).(d)The concept of pro-PROTACs is explored as a promising strategy for cancer therapy,combining the principles of prodrugs and PROTACs to enhance specificity and reduce toxicity.(e)The design of prodrugs through carbon-carbon bond cleavage is discussed,offering a new perspective for the activation of drugs with limited modifiable functional groups.(f)The targeting of programmed cell death pathways in cancer therapies with small molecules is reviewed,emphasizing the induction of autophagy-dependent cell death,ferroptosis,and cuproptosis.These insights collectively contribute to a deeper understanding of the dynamic landscape of drug discovery.
基金supported by grants from the National Key R&D Program of China(2022YFA1303400)Fundamental Research Funds for the Central Universities(KJJQ2024007)the National Natural Science Foundation of China(32270301)toQ.Z.
文摘Auxin controls multiple developmental processes and plant responses to environmental stimuli (Adamowski and Friml, 2015). The plasma membrane-localized PIN-FORMED (PIN) auxin efflux transporters govern directional cell-to-cell transport and the gradient distribution of auxin, and these processes are fine-tuned by reversible phosphorylation (Bassukas et al., 2022). The AGCVIII kinases PINOID (PID) and D6 PROTEIN KINASE (D6PK) have been identified for modulating PIN activity through direct phosphorylation in their central, hydrophylic loop (Zourelidou et al., 2014).
基金supported by the National Natural Science Foundation of China,No.81671243 and 81373429
文摘Spinal cord injury results in the loss of motor and sensory pathways and spontaneous regeneration of adult mammalian spinal cord neurons is limited. Chitosan and sodium alginate have good biocompatibility, biodegradability, and are suitable to assist the recovery of damaged tissues, such as skin, bone and nerve. Chitosan scaffolds, sodium alginate scaffolds and chitosan-sodium alginate scaffolds were separately transplanted into rats with spinal cord hemisection. Basso-Beattie-Bresnahan locomotor rating scale scores and electrophysiological results showed that chitosan scaffolds promoted recovery of locomotor capacity and nerve transduction of the experimental rats.Sixty days after surgery, chitosan scaffolds retained the original shape of the spinal cord. Compared with sodium alginate scaffolds- and chitosan-sodium alginate scaffolds-transplanted rats, more neurofilament-H-immunoreactive cells （regenerating nerve fibers） and less glial fibrillary acidic protein-immunoreactive cells （astrocytic scar tissue） were observed at the injury site of experimental rats in chitosan scaffold-transplanted rats. Due to the fast degradation rate of sodium alginate, sodium alginate scaffolds and composite material scaffolds did not have a supporting and bridging effect on the damaged tissue. Above all, compared with sodium alginate and composite material scaffolds, chitosan had better biocompatibility, could promote the regeneration of nerve fibers and prevent the formation of scar tissue,and as such, is more suitable to help the repair of spinal cord injury.
基金supported by the National Natural Science Foundation of China(32422041,32071226)the Foundation of Hubei Hongshan Laboratory(2021HSZD011)+1 种基金the Fundamental Research Funds for the Central Universities(2662023PY001)the HZAU-AGIS Cooperation Fund(SZYJY2022022).
文摘DNA double-strand breaks(DSBs)severely impact the integrity of the genome and cell homeostasis.To address DSBs,cells activate sophisticated mechanisms to repair this DNA damage.Non-homologous end joining(NHEJ)is a predominant pathway for repairing DSBs.p53 binding protein 1(53BP1)serves as a pivotal regulator in the NHEJ pathway.By locating and forming phase separation at DSB sites,53BP1 acts as a scaffold protein to recruit downstream components and facilitate DSB repair[1].
