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Source | Xiaoke Life Structure Biology is well-known to help understand the occurrence and development mechanism of macroscopic phenomena from the molecular level, especially due to the increasing maturity and wide application of single-particle cryo-electron microscopy technology
.
With the impressive record of AlphaFold2 in protein structure prediction, the research direction and future of structural biology have been heatedly discussed
.
It is undeniable that protein prediction will promote scientific research from other existing and potential perspectives, and structural biology based on experimental data needs to answer scientific questions from a more innovative and profound perspective
.
On September 7, 2021, the Cheng Yifan laboratory and David Julius laboratory of the University of California, San Francisco, USA published a research paper titled: Structural snapshots of TRPV1 reveal mechanism of polymodal functionality in Cell
.
Under the conditions of applying different natural stimuli and simulating different physiological environments, this study analyzed a series of intermediate state conformations and activation mechanisms of capsaicin receptor TRPV1 with the help of single-particle cryo-electron microscopy technology, and observed a variety of closed and open states , Reveals the structural elements related to the coupling of multiple ligand action sites, compares the protein behavior when cations of different sizes pass through, explores the quantitative relationship between agonists and endogenous lipid molecules competing for binding sites, and also describes Protein conformation rearrangement under acid conditions
.
The co-corresponding author of the study, Professor David Julius, has just won this year's Nobel Prize in Physiology or Medicine for his research on the capsaicin receptor TRPV1
.
TPRV1 is a tetrameric ion channel that transports cations non-specifically and is closely related to pain and inflammation.
It can be activated by a variety of naturally occurring stimuli and extracellular acidity
.
The natural stimulants of TPRV1 include capsaicin (Capsaicin), the active ingredient of peppers, polypeptide toxin (DkTx) produced by poisonous spiders, and gum lipotoxin (RTX) isolated from the resin Euphorbia.
It can also sense temperature changes (>43°C).
) To participate in the body's body temperature regulation
.
Because of the importance of TPRV1-mediated signal transmission, it has become a potential analgesic target with clinical significance
.
However, because of the complexity of its signal integration, the development and application of analgesics targeting TPRV1 still have side effects such as impairing thermoregulation
.
Therefore, under the action of different stimuli, it is necessary to explore the diversity, uniqueness and commonality of TRPV1 activation pathways, and it is expected to provide more profound and targeted guidance for the development of drugs targeting TPRV1
.
The author reorganized the protein TPRV1 into a lipid environment, expressed and purified the polypeptide toxin DkTx from in vitro, and prepared frozen samples of the two complexes
.
By optimizing the sample preparation conditions and data processing parameters, the author successfully identified a series of intermediate structures from pre-binding, single-binding, and double-binding when the channel is closed and opened
.
These progressive conformational changes, especially the outward shift of the S1-S4 domain from preliminary to full conformation, strongly explain how the peptide agonist DkTx bound on the extracellular side couples and triggers the low-gated opening of TPRV1
.
Different from the DkTx binding site, the vanillic acid agonist RTX binds to the region where the lower gate of TPRV1 is located, thereby directly regulating the open state of the lower gate
.
In the absence of ligand binding, the binding site of TPRV1 vanillic acid agonist is occupied by the endogenous lipid molecule PI
.
This means that the activation of TPRV1 by RTX must first competitively replace the PI in the binding pocket, and then play a regulatory role on ion channels
.
Under low-salt conditions, the author successfully revealed the various possibilities of RTX molecules competing with PI for four binding pockets, which are single RTX molecules, bimolecular ortho and para positions, and three and four RTX molecules binding
.
Each time the RTX molecule completes a binding pocket competition, it will cause the corresponding subunit conformational change, but until the four subunits are occupied by RTX and cause sufficient conformational changes, the gate opening of TPRV1 can be revealed
.
Acid accumulation in local tissues of the organism can also turn on the signal transduction of TPRV1
.
Past functional experiments have proved that the two amino acids on the extracellular side of TRPV1 constitute a key site in response to acid
.
Based on the resolved multiple intermediate state conformations, the author directly observed how these two amino acid positions undergo local structural changes under acid conditions and gradually affect the conformation of TPRV1
.
Although these intermediate states are not in a completely open state, the conformational changes of the S1-S4 domains similar to the action of DkTx interpret the acidic environment to promote the opening of TPRV1
.
The author further explored the transport mechanism of TPRV1 to large cations (such as NMDG)
.
By adding large cations to the solution and preparing frozen samples, the authors resolved multiple conformations of TPRV1
.
These conformations cover how NMDG causes the pore area outside the cell to expand and gradually enter the ion transport path
.
These findings confirm the adaptability of TPRV1 to different physiological environments and the mechanism of how to mediate the transport of ions of different sizes across the membrane
.
Dr.
Kaihua Zhang, a postdoctoral fellow at the University of California, San Francisco, is the first author of the paper.
Professor Yifan Cheng from the Department of Biochemistry and Biophysics at the University of California, San Francisco and Professor David Julius from the Department of Physiology are the co-corresponding authors
.
The David Julius laboratory discovered TRPV1 in 1997, and confirmed that it is an ion channel that can be activated by heat and capsaicin to cause pain
.
Cheng Yifan's laboratory has been engaged in research on cryo-electron microscopy methods and applications
.
The two laboratories have a long-term cooperation.
In 2013, the single-particle cryo-electron microscopy method was used to analyze the atomic structure of TRPV1 for the first time, which triggered a revolution in structural biology
.
In 2016, Dr.
Kaihua Zhang joined this cooperative team for postdoctoral research
.
He successfully applied the advantages of single-particle cryo-electron microscopy technology in analyzing the heterogeneity of samples, and further explained the relationship between TRPV1 structure and function through the study of the intermediate state structure, and interpreted the protein analysis machine from a biological perspective.
The importance of intermediate structure
.
These findings will help to understand more deeply the function of TRP family ion channels and even other signaling proteins, and provide new ideas for the development of drugs targeting TRPV1
.
As far as structural biology is concerned, especially in the context of the use of artificial intelligence for structure prediction, the use of single-particle cryo-electron microscopy to capture the intermediate state structure to explain the function of the protein may be a new research direction in the future.
.
Link to the paper: https://doi.
org/10.
1016/j.
cell.
2021.
08.
012 open for reprinting, welcome to forward to Moments and WeChat groups
.
With the impressive record of AlphaFold2 in protein structure prediction, the research direction and future of structural biology have been heatedly discussed
.
It is undeniable that protein prediction will promote scientific research from other existing and potential perspectives, and structural biology based on experimental data needs to answer scientific questions from a more innovative and profound perspective
.
On September 7, 2021, the Cheng Yifan laboratory and David Julius laboratory of the University of California, San Francisco, USA published a research paper titled: Structural snapshots of TRPV1 reveal mechanism of polymodal functionality in Cell
.
Under the conditions of applying different natural stimuli and simulating different physiological environments, this study analyzed a series of intermediate state conformations and activation mechanisms of capsaicin receptor TRPV1 with the help of single-particle cryo-electron microscopy technology, and observed a variety of closed and open states , Reveals the structural elements related to the coupling of multiple ligand action sites, compares the protein behavior when cations of different sizes pass through, explores the quantitative relationship between agonists and endogenous lipid molecules competing for binding sites, and also describes Protein conformation rearrangement under acid conditions
.
The co-corresponding author of the study, Professor David Julius, has just won this year's Nobel Prize in Physiology or Medicine for his research on the capsaicin receptor TRPV1
.
TPRV1 is a tetrameric ion channel that transports cations non-specifically and is closely related to pain and inflammation.
It can be activated by a variety of naturally occurring stimuli and extracellular acidity
.
The natural stimulants of TPRV1 include capsaicin (Capsaicin), the active ingredient of peppers, polypeptide toxin (DkTx) produced by poisonous spiders, and gum lipotoxin (RTX) isolated from the resin Euphorbia.
It can also sense temperature changes (>43°C).
) To participate in the body's body temperature regulation
.
Because of the importance of TPRV1-mediated signal transmission, it has become a potential analgesic target with clinical significance
.
However, because of the complexity of its signal integration, the development and application of analgesics targeting TPRV1 still have side effects such as impairing thermoregulation
.
Therefore, under the action of different stimuli, it is necessary to explore the diversity, uniqueness and commonality of TRPV1 activation pathways, and it is expected to provide more profound and targeted guidance for the development of drugs targeting TPRV1
.
The author reorganized the protein TPRV1 into a lipid environment, expressed and purified the polypeptide toxin DkTx from in vitro, and prepared frozen samples of the two complexes
.
By optimizing the sample preparation conditions and data processing parameters, the author successfully identified a series of intermediate structures from pre-binding, single-binding, and double-binding when the channel is closed and opened
.
These progressive conformational changes, especially the outward shift of the S1-S4 domain from preliminary to full conformation, strongly explain how the peptide agonist DkTx bound on the extracellular side couples and triggers the low-gated opening of TPRV1
.
Different from the DkTx binding site, the vanillic acid agonist RTX binds to the region where the lower gate of TPRV1 is located, thereby directly regulating the open state of the lower gate
.
In the absence of ligand binding, the binding site of TPRV1 vanillic acid agonist is occupied by the endogenous lipid molecule PI
.
This means that the activation of TPRV1 by RTX must first competitively replace the PI in the binding pocket, and then play a regulatory role on ion channels
.
Under low-salt conditions, the author successfully revealed the various possibilities of RTX molecules competing with PI for four binding pockets, which are single RTX molecules, bimolecular ortho and para positions, and three and four RTX molecules binding
.
Each time the RTX molecule completes a binding pocket competition, it will cause the corresponding subunit conformational change, but until the four subunits are occupied by RTX and cause sufficient conformational changes, the gate opening of TPRV1 can be revealed
.
Acid accumulation in local tissues of the organism can also turn on the signal transduction of TPRV1
.
Past functional experiments have proved that the two amino acids on the extracellular side of TRPV1 constitute a key site in response to acid
.
Based on the resolved multiple intermediate state conformations, the author directly observed how these two amino acid positions undergo local structural changes under acid conditions and gradually affect the conformation of TPRV1
.
Although these intermediate states are not in a completely open state, the conformational changes of the S1-S4 domains similar to the action of DkTx interpret the acidic environment to promote the opening of TPRV1
.
The author further explored the transport mechanism of TPRV1 to large cations (such as NMDG)
.
By adding large cations to the solution and preparing frozen samples, the authors resolved multiple conformations of TPRV1
.
These conformations cover how NMDG causes the pore area outside the cell to expand and gradually enter the ion transport path
.
These findings confirm the adaptability of TPRV1 to different physiological environments and the mechanism of how to mediate the transport of ions of different sizes across the membrane
.
Dr.
Kaihua Zhang, a postdoctoral fellow at the University of California, San Francisco, is the first author of the paper.
Professor Yifan Cheng from the Department of Biochemistry and Biophysics at the University of California, San Francisco and Professor David Julius from the Department of Physiology are the co-corresponding authors
.
The David Julius laboratory discovered TRPV1 in 1997, and confirmed that it is an ion channel that can be activated by heat and capsaicin to cause pain
.
Cheng Yifan's laboratory has been engaged in research on cryo-electron microscopy methods and applications
.
The two laboratories have a long-term cooperation.
In 2013, the single-particle cryo-electron microscopy method was used to analyze the atomic structure of TRPV1 for the first time, which triggered a revolution in structural biology
.
In 2016, Dr.
Kaihua Zhang joined this cooperative team for postdoctoral research
.
He successfully applied the advantages of single-particle cryo-electron microscopy technology in analyzing the heterogeneity of samples, and further explained the relationship between TRPV1 structure and function through the study of the intermediate state structure, and interpreted the protein analysis machine from a biological perspective.
The importance of intermediate structure
.
These findings will help to understand more deeply the function of TRP family ion channels and even other signaling proteins, and provide new ideas for the development of drugs targeting TRPV1
.
As far as structural biology is concerned, especially in the context of the use of artificial intelligence for structure prediction, the use of single-particle cryo-electron microscopy to capture the intermediate state structure to explain the function of the protein may be a new research direction in the future.
.
Link to the paper: https://doi.
org/10.
1016/j.
cell.
2021.
08.
012 open for reprinting, welcome to forward to Moments and WeChat groups
