Joseph P.

How Mitochondrial Dynamism Orchestrates Mitophagy

Authors Orian S. Shirihai, Moshi Song, Gerald W. Dorn II

@explainpaper

Understanding the Significance of Mitochondrial Fission and Fusion

Mitochondrial dynamics refers to the movement of within a cell. This includes , which is when mitochondria divide into two parts, , which is when two mitochondria join together, and , which is when mitochondria move from one part of the to another. This movement is important for maintaining the stability of the mitochondrial , which is the genetic material found in mitochondria, and for controlling the cell's . It can also be involved in programmed . In the , mitochondrial dynamics s, such as s, optic , and dynamin-related protein, are highly expressed and play an important role in maintaining the quality of the . Other roles for mitochondrial dynamics proteins in the include helping to move into the mitochondria and regulating the structure of the mitochondria.

are organelles in cells that are responsible for producing . They can change their structure by breaking apart () and reforming (). This process is complicated and energy intensive, so it is important to understand why it is necessary. One reason may be that when cells divide, the mitochondria need to be divided equally between the two daughter cells. This requires the to be broken apart and then reformed in each daughter . This process of breaking apart and reforming is more efficient than growing and budding the mitochondria. To help explain this process, the authors use the analogy of an army. Each soldier in the army is like a protein in the mitochondria, and the different units of the army are like the different parts of the . To increase the size of the army, units are added, rather than individual soldiers. This is similar to how mitochondria are modified, by adding or subtracting intact functional units, rather than individual s.

Mitochondria are s in cells that can change their physical structure by undergoing fission. Fission can be symmetrical, which is when mitochondria replicate and expand the number of in the , or asymmetrical, which is when damaged components of the mitochondria are removed. The major that helps with mitochondrial fission is called Drp1. It is mostly found in the , but it needs to be recruited to the outer mitochondrial to help with fission. Different factors can cause Drp1 to be recruited, such as phosphorylation by mitotic kinase cyclin B–cyclin-dependent-kinase (cdk) 1 complex during division, or interacting with Bcl-2–associated protein x during . Inhibiting Drp1 can protect cells from some, but not all, forms of programmed cell death.

Mitochondria, which are organelles in cells, can be partitioned in . The most efficient way to do this is by dismantling and then reconstituting the cellular network through sequential fission, distribution, and refusion. To explain this concept, the text uses an analogy of how military units are constituted and managed within an army's hierarchical organization structure. In this analogy, each soldier represents an individual respiratory complex , which are grouped together to form a squad (analogous to a respiratory complex). Squads are arranged into platoons, and approximately 6 platoons comprise a functional unit, the company (like 1 complete respiratory chain). The text suggests that it would be easier to add prefabricated supercomplexes to preexisting ones, as by fusing mitochondrial cristae, rather than trying to make a larger or different shaped mitochondrion through the wholesale incorporation of individual proteins. This is because making major structural modifications of respiratory supercomplexes on paracrystalline cristal membranes would first require destabilizing the , then incorporating additional individual components, and finally reconstructing the original highly organized structure, which is complicated and potentially disruptive.

are small organelles in cells that can change their physical structure by undergoing fission. Fission can be symmetrical, which means the are split into two equal parts, or asymmetrical, which means the mitochondria are split into two unequal parts. Symmetrical fission is used to replicate and expand the number of mitochondria in the , while asymmetrical fission is used to remove damaged mitochondria from the cell. The major responsible for mitochondrial fission is called Drp1. Drp1 is mostly found in the cytosol, but it needs to be recruited to the outer mitochondrial to promote fission. Different factors can stimulate Drp1 to move to the outer mitochondrial , such as phosphorylation by mitotic kinase cyclin B–cyclin-dependent-kinase (cdk) 1 complex. In addition, the endoplasmic reticulum (ER) is often found at the sites of mitochondrial fission. If Drp1 is not present, the mitochondria can still fragment during , suggesting that there are other mechanisms that can promote mitochondrial fission.

The text is talking about the process of mitochondrial fission, which is a process that involves connecting and separating parts of a . The author uses the metaphor of making sausage links to explain the process, but then goes on to explain that mitochondria are actually more like a turducken, which is a dish made of a chicken stuffed inside a duck stuffed inside a turkey. This creates layers of poultry, which is similar to the double /double space structure of . The author then explains that the process of mitochondrial fusion involves connecting the two mitochondria layer by layer, using proteins called mitofusins. Mitofusins have a domain, two hydrophobic heptad repeat coiled-coil domains, and a small hydrophobic transmembrane domain. These proteins insert into the outer of the , and can interact with other proteins in the cytosol. The process of mitochondrial fusion is GTP-independent and reversible, but is essential for irreversible outer membrane fusion.

are proteins that are essential for the first two stages of mitochondrial fusion, which is the process of two mitochondria joining together. This process is important for the exchange of information between the and the . If the mitofusins are deleted or suppressed, the mitochondria become abnormally small and are unable to undergo normal fusion. This can have serious implications for the health of the .

Membrane-by-membrane mitochondrial fusion is a process that helps to keep the structure of the inner and outer membranes of intact. This helps to preserve the process of oxidative phosphorylation, which is important for providing energy to cells. Without this process, molecules that can be toxic to cells can form and interrupt the electron transport chain. This process is also important for maintaining the normal shape of the crista, which is necessary for the proper assembly and functioning of electron transport chain supercomplexes. In addition, it has been shown that interrupting Mfn-mediated OMM fusion can cause a ER stress response, while interrupting Opa1-mediated IMM fusion can compromise mitochondrial function.

Mitochondrial fission and fusion are important processes in , as evidenced by the fact that mutations in genes related to these processes can cause serious diseases in humans. Altering the balance between fission and fusion can have an effect on the shape of , with more fusion leading to longer, more interconnected mitochondria, and more fission leading to shorter, less interconnected mitochondria. It is generally thought that more interconnected are healthier, but this is not always the case. In some cases, mitochondrial can be beneficial, and it is important to understand the interplay between mitochondrial fragmentation and other processes, such as , in order to understand the effects of mitochondrial fission and fusion.

Mitophagy is a process by which cells eat their own . Mitochondria are organelles that produce energy in the form of , which is used to power most biological processes. Over time, mitochondria can become damaged and produce toxic levels of reactive oxygen species ( ). To protect the from this damage, it has developed a sophisticated system to identify and remove these dysfunctional . This process is called mitophagy. is a combination of the words mitochondria and , which means "self-eating". It is a way for cells to selectively target and remove damaged mitochondria, while still keeping healthy ones. This helps to maintain the balance between having enough energy-producing and getting rid of the ones that are no longer functioning properly.

Pulse chase experiments are a type of scientific experiment used to study the behavior of molecules over time. In this particular experiment, researchers found that when (the energy-producing organelles in cells) are targeted for (a process of removing damaged mitochondria from the cell), they have a relatively depolarized potential before being removed. This means that the have a lower electrical charge than normal, and they are less likely to be involved in events (when two mitochondria join together). The time between the mitochondria becoming depolarized and being removed from the cell can range from less than an hour to about three hours, suggesting that there is a population of preautophagic (mitochondria that are about to be removed). This pool helps to explain the variation in mitochondrial potential in different cell types. The process that feeds mitochondria into the preautophagic pool is important for determining how quickly are removed from the . Scientists have developed a technology to label individual mitochondria and track their potential, which has allowed them to identify the event at which depolarized are produced. This event is called asymmetrical fission, and it occurs when the daughter mitochondria produced by the fission event have different potentials - one daughter has a higher membrane potential than the mother mitochondrion, while the other daughter has a lower membrane potential. This process of asymmetrical fission helps to separate damaged components from healthy components before they are removed from the .

The concept of mitochondrial fission and fusion and how it affects mitochondrial quality. It suggests that when the fusion factors Mfn1 and Mfn2 are both absent, unusually small and degenerated accumulate in adult mouse hearts. This was associated with impaired respiration, but not with measurable alterations in consumption. It was later discovered that the isolation procedure used was not capturing the fragmented produced by interrupting mitochondrial fusion. This led to the discovery that Mfn2 is essential to -mediated , which is a process that helps to maintain mitochondrial quality. Three recent papers have also implicated the mitochondrial fission protein Drp1 in cardiac , and it is suggested that if asymmetrical mitochondrial fission normally precedes mitophagy, then chronic suppression of fission by ablating Drp1 would have different consequences on depending on when it is assayed.

Mfn2 and PINK1–Parkin Mitophagy Signaling is a mechanism for controlling the quality of in the body. and are proteins that are linked to 's disease, and mutations in their genes were the first to be identified as causing the disease. Scientists have studied how PINK1 interacts with Parkin, and how this interaction can lead to the destruction of damaged , which is called . is like an ignition switch that senses when mitochondrial damage has occurred, and then activates Parkin-mediated mitophagy. PINK1 is normally not present in healthy , but when mitochondrial damage occurs, PINK1 accumulates and triggers the destruction of the damaged .

PINK1 is a protein that accumulates on damaged mitochondria and helps to promote mitophagy, which is the process of getting rid of damaged mitochondria. PINK1 does this by inducing the cytosolic protein Parkin to move to the mitochondria and ubiquitinate proteins on the outer membrane of the mitochondria. This helps to prevent the spread of damage from the damaged mitochondria to the healthy ones. PINK1 also inhibits the fusion of the damaged mitochondria. There are different theories about the biochemical events that cause Parkin to move to the mitochondria and stop the fusion. It is thought that PINK1 phosphorylates Parkin on certain sites, which helps Parkin bind to the mitochondria. It is also thought that PINK1 phosphorylates ubiquitin, which helps Parkin bind to the mitochondria and ubiquitinate proteins on the outer membrane. Finally, it is thought that PINK1 phosphorylates Mfn2, which helps Parkin bind to the mitochondria and ubiquitinate proteins on the outer membrane. All of these processes help to promote mitophagy and prevent the spread of damage from the damaged mitochondria to the healthy ones.

is a protein that plays an important role in a process called , which is a form of quality control for mitochondria. Mutations in the have been linked to hereditary 's disease in humans, but when the PINK1 gene is deleted in mice, it does not cause the same pattern seen in humans. Even when the genes for PINK1, Parkin, and DJ-1 are all deleted in mice, it still does not cause the same loss of dopaminergic s seen in 's disease patients. This suggests that there may be other pathways that can compensate for the loss of and , such as increased transcription of other E3 ligases in the hearts of Parkin-knockout mice.

The text is discussing the idea of mitochondrial quality control pathways, which are processes that help keep mitochondria healthy. The text is suggesting that there may be alternate pathways that can be used to maintain mitochondrial health, rather than waiting until the mitochondria are completely depolarized before triggering their removal. It is comparing this idea to the idea of maintaining a car, where it is better to perform regular maintenance and repairs rather than waiting until the car is completely broken down before replacing it.

Like a car, mitochondria can be maintained through preventative maintenance, such as replacing worn parts, and that more serious damage can be repaired by removing and replacing individual components. It also suggests that, like a car, can be repaired by removing and replacing damaged parts, but on a smaller scale. The different types of maintenance and repair may be part of a continuum, rather than distinct categories.

and mitochondrial dynamism are two processes that are closely connected. Mitophagy is the process of removing damaged from the , while mitochondrial dynamism is the process of mitochondria fusing together and separating. The two processes work together to keep the cell healthy by eliminating damaged mitochondria and preventing healthy mitochondria from being contaminated by the damaged ones. The protein plays a role in both processes, acting as a factor for mitochondrial fusion when it is not acted on by and as a receptor for when it is. This suggests that the two processes are mutually exclusive, meaning that they cannot happen at the same time. This helps to protect healthy from being contaminated by the damaged ones. Finally, the involvement of PINK1 and Parkin in multiple mitochondrial quality control mechanisms shows that there are multiple ways to keep the healthy, which is important for preventing chronic degenerative diseases and providing opportunities for intervention.

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Joseph P.

@explainpaper

Tumoral Immune Cell Exploitation in Colorectal Cancer Metastases Can Be Targeted Effectively by Anti-CCR5 Therapy in Cancer Patients

Niels Halama, Inka Zoernig, Anna Berthel, Christoph Kahlert, Fee Klupp, Meggy Suarez-Carmona,Thomas Suetterlin, Karsten Brand, Juergen Krauss, Felix Lasitschka, Tina Lerchl, Claudia Luckner-Minden, Alexis Ulrich, Moritz Koch, Juergen Weitz, Martin Schneider, Markus W. Buechler, Laurence Zitvogel,
Thomas Herrmann, Axel Benner, Christina Kunz, Stephan Luecke, Christoph Springfeld, Niels Grabe, Christine S. Falk, and Dirk Jaeger

Targeting Tumor-Promoting Microenvironment Through CCR5 Blockade in Metastases

progression is a process in which cancer cells and cells interact with each other in a way that can lead to the growth and spread of cancer. In cancer, when the cancer has spread to other parts of the body, it is called and it is very difficult to treat. Treatments such as PD-1/PD-L1 blockade and modulation have been successful in modifying the interactions between the immune system and cancer, leading to the rejection or suppression of progression. Cancer cells can also alter the immune microenvironment, leading to and evasion. In this research paper, the authors studied the microenvironment in metastases and identified a network of cells and immune cells that exploit the CCL5-CCR5 axis. They then investigated and characterized the effects of blocking the CCL5-CCR5 axis.

the microenvironment of metastases of cancer ().

the environment induces migration of T lymphocytes, which produce a called CCL5. This CCL5 then supports tumor growth and spread by influencing macrophages and cells. The environment is immunosuppressive and the tumor cells are exploiting the host's cells to their advantage. In other words, the tumor cells are using the host's immune cells to help them grow and spread.

the effects of CCR5 blockade on the level.

Tumor death and a specific pattern of and modulation are observed in the and in biopsies from a . Macrophages are the key for these anti-tumoral effects, as they produce IFNs and reactive oxygen species which cause tumor cell death. blockade induces a phenotypic shift in the macrophages, which is referred to as a switch from an M2 to an M1 phenotype. This repolarization also reduces levels of CD163+ cells, reshaping the cell composition in the microenvironment. The influx of new effector cells due to CCR5 inhibition can shift the effects of CCL5 towards beneficial effects, such as reduction of , , and resistance.

The microenvironment of the invasive margin of metastases.

There was no relevant Th1, Th2, or Th17 signature present in any of the samples. However, the authors did find that and -related cytokines were significantly increased at the invasive margin. Chemokines are molecules that help to attract cells to the area, and macrophage-related cytokines are molecules that help to regulate the activity of , which are a type of immune cell. 98% of the CD3+ s in the resection specimens were positive for PD-1, which is a molecule that helps to regulate the activity of the immune system.

is a protein produced by T cells, which are a type of white blood cell. is a receptor found on metastatic tumor cells, which are cancer cells that have spread from the primary to other parts of the body. In this research paper, it was found that CCL5 has tumor-promoting effects on cells and tumor-associated s. This means that CCL5 has multiple effects on both the cancer cells and the macrophages, which are a type of white , that are associated with the . CCL5 was produced mainly by T cells located at the invasive margin and stroma of metastases, and that CCR5 was dominantly expressed by metastatic tumor cells. CCL5 also had effects on tumor , invasive tumor , and increased production of matrix es by tumor-associated macrophages. Finally, they found that CCR5 inhibition had an effect on key molecules of to transition ( ).

The researchers wanted to test the effects of blockade, which is a way of blocking the CCR5 receptor on cells, using a drug called maraviroc. They used human s, which are samples of from advanced patients with metastases. Maraviroc led to morphologically overt tumor in the , which means that the tumor cells died and changed in appearance. The researchers then tested the hypothesis that s, (type of white blood cell), were required for the tumor cell death-inducing effects of CCR5 blockade. They used clodronate s to deplete CD163+ TAMs, ( s associated with tumors) and found that combining clodronate with CCR5 inhibition abrogated the immediate tumor cell death-inducing effects of inhibition. This confirmed the role of macrophages in this process. IFN-g induced stromal CD163+ death and led to a reconfiguration of the cell compartment. Inhibition of macrophage-derived reactive oxygen species could partially block the anti-tumoral effects of CCR5 inhibition. Finally, they tested the effects of CCL5/CCR5 inhibition and found that both a CCL5 neutralizing antibody and a CCR5 blocking had similar functional effects to maraviroc.

A (MARACON) was conducted to test the effects of a drug called maraviroc on patients with advanced-stage colorectal . The involved taking biopsies of the patients before and after treatment with maraviroc, and the results showed that the drug had beneficial effects on the tumor-promoting and led to objective clinical responses. These responses included induction of central , reduction of tumor cell death, and reduction of key s and growth factors that promote tumor growth. The drug was also found to be very well tolerated, with mild elevation of enzymes being the most common side effect. Finally, the trial showed that partial responses were achieved in patients with previously refractory disease.

CCR5 blockade, is a type of used to treat .

The MARACON clinical trial, showed that CCR5 blockade had a positive effect on the tumor microenvironment and led to a higher response rate in subsequent chemotherapies. The authors suggest that this effect is not limited to the metastases, but is a systemic feature. They also suggest that the local presence of multiple layers of subversion in cancers depends on the individual tissue, , tumor type, and the difference between primary and metastatic lesion. The authors also found that the results of the were in line with the results of a fully human organotypic tumor , which is a simple model with a straightforward approach. The authors also note that the survival data from the trial is not conclusive due to the limited number of patients, but that the objective treatment responses are very encouraging. They suggest that CCR5 blockade may be a promising approach and needs to be evaluated further scientifically and clinically.

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Joseph P.

Using Human Pluripotent Stem Cells to Create Human Skeletal Muscle Organoids for Repair and Regeneration 

Skeletal is a type of tissue that makes up a large part of the human body. It is made up of many different cells that are able to contract and move. Skeletal muscle has the ability to itself when it is damaged due to , exercise, or diseases like . A small group of cells called s help with the repair process. Scientists have been trying to create models to study how develops and regenerates. Recently, they have been using human pluripotent to create 3D models of skeletal muscle tissue. However, these models have not been able to recreate the full process of muscle regeneration. In this research paper, the authors introduce a new method of using human pluripotent stem cells to create 3D models of skeletal muscle tissue that can retain the ability to repair itself.

Over the past decades, scientists have used to study , which is regulated by s. These animal models have been very helpful in understanding the mechanisms of muscle , but they don't always accurately reflect the same range of diseases that humans experience. Therefore, researchers have suggested creating reliable in vitro models using human muscle cells. ( s) could be used to create 3D human skeletal muscle s ( s) that contain sustainable and distinct myofibers with the same proteins and structure as adult muscles. Previous approaches to skeletal muscle differentiation have been developed using 2D systems, but these lack the natural environment and niche that are necessary to model adult and muscle .

s ( s) can be used to repair damaged muscle tissue. They explain that SCs can be activated in response to muscle injuries and that other types can contribute to the process of . The author then goes on to explain that s, such as IL-4, can influence the and promote SCs differentiation, which helps with muscle regeneration. While s generated from s have potential, they do not fully replicate the in vivo native microenvironment. To address this, treat the s with extrinsic s to promote . s might then be used to study aspects of human muscle and to identify novel candidates for muscle-wasting disorders.

To create a 3D structure of muscle tissue. They used activator and inhibitors at the beginning of the differentiation process to induce paraxial s. They then added to the Matrigel to promote the 3D structure. and IGF1 were added later to accelerate the specification and further differentiation. They optimized the timing of the Matrigel embedding to day seven. After this, they observed s and withdrew FGF2 to focus on muscle tissue development. They then prolonged the HGF and IGF1 treatment to propagate s. They found that 62% of the was tissue and that it contained PAX7+ / cells, MYOD+ activated/committed s, and MYOG+ s. They also found that 31% of PAX7+/Ki67− and 29% of MYOD−/PAX7+ non-dividing quiescent SCs were present in the mature s. This indicates that the s were able to effectively recreate nic and have regenerative potential. Future studies using sequencing may be necessary to further characterize the different types of cells in s.

The stepwise process to generate human skeletal muscle organoid s (hSkMOs) from human pluripotent stem cells (hPSCs)

The process begins with dissociating s into s and allowing them to form bodies ( s) in low-attachment V-shaped 96-well plates. Then, paraxial differentiation is promoted with activation, BMP inhibition, and FGF2 signaling. The expression of pluripotency markers OCT4 and NANOG decreases, and the expression of markers Brachyury, T-Box transcription factor 6 (TBX6), and mesogenin 1 (MSGN1) increases. To further characterize paraxial al differentiation, TBX6 is ed. After paraxial induction, the s are embedded with growth factor-reduced Matrigel and transferred to a six-well plate on an orbital shaker. Growth factors are then added to the specification media, and s are cultured until the day of analysis. The orbital shaker improves the viability, survival, and differentiation of hSkMOs by increasing the penetration rate of oxygen and nutrients into the core area of hSkMOs. The gradually grow to more than 1.5 mm in diameter by day 60, appearing round-shaped, uniformly sized, and having relatively homogenous morphology. PAX3 and PAX7 are progenitor markers, and their expression is verified by qRT-PCR and sections. The cells appear as clusters, and approximately 9% of PAX7+ cells are double-positive for Ki67 at day 30, demonstrating that proliferating cells are s in hSkMOs. This indicates that the in vitro is able to recapitulate the features of embryonic skeletal development.

The different types of stem/progenitor cells that are involved in myogenesis, the process of muscle formation.

The researchers used qRT-PCR analysis and to identify and characterize the different types of cells. They found that PAX3 and PAX7 (SC markers) were the major population during the early stage of , and that MYOD (proliferating and activated SC marker) and MYOG (differentiated myocyte marker) increased over time. They also observed that MYOD−/PAX7+, MYOD+/PAX7+, and MYOD+/Ki67+ cells accounted for 29%, 6%, and 8% of the putative quiescent, activated, and proliferating s, respectively. MYOD+/PAX7− cells constituted 39% of differentiating myoblasts, and MYOG−/PAX7+ cells constituted 23% of putative quiescent SCs. MYOG+/PAX7− cells accounted for 30% of differentiated s, and 8% and 6% of the MYOG+ cells in s co-expressed PAX7 and Ki67, respectively. This data shows that the researchers were able to identify and characterize different types of skeletal muscle stem/progenitor cells during .

The text is discussing the results of a research study that used hSkMOs (human skeletal muscle s) to study the development of skeletal muscle . The study found that the s grew exponentially in size within two months, and the growth rate then steadily decreased. The researchers then used scanning electron microscopy (SEM) imaging and confocal microscopy to examine the cytoarchitecture of the hSkMOs. They found that the hSkMOs contained a large population of terminally differentiated cells and a small population of preserved myogenic stem/progenitor cells. They also found that the hSkMOs contained a substantial proportion of TITIN+ muscle cells and MAP2-positive s. To further characterize the presence of sustainable stem cells within the mature hSkMOs, they quantified the amount of dormant stem cells by imaging. The results showed that approximately 56%, 31%, and 5% of PAX7+/Ki67- putative dormant stem cells existed throughout the differentiation of hSkMOs at days 30, 70, and 130, respectively. This indicates that the hSkMOs contained mature skeletal muscle properties and had the potential for .

The researchers wanted to see if the s (human muscle s) had the ability to regenerate after damage. To test this, they treated the hSkMOs with a cardiotoxin (CTX) which is known to induce muscle inflammation and damage. They then observed a decrease in PAX7+ and MYOD+ cells in the hSkMOs. To further test the potential of the s, they added interleukin-4 (IL-4) to the medium to promote . After 14 days, they observed a significant increase in MYOG+ myocytes in the CTX-injured hSkMOs with the treatment of IL-4 compared to the CTX-injured hSkMOs without the treatment. This suggests that the hSkMOs have the potential to regenerate muscle tissue after damage.

Generation of Skeletal Muscle Organoids from Human Pluripotent Stem Cells to Model Myogenesis and Muscle Regeneration

Authors :

Min-Kyoung Shin , Jin Seok Bang , Jeoung Eun Lee , Hoang-Dai Tran , Genehong Park , Dong Ryul Lee and Junghyun Jo

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Joseph P.

ATP-Driven Molecular Chaperone Machines

are proteins that help maintain the balance of proteins in the , which is essential for the cell to stay alive. Chaperones are always present in the cell, but they can also be activated in response to . They interact with proteins that are not folded correctly, preventing them from clumping together and helping them to fold correctly. Chaperones don't usually interact with proteins that are already folded correctly. They use from binding and/or hydrolysis to help with and unfolding proteins. Because chaperones are involved in keeping protein balance, they are linked to diseases caused by misfolding, such as and . Therefore, understanding how chaperones work is important for understanding and treating these diseases.

The Hsp70 system is a group of proteins that are found in , cells, and some . They are responsible for binding to unfolded or partially unfolded proteins to prevent them from aggregating and to help them fold correctly. Hsp70 proteins are made up of two parts: a 44 kDa N-terminal ATPase domain and a 28 kDa substrate binding domain with a C-terminal lid subdomain. The domain helps the protein bind and release substrates, while the substrate-binding domain binds to extended chains. Hsp40 proteins, which are also known as J-domain proteins, act as co-chaperones to Hsp70 and help recruit substrates and stimulate the ATPase activity of Hsp70. Hsp40s can also direct Hsp70 to specialized functions and sub-cellular regions.

Hsp90 is a type of molecular chaperone that helps proteins fold correctly. It is made up of three conserved domains: the ATP binding N-terminal domain, the middle domain, and the C-terminal dimerization domain. Hsp90 works by binding to proteins that need to be folded correctly and preventing them from aggregating in an ATP-dependent manner. It also interacts with other proteins, called co-chaperones, which help regulate its ATPase cycle and determine which proteins it binds to. Hsp90 can also act as a buffer for genetic variation by rescuing mutated proteins with altered properties.

The different functions of the Hsp100/Clp proteins.

These proteins contain one or two conserved ATPases Associated with various cellular Activities (AAA1) domains and can act as or . Unfoldases help to unfold proteins and deliver them to a ring , while disaggregases have the unique ability to recover proteins from both amorphous and aggregates. The main difference between the two is the presence of a coiled-coil insertion in the first AAA1 domain in the disaggregases. The Hsp100 proteins usually form hexamers which hydrolyze ATP in either a sequential/random or a concerted manner. structures have been determined of monomeric forms of several Hsp100 proteins, and of the hexamer forms of HslU, ClpX, and ClpC unfoldases. Hexameric forms of various Hsp100’s have been observed at intermediate resolutions by cryo-EM. These structures suggest a typical AAA1 packing arrangement for the unfoldases and an expanded conformation for the Hsp104 disaggregase. The central channels of the Hsp100s are lined by tyrosine residues, located on mobile loops, which bind substrates non-specifically. It is thought that rotations of the AAA1 domains provide the force to unfold the bound substrate and pull it through the channel. Disaggregation and unfolding functions are coupled and regulated via an interaction between the Hsp70 nucleotide-binding domain and the coiled-coil insertion. Recent biochemical and structural data suggest that it is docked on the outside surface of the AAA1 ring. Hsp100/Clp proteins are proteins that have one or two conserved ATPases Associated with various cellular Activities (AAA1) domains. These proteins can act in two different ways: as unfoldases or disaggregases. Unfoldases help to unfold proteins and deliver them to a ring protease, while disaggregases have the ability to recover proteins from both amorphous and amyloid aggregates. The main difference between the two is the presence of a coiled-coil insertion in the first AAA1 domain in the disaggregases. The Hsp100 proteins usually form hexamers which hydrolyze ATP in either a sequential/random or a concerted manner. Structures of these proteins have been determined, which suggest a typical AAA1 packing arrangement for the unfoldases and an expanded conformation for the Hsp104 disaggregase. The central channels of the Hsp100s are lined by tyrosine residues, which bind substrates non-specifically. It is thought that rotations of the AAA1 domains provide the force to unfold the bound substrate and pull it through the channel. Disaggregation and unfolding functions are coupled and regulated via an interaction between the Hsp70 nucleotide-binding domain and the coiled-coil insertion, which is docked on the outside surface of the AAA1 ring.

GroEL is a molecular chaperone machine that binds to proteins to prevent them from aggregating. It is estimated that GroEL binds to around 10% of the proteins in E. coli. The binding site is hydrophobic in character and contains essential hydrophobic residues that line the cavity-facing surface of the apical domain. If one of these residues is changed from hydrophobic to hydrophilic, the binding is abolished. Studies have shown that multiple binding sites act together as a continuous hydrophobic binding surface. It has also been shown that proteins stably bound to are unstructured and that binding of non-native proteins to GroEL can be associated with unfolding. X-ray crystallographic studies have revealed structures of extended or helical peptides bound in the groove formed by helices H and I via hydrophobic interactions. Cryo-EM has also been used to probe the structure of non-native proteins bound to GroEL, which showed that the substrates were bound to helices H and I, with substrate density protruding from the GroEL ring. There is an upper limit, around 60 kDa, to the size of substrate that can fit inside the folding chamber. In summary, GroEL is a molecular chaperone machine that binds to proteins to prevent them from aggregating. It has a hydrophobic binding site that contains essential hydrophobic residues. Studies have shown that multiple sites act together as a continuous hydrophobic binding surface and that proteins stably bound to GroEL are unstructured. X-ray crystallographic and cryo-EM studies have revealed structures of extended or helical peptides bound in the groove formed by helices H and I via hydrophobic interactions. The upper limit to the size of substrate that can fit inside the folding chamber is around 60 kDa.

Structural, biochemical, and biophysical studies have shown how proteins interact with GroEL, a protein-folding machine, and how ATP (a molecule that provides energy for many processes in cells) induces changes in GroEL's shape that allow it to switch between binding to proteins and folding them. Mutational analysis and cryo-EM studies (a type of imaging technique) have revealed that proteins primarily bind to a specific part of GroEL, and that multiple parts of GroEL bind to the protein at the same time. This binding causes the parts of GroEL to extend and expand, which helps to unfold the protein. Additionally, the protein's binding to GroEL provides a mechanical load on GroEL, which helps to further unfold the protein. Finally, when ATP is added, the parts of GroEL rotate, which removes the binding sites from the inside of the chamber and traps the protein in the chamber, which is now capped by GroES (another protein-folding machine). Group 2 are similar to GroEL, but have a slightly different structure. They are found in both eukaryotes (organisms with a nucleus, like humans) and archaea (a type of single-celled organism). They form back-to-back rings and have a high degree of sequence identity/similarity to GroEL. The main difference is an extension in the part of GroEL that forms the lid of the folding chamber. This extension helps to further unfold the protein.

The structural similarities between the Group 2 chaperonins and GroEL, both essential for folding proteins. Group 2 chaperonins have 8- or 9-fold symmetry, meaning that they form back-to-back rings with the same domain structure and a high degree of sequence identity/similarity to GroEL. The main difference between the two is an extension in the helix H equivalent in the apical domain of the Group 2 chaperonin, which removes the need for a GroES co-chaperone. Structural studies of the Group 2 chaperonins in different nucleotide bound states have revealed open, substrate binding and closed, substrate folding conformations similar to GroEL. These conformations involve a large clockwise twist of the apical domains and an inward tilt of the whole subunit, which brings the catalytic Asp in the intermediate domain close to the ATP binding site and closes the folding chamber. The ring expansion/contraction of Group 2 chaperonins is facilitated by the 1:1 nature of their inter-ring interface, allowing the equatorial domains to move more freely than in GroEL.

ATP-driven chaperones are proteins that help other proteins maintain their structure and function. They do this by binding, unfolding, refolding, and disaggregating proteins that are not in their native state. The Hsp70 system uses ATP binding and hydrolysis to regulate the binding and release of substrates. It is also regulated by co-chaperones. Hsp90 uses its ATPase cycle to induce multiple conformations that bind and stabilize or help mature the substrate proteins. It is also regulated by co-chaperones. The Hsp100s use ATP to unfold, thread, and disaggregate substrate proteins. In ATP-dependent proteolysis, the unfoldase is connected to a protease which breaks down the unfolded substrate proteins. The disaggregases, in combination with the Hsp70 system, use ATP-induced conformational changes to disaggregate and unfold substrate proteins. GroEL-GroES uses ATP binding to induce conformational changes to convert from a substrate binding to a substrate folding complex. It may also use the ATP-induced conformational changes to force the substrate to unfold. GroES binding then ejects the substrate from the binding surface, giving it a chance to fold in isolation during the slow ATP hydrolysis step. The archaeal Group 2 chaperonins use ATP-induced domain rotations that are similar to GroEL, but the conformational changes are not in the same order. The eukaryotic cytosol Group 2 chaperonin is similar to the archaeal system, but its ATPase cycle and action appear to be more complex and specific to the substrate.

In conclusion, ATP-driven chaperones are proteins that help other proteins maintain their structure and function by binding, unfolding, refolding, and disaggregating proteins that are not in their native state. Structural studies of GroEL and Group 2 chaperonins have revealed ATP-induced conformational changes that bind, unfold, and refold proteins in the ATP-dependent folding process. GroEL uses ATP binding to induce a conformational change that switches between the substrate binding and substrate folding states. The archaeal Group 2 chaperonins have a similar mechanism, but with a different order of conformational changes. The eukaryotic cytosol Group 2 chaperonin is more complex, indicating different substrate-specific functions. In general, ATP-driven chaperones help to ensure the proper folding of proteins and support the lifecycle of proteins.

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Joseph P.

So i’m wholly convinced has a pretty huge part to play in the future of education. Something like let’s you have a didactic conversation about a lot of surface level topics. But beyond that you can give it personality by for example -ing the output to improve interest, for example in kids.

AI could help teachers in preparing materials and , reducing the amount of time spilling out of their day.

I see AI as the logical next step in improving the system, by making it more efficient and productive while also providing a way to personalize . AI can be used to create personalized learning paths, tailor-made to the style of learning of each , making sure they continue to nurture every one of their interests and passions. AI can also detect symptoms of or disengagement, and suggest activities to smooth their .

For Example a student might be interested in a particular topic , but their parents not so much or their situation makes it hard to connect with s , s, role models, well with something like this they can really enjoy educating themselves on a given subject matter.

within a matter of seconds the AI dreamed up a text based to teach folks about .

jos****@****.***
create a text based decision game to help me learn about cell metabolism

Sure, I can help you create a text-based decision game to help you learn about cell metabolism. Here's a basic outline for the game:

Introduction: The game begins by introducing the player to the concept of cell metabolism and explaining the main objective of the game, which is to help a cell maintain its metabolic balance.

Decision-making: The player is presented with a series of choices that affect the cell's metabolic processes. For example, the player might be asked whether to increase or decrease the cell's production of a particular enzyme, or whether to activate a certain metabolic pathway.

Consequences: Each decision the player makes has consequences for the cell's metabolism. For example, increasing enzyme production might increase the cell's energy production, but it might also increase the cell's demand for oxygen. The player must weigh the pros and cons of each decision and decide which course of action to take.

Feedback: After each decision, the game provides feedback on the cell's metabolic status. This can include information on the cell's energy levels, oxygen levels, and other metrics that reflect the cell's overall health.

Repeat: The game continues in this manner, with the player making decisions and receiving feedback, until the cell's metabolism is in balance. At that point, the game is complete.

I hope this helps! Let me know if you have any other questions.

jos****@****.***
that sounds fun ! let's play the game I have 100 ATP points, let's use ATP to help balance the cell metabolism

Great! To start the game, you have 100 ATP points to use to help balance the cell's metabolism. In each round of the game, you will be presented with a decision that affects the cell's metabolism. For example, you might be asked whether to increase or decrease the production of a particular enzyme, or whether to activate a certain metabolic pathway.

Each decision you make will have consequences for the cell's metabolism. For example, increasing enzyme production might increase the cell's energy production, but it might also increase the cell's demand for oxygen. You must weigh the pros and cons of each decision and decide which course of action to take.

After each decision, the game will provide feedback on the cell's metabolic status. This can include information on the cell's energy levels, oxygen levels, and other metrics that reflect the cell's overall health.

The game continues in this manner, with you making decisions and receiving feedback, until the cell's metabolism is in balance. At that point, the game is complete.

Good luck! Let me know if you have any questions as you play the game.

jos****@****.***
I decide to spend some ATP to produce NAD+

Spending ATP to produce NAD+ is a good decision, as NAD+ is an important cofactor that is involved in many cellular processes, including energy metabolism. Producing NAD+ can help the cell maintain its metabolic balance and support its overall health.

However, it's important to consider the potential costs and benefits of this decision. For example, increasing NAD+ production might require the cell to use more ATP, which could deplete its energy stores. It's also possible that increasing NAD+ production could affect other metabolic processes in the cell, such as oxygen levels or the production of other enzymes.

Therefore, it's important to carefully consider the potential consequences of your decisions and weigh the pros and cons before making a decision. Good luck! Let me know if you have any other questions.

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Joseph P.

Track all cellular agriculture companies around the world

newfarms.io/#companies

Really interesting list when you consider what all is at stake here. Thanks to
@newfarms_io
, I dont know you yet but thanks!

0

cell

6

biomanufacturing

1

med

1

heart

1

biofabrication

1

neuro There is nothing here!

0

eye There is nothing here!

0

proteomics There is nothing here!

0

omics There is nothing here!

0

genomics There is nothing here!

0
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