Biochemical controls: the kidney (Introduction)

by David Turell @, Monday, April 25, 2022, 20:47 (218 days ago)

The kidney does manythings at once to produce proper urine:

"Proper function of the kidney is critical for concentrating urine, regulating blood pressure, and for the tight control of electrolyte levels in the blood. The kidney achieves these important functions through many microscopic functional units, called nephrons. These nephrons consist of different segments with distinct functions. How these segments form during development and how their function is maintained in the adult is only partially understood.


"The distal nephron is particularly important for the ability of the kidney to concentrate urine, regulate blood pressure, and control calcium and magnesium blood levels. Parts of the distal nephron have specific salt transporters, which are the main targets of medicine's most effective diuretics, used in the treatment of hypertension and chronic kidney disease. Thus, understanding how their function is regulated has important implications for these common diseases.


"Previously, Marneros showed in work published in Developmental Cell in 2020 that AP-2β is required for the formation of the segment of the distal nephron that is targeted by thiazide diuretics: the distal convoluted tubule. This prompted him to ask whether the closely related protein AP-2α also has a function in the kidney. His team found that while AP-2β function in the kidney is required for survival by regulating the development and function of distal convoluted tubules, AP-2α is important for the proper function of a different segment of the distal nephron, called the collecting duct, which is involved in the kidney's ability to concentrate urine. Notably, loss of even only half of AP-2β levels causes progressive kidney disease, whereas complete loss of AP-2α resulted in less severe kidney abnormalities.

"'These findings show that AP-2α and AP-2β are important regulators of distinct segments of the distal nephron. These new observations in genetic mouse models are important contributions to our understanding of how specific segments of the kidney are regulated on a molecular level," says Marneros."

Comment: As in all these situations, everything must work together from the start, or it won't work. That is irreducible complexity as must be fully designed from the start to work properly. Mutating it bit by bit is impossible. This intact functkon had to first appear in the Cambrian explosion.

Biochemical controls: how enzymes work

by David Turell @, Monday, April 25, 2022, 21:08 (218 days ago) @ David Turell

Picking their activity apart:

"This concept is known as "electrostatic stress." For example, if the substrate (the substance upon which the enzyme acts) carries a negative charge, the enzyme could use a negative charge to "stress" the substrate and thus facilitate the reaction. However, a new study by the University of Göttingen and the Max Planck Institute for Multidisciplinary Sciences in Göttingen has now shown that, contrary to expectations, two equal charges do not necessarily lead to repulsion, but can cause attraction in enzymes. The results were published in the journal Nature Catalysis.

"The team investigated a well-known enzyme that has been studied extensively and is a textbook example of enzyme catalysis. Without the enzyme, the reaction is extremely slow: in fact, it would take 78 million years for half of the substrate to react. The enzyme accelerates this reaction by 1017 times, simply by positioning negative and positive charges in the active centre. Since the substrate contains a negatively charged group that is split off as carbon dioxide, it was assumed for decades that the negative charges of the enzyme serve to stress the substrate, which is also negatively charged, and accelerate the reaction. However, this hypothetical mechanism remained unproven because the structure of the reaction was too fast to be observed. (my bold)


"Unexpectedly, the negative charges of enzyme and substrate did not repel each other. Instead, they shared a proton, which acted like a kind of molecular glue in an attractive interaction. "The question of whether two equal charges are friends or foes in the context of enzyme catalysis has long been controversial in our field, and our study shows that the basic principles of how enzymes work are still a long way from being understood," says Tittmann. The crystallographic structures were analysed by quantum chemist Professor Ricardo Mata and his team from Göttingen University's Institute of Physical Chemistry. "The additional proton, which has a positive charge, between the two negative charges is not only used to attract the molecule involved in the reaction, but it triggers a cascade of proton transfer reactions that further accelerate the reaction," Mata explains.

"'We believe that these newly described principles of enzyme catalysis will help in the development of new chemical catalysts," says Tittmann. "Since the enzyme we studied releases carbon dioxide, the most important greenhouse gas produced by human activities, our results could help develop new chemical strategies for carbon dioxide fixation.'"

Comment: this shows how enzymes work, as if they knock two heads together, and demand cooperation. Enzymes force reactions to occur at the high-speed life's biology requires. Each giant enzyme molecule is precisely designed for each reaction it speeds up. Organic chemistry uses molecules that won't react quickly by themselves. Unfortunate, but those molecules are the only ones that will work. God knows what He is doing even if dhw has doubts with his second-guessing. It seems agnostics know better than God how to do things.

Biochemical controls: the kidney pumps blood

by David Turell @, Wednesday, May 18, 2022, 15:24 (196 days ago) @ David Turell

The kidney doesn't just filter blood, it pumps it along:

"Human kidneys are an intricate network of tubes that process roughly 190 quarts of blood every day. Lining these tubes are epithelial cells that transport blood through the kidneys and circulate it back into the body. How these immobile cells generate the mechanical force needed to do their job is not fully understood. To unlock the secrets of this fluid transport process, a Johns Hopkins mechanical engineer has created a device that measures mechanical forces generated by both healthy and diseased kidney cells.

"'Fundamental physical laws say that you need forces to move things. In this case, the cells are not moving, but they are moving fluid. The question then becomes how do they do this?" said Sean Sun, a professor in the Whiting School of Engineering's Department of Mechanical Engineering and a core member of the Institute for NanoBioTechnology.


"The researchers noticed that kidney epithelial cells behave like mechanical fluid pumps and actively generate a fluid pressure gradient. The fluid pumping behavior is characterized by a pump performance curve, which is very much like a water pump in a house. Most people believe that kidneys behave like a conventional filter, which needs external pressure to move fluid. However, Sun and his team showed that cells can actually generate the needed pressure themselves—an insight with important implications for understanding kidney physiological function.

"'Everyone hears that kidneys filter blood, but conceptually that is incorrect. What we showed is that kidney cells are pumps, not filters, and they are generating forces," Sun said."

Comment: kidney blood vessels are extremely tiny, and the arterial blood delivered to them under pressure must be reduced to almost zero for proper filtration. That an extra push is designed into kidney cells is not surprising, but is necessary. Such complexity is irreducibly complex as it must be designed all at once for the kidney system to work.

Biochemical controls: controlling cell protein output

by David Turell @, Tuesday, May 31, 2022, 19:20 (183 days ago) @ David Turell

The body has control systems that drive production and slow production in a tight fashion:

"Cells produce proteins like little factories. But if they make too much at the wrong times it can lead to diseases like cancer, so they control production with a process called RNA interference (RNAi).


"They [a research group] recently discovered how RNAi's workhorse protein Argonaute (Ago) leverages limited resources to keep protein production on track.

"It's important to understand exactly how RNAi works because it's such a basic and heavily used process, Joshua-Tor said. It also offers a kind of safety net for therapeutics because it doesn't make permanent changes to cells and can be reversed.


"Ago helps cut off protein production by finding, binding, and destroying molecules called mRNA—which tell cells to make proteins. But the amount of Ago in the body pales in comparison to the amount of mRNA it must target. After destroying one MRNA molecule, the protein is still capable of finding another but it can't move on without help. Bibel discovered how cells use a process called phosphorylation to break Ago's grip on a mRNA target, allowing it to commute to the next.

"Bibel explains that their "theory is that having phosphorylation promote release is a way that you could free up Argonaute because when the target gets released, the guide's still there and it's super duper stable. So our thinking is that by phosphorylating it, you're going to free it to go repress other targets—because it's still totally capable of doing that work.'"

Comment: more evidence of purposeful design. Controlling production rates is vital, so start and stop controls must be designed together all at once.

Biochemical controls: intracellular electrical controls

by David Turell @, Saturday, September 10, 2022, 15:54 (81 days ago) @ David Turell

Using very advanced techniques:

"New findings reported in PNAS by Toyama et al. are uncovering a role for electrostatics in enzymatic activity. Simultaneously, the discovery may offer insight into the function of so-called “disordered proteins” that never fold into stable structures, and other proteins containing disordered regions that would seem to flail about like loose cables. But there is order in the disorder! How big is this discovery?

"Electrostatic interactions play important roles in regulating a plethora of different biochemical processes and in providing stability to biomolecules and their complexes (my bold)

"What the team from the University of Toronto found, discussed below, was only made possible by “solution NMR spectroscopy.” This technique allows them, for the first time, to measure the near-surface electrostatic potentials of individual atoms in proteins and follow changes in those potentials during an enzyme’s action.

"Our results collectively show that a subtle balance between electrostatic repulsion and interchain attractive interactions regulates CAPRIN1 phase separation and provides insight into how nucleotides, such as ATP, can induce formation of and subsequently dissolve protein condensates.

"CAPRIN1 (cell cycle associated protein 1) is an RNA-binding protein “localized to membraneless organelles playing an important role in messenger RNA (mRNA) storage and translation.” It may act as a negative regulator of translation, confining mRNAs in condensates at times to prevent overproduction of proteins. “CAPRIN1 is found in membraneless organelles, such as stress granules, P bodies, and messenger RNA (mRNA) transport granules, where, in concert with a variety of other RNA-binding proteins, it plays an important role in regulating RNA processing,” the paper explains.

"CAPRIN1 contains IDP tails at both ends which, it turns out, are the key to condensate formation. The Toronto team found, importantly, that ATP plays a dynamic role in the electrostatic changes of CAPRIN1, especially in its IDP regions. In brief, here is what happens (see Figure 5 in the paper). Specific amino acid residues in the IDP regions confer on them a net positive charge. This makes the tails repel each other, resisting condensate formation (and preventing self-association of the tails). When ATP attaches to the IDP regions, however, the net charge is reduced, permitting intermolecular interactions. As more ATP is added, the collection becomes neutral, and a condensate forms. Additional ATP inverts the electrical potential, making it negative. Electrostatic repulsion ensues again, causing breakup of the condensate, separating the contents and freeing them up for the next round.

"This implies that condensate formation has an electrical aspect to it. Since it relies on the sequence and position of specific amino acid residues, one might even call it an electric code.


"The information in the sequence of amino acids, and of the codons in the genes that encode them, appears to play critical roles in condensate formation and, simultaneously, in enzymatic behavior. Some amino acids they dub “stickers” promote phase separation. The specific electrostatic attractions and repulsions that give rise to the enzyme’s function during condensate formation and dissolution is dependent on the positions of these stickers.

"This remarkable revelation begins to give insight into the participation of cell coding with electrophysics. Get a charge out of that!

"CAPRIN1 coexists with negatively charged RNA molecules in cells and, along with FMRP and other proteins, is implicated in the regulation of RNA processing and translational activity. Thus, electrostatics play a central role in modulating the biological functions of this protein, and measurement of electrostatic potentials at each site along its backbone, as reported here, provides an opportunity to understand in more detail the important role of charge in this system. (my bold)

"The paper only investigated one enzyme, so caution is advised before generalizing. The authors feel, though, that this electrical code model will help explain many other processes that require molecules to come together, perform their work, and then separate. It’s the new Electric Cell."

Comment: electrostatic controls add another amazing layer to the complexity of the cell. Since all proteins contain charged areas the use of electrostatic charges to control molecular movements makes perfect sense.

Biochemical controls: reading DNA

by David Turell @, Saturday, September 10, 2022, 16:16 (81 days ago) @ David Turell

At enormous speeds:

"This team worked on a helicase enzyme named PcrA, which unwinds DNA for transcription. This enzyme works so fast (1000 bases per second!) it’s been like trying to describe the blur of a racecar speeding down a track. Using a new technique called “single-molecule picometer-resolution nanopore tweezers” (SPRNT), they were able to slow down the action and watch the racecar move with its “inchworm mechanism” one base at a time. This blends chemistry with another branch of physics, mechanics: “mechanochemistry.” (my bold)

"We recorded more than two million enzyme steps under various assisting and opposing forces in diverse adenosine tri- and diphosphate conditions to comprehensively explore the mechanochemistry of PcrA motion.…Our data reveal that the underlying DNA sequence passing through the helicase strongly influences the kinetics during translocation and unwinding. Surprisingly, unwinding kinetics are not solely dominated by the base pairs being unwound. Instead, the sequence of the single-stranded DNA on which the PcrA walks determines much of the kinetics of unwinding.

"The authors are not clear why this is. What is evolution up to? They figure that there must be a reason.

"Unlike protein filaments (e.g., actin), DNA is not a homogeneous track; sequence-dependent behavior may be the norm rather than the exception. Strong sequence-dependent enzyme kinetics such as those observed in our data likely affect PcrA’s role in vivo and could thereby exert selective pressure on both DNA and protein evolution. Therefore, sequence-dependent behavior should be carefully considered in future studies of any enzyme that walks along DNA or RNA, since the sequence-dependent kinetics may reveal essential features of an enzyme’s function. Such effects are almost certainly used by life to achieve various ends, and SPRNT is well suited to discovering how and why such sequence dependence occurs and opens the possibility of uncovering enzyme functions that were hereto unknown.

"Why are they giving the credit to blind evolution? If life uses “sequence-dependent kinetics…to achieve various ends,” that sounds like intelligent design, not evolution. Design advocates are accustomed to forgiving logical malapropisms like this. They look past the magical thinking and see the operation of a designing mind with foresight and purpose, intimately familiar with the laws of physics, able to write code to utilize those laws in precision operations. Now, it becomes clear that the precision goes deeper than previously known."

Comment: The final paragraph is pure ID thought. The unwinding speed of PcrA is amazing. What should be mentioned is all enzymes are giant molecules of thousands of amino acids. How did natural evolution find it?

Biochemical controls: an enzyme controls growth

by David Turell @, Monday, October 31, 2022, 17:10 (30 days ago) @ David Turell

Its form is discovered:

"Danish researchers have determined the three-dimensional structure of the proteolytic enzyme PAPP-A. The results may allow us to better understand the basic biology that regulates linear growth of vertebrates. The same regulatory mechanisms are also involved in several age-related diseases, and thus, the research is an important step towards the development of novel types of drugs.

"The growth factor IGF plays a key role in human growth. In the absence of IGF signaling, we become dwarfs. Later in life, IGF is involved in age-related diseases, such as cancer and cardiovascular disease. In both cases, IGF must be converted from an inactive to an active form. This is what PAPP-A is able to do.

"'Seven years ago we discovered that the protein STC2 blocks the activity of PAPP-A, thus indirectly inhibiting the activity of the IGF growth factor. To block the activity, STC2 must form a complex with PAPP-A. We have studied this complex, and we now know its three-dimensional structure," Professor Claus Oxvig explains.

"'It is fascinating to see what a molecule, we know biochemically very well, actually looks like. PAPP-A is heart-shaped with an inner 'chamber'. But from a research point of view, the shape is not the most interesting feature. Rather, it is the interactions between the different elements of the molecule."

"There are still many unanswered questions about the molecular mechanisms, which regulate how much IGF is converted into the active form. It is likely that complex formation between PAPP-A and STC2 is highly regulated. Such a hypothesis is supported by earlier findings showing that natural human variants of STC2, in which just a single amino acid is substituted, form the complex with PAPP-A slightly slower. The consequence of this is that slightly more IGF can be activated by PAPP-A, resulting in an increase in height of up to 2.1 cm."

Comment: Same old point: this must be a designed mechanism because of the complexity of the enzyme molecule and the feed-back controls.

Biochemical controls: dumping cell waste

by David Turell @, Monday, October 31, 2022, 18:25 (30 days ago) @ David Turell

A new control found:

"A vast number of biological reactions occur inside cells, generating various byproducts. Some of these can be highly reactive molecules, and if they build up inside cells they can cause stress and damage. One class of these molecules, reactive sulfur species (RSS), are known to play biological functions, but it was unknown how cells respond to an accumulation of RSS. Now, researchers have described a system by which excess RSS can be actively transported out of cells.

"Chemical reactions constantly occur in cells, including two opposing reactions known as oxidation and reduction, and so it is key that this balance, known as "redox homeostasis," is maintained for the health of cells. RSS have been shown to act as antioxidants to protect against oxidative stress and maintain redox homeostasis, but an excess of RSS can also lead to sulfur stress.

"By creating a strain of mice that generated excessive RSS, the team were able to show that the levels of RSS rose in the extracellular space but not inside the cells, suggesting an active mechanism to transport RSS out of cells. "The strict regulation of the cellular levels of RSS that we observed suggests the presence of an adaptive cellular mechanism controlling the RSS levels, which most likely exists to protect against sulfur stress," explains senior author Professor Yoshito Kumagai.

"Transporter proteins are responsible for moving molecules out of cells. The team found that an amino acid called cystine was key in the export of RSS, suggesting that a particular transporter called SLC7A11 is involved in the transport of RSS. SLC7A11 is known to bring cystine into the cell while pumping another amino acid called glutamate out. As cystine is a sulfur-containing molecule, it was a surprising finding that SLC7A11 both imports cystine and exports RSS.

"Sulfur stress caused by high levels of RSS can lead to cell death. This is thought to be involved in a variety of human health conditions, including diseases of the heart (cardiomyopathy) and muscles (muscular dystrophy). Therefore, the surprising and significant results of this study will open new and previously unconsidered avenues for research into sulfur stress and related diseases."

Comment: this new system fits the definition of irreducibly complex. It had to be designed all at once.

Biochemical controls: protein folding follows rules

by David Turell @, Monday, October 31, 2022, 22:06 (29 days ago) @ David Turell

As shown by an AI program:

"There’s an age-old adage in biology: structure determines function. In order to understand the function of the myriad proteins that perform vital jobs in a healthy body—or malfunction in a diseased one—scientists have to first determine these proteins’ molecular structure. But this is no easy feat: protein molecules consist of long, twisty chains of up to thousands of amino acids, chemical compounds that can interact with one another in many ways to take on an enormous number of possible three-dimensional shapes. Figuring out a single protein’s structure, or solving the “protein-folding problem, can take years of finicky experiments.

"But earlier this year an artificial intelligence program called AlphaFold developed by the Google-owned company DeepMind, predicted the 3-D structures of almost every known protein—about 200 million in all.


"There are 32 different component algorithms, and each of them is needed. It’s a pretty complicated architecture, and it needed a lot of innovation. That’s why it took so long. It was really important to have all these different inputs from different backgrounds and disciplines. And I think something we do uniquely well at DeepMind is mix that together—not just machine learning and engineering.


"One of the things we built in was this understanding of chemical bond angles and also evolutionary history using a process called multisequence alignment. These bring in some constraints, which help to narrow the search space of possible protein structures. The search space is too huge to do by brute force. But obviously, real-world physics solves this somehow because proteins fold up in nanoseconds or milliseconds. Effectively, we’re trying to reverse engineer that process by learning from the output examples. I think AlphaFold has captured something quite deep about the physics and the chemistry of molecules."

Comment: the underlying principle is every atom has a charge which dictates its contribution
to the folding by the attraction of the different charges. The AI program understand this. So, in thinking about design folding is not much of a design problem. It is the sequence of atoms in the protein that is required to be designed with an anticipated understanding of the desired protein function to be expressed. Not by chance.

Biochemical controls: plant wound signals

by David Turell @, Saturday, October 22, 2022, 16:57 (39 days ago) @ David Turell

How plants signal damage:

"John Innes Center researchers have shown that calcium waves are not a primary response, but rather they are a secondary response to a wave of amino acids released from the wound.


"It has been observed for many years that wounding, and other trauma, initiates calcium waves that travel both short distances from cell to cell, and longer distances from leaf to leaf.

"These calcium waves are reminiscent of signaling seen in the nerves in mammals, but since plants do not have nerve cells, the mechanism by which this happens has been in question.

The new findings, which appear in Science Advances, suggest that when a cell is wounded, it releases a wave of glutamate, an amino acid. As this wave travels through plant tissues, it activates calcium channels in the membranes of the cells it passes. This activation appears like a calcium wave but is a passive response, or "readout'' of the moving glutamate signal.


"Dr. Faulkner's group specializes in the study of plasmodesmata, the channels or bridges that connect cells and the team speculated that a wound signal would travel from cell to cell through plasmodesmata. However, using quantitative imaging techniques, data modeling and genetics they found that the mobile signal is a glutamate wave that travels outside of cells, along the cell walls.

""The glutamate and calcium waves are connected—glutamate triggers the calcium response. You could imagine it with an analogy of a corridor. The glutamate rushes down the corridor and as it passes a door it kicks it open. The calcium response is the door opening. Up to now the assumption has been that what moved down the corridor was hydraulic pressure or a series of propagating chemical reactions, but our study shows that this is not the case," said Dr. Faulkner."

Comment: a different way to spread information without nerves.

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