Category: Biochemistry

What collaboration is currently taking place in protein chemistry and protein folding research?

Answered Dec 21

A recent example is:

Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction

They run an annual competition, where they publicly post primary sequences of proteins.

If I understand correctly, they already know the 3-D structures, but haven’t publicly released those.

Then, many research groups around the world use the primary sequences to attempt to solve the final structures, and submit their predictions.

This year’s winner, by far, was Google’s Deep Mind AI AlphaFold project.

AlphaFold apparently uses a large database of publicly known sequence and structure solutions. Then, it compares those solved sequences with the new sequences. Apparently it makes a number of possible predictions, and finds the one with the lowest final Gibbs energy level.

It’s pretty cool, although it isn’t clear whether their system is just trying to go directly from primary sequence to final structure. Or whether it attempts to find the series of intermediary conformations that real proteins go through. That is important, since one intermediary fold may be required to trigger the next fold.

Is it possible to use machine learning to make predictions with little understanding about the underlying mechanisms, such as predicting the 3D structure of proteins out of the amino acid sequences?

Updated Nov 5

Predictions are already made mathematically, but they are only guesses.

An example is looking for portions of a protein that might be trans-membrane helices, where there is a numerical calculation of hydrophobic side chains in a certain segment. Basically, if you have hydrophobic side chains in a row for 19 or more residues, then they may compose an alpha-helix facing a lipid membrane.

Another version is looking for helices that are hydrophobic on one side, and hydrophilic on the other side.

There are certain “motifs” which appear in many proteins, and you can mathematically look for them, based on previously solved structures, and numerically scoring each side chain. Then you could guess, “This may be a member of such-and-such category”. Or, “This has a domain that is structured similarly to other known proteins”.

You might also be able to say, “some beta-sheets and beta-barrels look like…”mathematically.

I think you can also look for a feature like an ATPase domain that might be predicted from the sequence.

It gets more and more complicated past that.

These predictions are only very general. There might never be a way to confidently machine-predict individual salt-bridges or metal interactions. Things which are physically close together in the native conformation may be very far apart in the primary sequence.

Predicting is vague guess, that is still a long way from solving the structure.

If you have a solved a protein structure already, then pharmaceutical companies already use computer models to run through possible drug candidates, seeing if they might bind to a receptor or enzyme.

What is the sequence of energy utilization from protein, lipids, carbohydrates, which comes first, second and third for providing energy for our body?

Answered Oct 26

The first option is to burn glucose, because it is the least complex, and more direct.

If you run short on glucose, you have a store of glycogen in your liver and muscles. Glycogen is made of linked glucose monomers, which can be separated and burned.

You would also use other sugars, such as lactose, which take a bit more energy input to do.

Next, you would burn lipids. These are disassembled into 2-carbon units.

Last, you would start burning proteins. This may be a bad thing, for a couple of reasons. You need to get rid of the excess nitrogen, which takes resources. And, ultimately, you would start cannibalising things like your muscle tissue. In a starvation scenario, your body would be simultaneously burning tissue proteins, and using those carbon skeletons to manufacture glucose to send to the brain, which can only use glucose.

What elements differentiate the amino acids of a protein from the sugars of a carbohydrate?

Answered Oct 25

Carbohydrates and lipids are all CHO, which includes Carbon, Hydrogen, and Oxygen. These can be in different proportions, depending on the specific molecule.

Amino acids, by definition, have an amine group, which includes a Nitrogen. They all have an N on their backbone, and some have an N on the side chain. Cysteine and Methionine have a Sulfur on the side chain.

A few enzymes use an amino acid with Selenium instead of Sulfur.

What are the best biochemistry videos for the USMLE Step 1?

Answered Oct 25

There isn’t just one best channel, but I have compiled listings for university students at:

Resources For Science Students

There are various YouTube channels, plus other videos, which I have personally checked, and are good for students in various biological fields. There are also links to other academic sites in these fields.

Please feel free to message me with any possible additions to this directory.

What needed more energy, the secretory cell or the sensation cell?

Updated Jul 1

When a nerve cell fires, it depolarises its plasma membrane (in a wave, which is how the signal travels down the length of the cell). Then, it has to repolarise the membrane (using the sodium-potassium pump, which uses a lot of energy) before the next firing. A very large percentage of your body’s glucose is used by your brain.

On the other hand, a secretory cell is, by definition, sending out products and materials. Those products take energy to assemble, and then they are spewed out, and cannot be recycled.

A secretory cell will have a lot of carbon and carbon skeletons leaving its system, as they are assembled into final products. It will need a lot of energy (in terms of burning glucose, etc) in order to disassemble, and then reassemble, and export more of these things.

Every time a cell assembles something (down to just each residue in a peptide, or each 2-carbon unit in a fatty acid) consumes an energy unit, and burns an ATP.

Secretory cells also need a large number of Golgi stacks and other export machinery. Plus, raw materials like amino acids need to be replaced, so the cell will be using energy for importing from the environment

So it’s hard to say. Maybe it depends on how active the cells are at that particular moment.

Thermodynamically speaking, is the process of protein folding entropy driven or enthalpy driven and why?

Updated Feb 6

It isn’t an either/or type issue. Both factors are involved.

However, it is apparently sequential. The folding tends to occur in a certain order.

As I vaguely recall, the first secondary structure to appear is the alpha-helix (if there is one), and this can start forming at the N-terminus, as it is still coming out of the ribosome. Then, the beta-sheets form a bit later.

I expect that the formation of individual alpha-helices and beta-sheets would based on enthalpy, since they are held together with hydrogen bonds.

Later, the alpha-helices and beta-sheets need to be arranged in tertiary structure, in relation to each other, with certain areas facing certain other areas.

This stage of folding is mainly based on the hydrophobic effect, which is driven by entropy.

It is a bit counter-intuitive at first. When hydrophobic amino acids (Phe, Val, etc) are facing the water environment, this forces the surrounding water molecules to become more ordered into a “cage”. That means lower entropy.

When those hydrophobic side chains are folded inwards, to the core of the protein, this allows the water molecules to become more free and entropic. That increase in the water entropy is larger than the decrease in the protein entropy.

Then, you may get the sort of mixed effect of an alpha-helix or a beta-barrel that is hydrophobic on one side, and hydrophilic on the other. This arrangement is used in membrane channels.

My understanding is that, early formation of these large entropy-driven structures then brings together smaller areas that can later form enthalpy-based hydrogen bonds, salt-bridges, disulfide bonds, and interactions with co-factors (e.g. a metal).

So, you need both forces, acting at different times, on different levels of the folding process.

As always, there is more complexity around the corner. If there are chaperones involved in the folding process, it seems to be mainly about controlling the hydrophobic vs hydrophilic exposure.

Also, with a protein that is normally associated with a membrane, the final stage of the folding process may need to occur when it is in that lipid environment (so that the hydrophobic side chains can point outwards).

Disclaimer: Thermodynamics and chemical energetics are among my least-favourite areas of science, so there are certainly people who know much more than I do about them.

What is the best YouTube channel to study microbiology?

Answered Dec 20, 2017

Thanks for the A2A.

On YouTube (or the internet in general), there isn’t just one single resource that I can recommend.

However, I have a page of links for science students (of all levels) at:

Links For Science Students

Please excuse the formatting, as I still need to work on that. However, these are the best links that I have found so far, and are somewhat categorised by field of study, with a few comments.

This page will improve in the near future, but generally, these are the links that I have appreciated, for biology, biochemistry, chemistry, mathematics, and , of course, microbiology.