What factors influence the folding of proteins and biomolecules?

[mktsgm]

TL;DR

What factors determine a particular molecular structure and its typical folding?

What determines protein/biomolecule folding or why it folds in a particular way?

For instance, both glucose and fructose have same molecular formula (C6H12O6) with same chemical constituents (CHO) . But glucose has its carbonyl group at the end of the carbon chain, but fructose has its carbonyl group within the carbon chain.

Their hydroxyl groups are also differently attached to the carbon atoms, leading to different ring formation. But what makes the hydroxyl groups to attach differently in the first place?

Can someone throw light on what primary factors are involved in such a different attachment sites for functional groups and their subsequent structural formation in glucose and fructose (in spite of them having same chemical constituents)?

Can you help me clarifying this? Thanks in advance.

 

[pinball1970]

TL;DR Summary: What factors determine a particular molecular structure and its typical folding?

What determines protein/biomolecule folding or why it folds in a particular way?

For instance, both glucose and fructose have same molecular formula (C6H12O6) with same chemical constituents (CHO) . But glucose has its carbonyl group at the end of the carbon chain, but fructose has its carbonyl group within the carbon chain.

Their hydroxyl groups are also differently attached to the carbon atoms, leading to different ring formation. But what makes the hydroxyl groups to attach differently in the first place?

Can someone throw light on what primary factors are involved in such a different attachment sites for functional groups and their subsequent structural formation in glucose and fructose (in spite of them having same chemical constituents)?

Can you help me clarifying this? Thanks in advance.

I would Associate folding with proteins not simple sugars.

Glucose comes in different forms, isomers depending on the initial conditions cell types enzymes and I would look at "Van 't Hoff's theory of asymmetrical carbon atoms." - wiki article.

Also the polyol pathway which converts Glucose to Fructose. Again whatever enzymes are available and whatever is ergonomically favourable.

 

[pinball1970]

TL;DR Summary: What factors determine a particular molecular structure and its typical folding?

What determines protein/biomolecule folding or why it folds in a particular way?

I trust you have consulted wiki.

Amino acid sequence, Shape, size and charge is the short answer but this discipline is extremely complex. Ai has made advances.

A few examples here.

https://phys.org/news/2024-02-state-protein.html

https://www.researchgate.net/public...l_for_Predicting_Protein_Folding_and_Dynamics

 

[Philip Koeck]

I trust you haver consulted wiki.

Amino acid sequence, Shape, size and charge is the short answer but this discipline is extremely complex. Ai has made advances.

A few examples here.

https://phys.org/news/2024-02-state-protein.html

https://www.researchgate.net/public...l_for_Predicting_Protein_Folding_and_Dynamics

Not exactly my field but I've been working with biologists for a few years.

Isn't it true that prions are misfolded proteins that have exactly the same amino acid sequence as their healthy counterparts? That would mean that the folding is not completely determined by the sequence, but also depends on external factors, in this case other prions nearby.
Is the same true for amyloid fibrils in Alzheimers, for example?

So predicting a protein structure from the sequence alone might not be possible, strictly speaking.

 

[pinball1970]

Is the same true for amyloid fibrils in Alzheimers, for example?

Pretty sure I have read something in the literature regarding this. I will check and feedback.

 

[BillTre]

Isn't it true that prions are misfolded proteins that have exactly the same amino acid sequence as their healthy counterparts? That would mean that the folding is not completely determined by the sequence, but also depends on external factors, in this case other prions nearby.

Yes, this happens with proteins susceptible to to doing prion-like things.

In general proteins are made by the ribosomes. Amino acids are added at one end and the growing protein chain is extruded out of the ribosome. As the growing protein chain comes out, it interacts with whatever is around it (its local environment) as part of the process of folding into its final shape. Many proteins interact with special chaperon proteins as they come out of the ribosome. This helps them for into their appropriate shape.
A similar set of interactions (with the signal recognition particle (SRP) mechanisms) occurs if the protein is destined to be in or on the other side of the cell membrane. It is determined by the first few amino acids of the new protein (the signal part) which interact with components of the SRP mechanisms.

Any interactions with prions would occur after this initial folding stage to make changes in their shape.

Here is a wikipedia page on protein folding: https://en.wikipedia.org/wiki/Protein_folding

When searching one of the hits was some AI assembled information that was an over-simplification.
So use a real source.

 

[mktsgm]

Protein as it is building up in the ribosomes, amino acid sequence plays a role in determining its shape. Even here, as Philip Koeck pointed out, some other factor has a role in its misfolding (in spite of the same amino acid sequence). I too wanted to know, what is that "some other factor?"

Just as the amino acid sequence here, glucose and fructose being the same atomic constituents of molecule, has its structure differently. Why it is so? What factors determine their carbonyl group attaching to different carbons. This was my original question.

I understand that there is a branch of chemistry that explains different types of isomers. But they seem to me that they explain after they're formed. I want to know the factors that determine/cause isomers.

Can I presume that similar factors (that participated in the protein misfolding) can also play in the glucose/fructose isomeric differentiation too? I just try to compare these two different processes to find out a pattern here.

Pardon me my stickiness. This was my original question. Thanks.