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Re:More Protein Folding Progress – What’s It Mean? by ramraj07 on Monday July 26, 2021 @04:31PM (#27965047)
Can you explain further what your second paragraph means?
Re:More Protein Folding Progress – What’s It Mean? by G3rn0ti on Monday July 26, 2021 @05:09PM (#27965514)
I think parent meant conservation of the amino acid is weak and still the structure remains the same overall. So sequence similarity is not everything.

Reason might be the overall protein fold is guided also by something else than detailed side chain contacts.

BTW: Hydrogen bonding and salt contacts do not drive protein folding at least not thermodynamically because it does not matter whether polar/charged residues interact with others or with water. Rather, the reason why proteins fold is the same why oil and water do not mix: Hydrophobic amino acids avoid water. This is an entropy driven process where electrostatic interactions do not matter. See also the „molten globules“ model. Basically it means a predecessor of the protein folds early on due to a collapse of the hydrophobic core. Tertiary structure is then refined due to residue/residue interactions. In the end, it’s the distribution of hydrophobic amino acids in its sequence that’s most important for the conservation of a structure. Surface residues can vary quite a lot.

Re:More Protein Folding Progress – What’s It Mean? by dekhn on Monday July 26, 2021 @05:32PM (#27965774)
your "BTW" is still a huge area of argument in protein folding, the claim you are making is just one perspective and is not well-established.