Will these two peptides fold in the same way ?
P1: [N-Term]-ALKIMNTRCA-[C-Term]
P2: [N-Term]-ACRTNMIKLA-[C-Term]
Please note that the amino acid residues and their sequence is exactly the same, the only difference lies in N to C terminal directional arrangement. Please share your views if these two peptides will share a similar folding pattern/structure ? Why/Why not ?
Most amino acids are asymmetric, thus interactions between adjacent residues will be different when the connectivity is reversed.
the folding mechanism mainly based on the bond between hydrogen and hydrogen , suphure sulphure bonds , and hydrophobic nature develeped between the amino acids in that protein.
The sequence which u have given doesnot share similar folding patern or structure, in between they are diferent amino acids which depends on H-H and S-S bonds,
i hope you might understand what i have answers. all the best
The peptides are too short and rich in acid-base residues, therefore, their structural organization is strongly pH dependent. However, their net charge at neutral pH (+ 2) and the small size of the peptide, which allows a strong dispersion of the charge, do not authorize any easy folding prediction. What is certain is that these peptides will be strongly fluctuating with strong exchange between conformers at equilibrium. Moreover, they should be considered as polycations, and then as polyelectrolytes, not as weak polyampholytes (such as the classic globular proteins). I imagine that their representation in aqueous solution should be through the conformational ensembles. An explanation about this problem can be reasonably obtained by molecular dynamics.
Yes, they will fold differently, basically because of the fact amino acids are asymetrical, and so it is impossible to get the same structure by reversing their order.
There is actually a nice example to illustrate this - in the 90s, when protein x-ray crystallography was using only R-factors to check structures, it was shown (by Gerard Kleywegt, if I remember correctly) that if a protein sequence was purposedly reverted to be fitted into a low-resolution electron density map, it would yield not so bad R-factors. Such error can be detected either by using R-frees or by using profile based methods such as Verify3D, which, in a nutshell, checks if a given stretch of amino acids "makes sense" in a structure by looking at their chemical environment and secondary structure. Which indirectly proves that reversed sequence do not produce the same fold, because if you actually force a reversed sequence into the original fold it simply won't fulfill the expected properties of a folded protein (in the case of a globular protein, at least having a stable hydrophobic core with a polar external surface).
Trevor and Lucas are correct. One way to understand this is to just write a dipeptide strucutre on paper. You will quickly see that AB and BA are very different. If you have access to a organic chemistry or Biophysics department, you can build a ball and stick model and appreciate the logic.
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