Proline cis/trans isomers

[PabloHNieto]

hello,

recently I found that some of my simulations had some residues in cis conformations Could it be possible to add a warning in ProteinPrepare or in other convenient place to inform about cis residues?

Thanks

[stefdoerr]

Theoretically the simulations that changed the conformations happened after proteinPrepare and a user would not really run it through proteinPrepare or HTMD again once he has a built system I think, no?

[giadefa]

that is probably true. Maybe some kind of validate. It is quite easy to do this mistake. As one equilibrate a protein at high temperature the proline do flip.

On Tue, 6 Nov 2018 at 16:09, Stefan Doerr notifications@github.com wrote:

Theoretically the simulations that changese the conformations happened after proteinPrepare and a user would not really run it through proteinPrepare or HTMD again once he has a built system I think, no?

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[stefdoerr]

The only place you could do this is in the Production protocol which seems...ugly?

[giadefa]

the alternative is to waste a lot of simulations

On Tue, 6 Nov 2018 at 16:20, Stefan Doerr notifications@github.com wrote:

The only place you could do this is in the Production protocol which seems...ugly?

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[j3mdamas]

@PabloHNieto, were the cis conformations in the starting structure? If so, how did you generate the starting structure (to have cis conformers)?

[stefdoerr]

No, he unfolded them at high temperature in an initial simulation and they flipped there

[j3mdamas]

OK; my opinion is that we don't need a check.

Check this paragraph from here:

Although most amino acids form peptide bonds that are in their trans-isomer conformations (> 99.5%),56,57 Xaa-Pro peptide bonds populate both cis- and trans-states. Xaa-Pro trans isomers are indeed less favored because of relatively high steric conflicts between Xaa-Cα atoms and Pro-Cδ’s (see Fig. 2). The energy differences between proline cis/trans conformers are less pronounced than in other amino acids, which, in connection with a high energy barrier between the two isomers (~20 kcal/mol)58,59 results in slow cis/trans interconversion rates (10−3 s−1).56 Hence, on average, ordered proteins contain 5–10% cis-conformers of the Xaa-Pro peptide bonds, whereas the occurrence of cis-isoforms of usual amide bonds in proteins is typically below 0.5%.56,57 The cis-isomer content is influenced by the nature of the surrounding residues and by the types of surrounding secondary structure.60-62 Despite these similar energy levels in disordered peptides, prolines in natively folded proteins tend to display exclusive cis-, or trans-conformations, which are primarily established via the protein fold and the resulting specific interactions with residues close in space.63,64 Within protein Xaa-Pro motifs, Cα(Xaa)/Cα(Pro) distances of trans-proline conformations are on average 1.5 Å larger than for cis proline isomers;65,66 however, these effects are not systematic and strongly influenced by the nature of Xaa. In most folded proteins, isomer-specific structural changes are local, and vanish at a distance of 2–3 residues from the proline of interest. More extended conformational rearrangements have only been observed for a few cases.67 From a local point of view the effects that proline cis/trans isomers induce in polypeptide chains are important. Cis-isoforms result in turn-like structures, whereas trans-isoforms favor locally extended conformations (see Fig. 2). In protein folding cis/trans isomerization plays an important role and often functions as the rate limiting step in the overall folding process.64 Important cellular enzymes such as peptidyl-prolyl isomerases (PPIases) accelerate proline isomerization processes and thereby enhance the kinetic rates with which thermodynamic equilibrium states are reached. The relationships between PPIases and IDPs will be discussed in more detail, later in the article. One aspect that we want to stress is that proline cis-trans characteristics and behaviors of IDPs are similar to those of peptides. IDPs display cis population averages of ~5–10% and, therefore, IDPs with 10 or more prolines have high probabilities for multiple cis conformations. This creates substantial diversity in population conformers that sample a vast conformational space.

References 56,57 show that we can still find 5 to 10% cis conformations for X-Pro, even in ordered proteins. So, I believe this is rather an issue that is the concern of the person running the simulations.

[giadefa]

in practice because proline does not switch back within the time frame of molecular simulation, your argument does not hold. We are not simulating at equilibrium, so we need a check.

On Tue, 6 Nov 2018 at 17:26, João M. Damas notifications@github.com wrote:

OK; my opinion is that we don't need a check.

Check this paragraph from here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424786/:

Although most amino acids form peptide bonds that are in their trans-isomer conformations (> 99.5%),56,57 Xaa-Pro peptide bonds populate both cis- and trans-states. Xaa-Pro trans isomers are indeed less favored because of relatively high steric conflicts between Xaa-Cα atoms and Pro-Cδ’s (see Fig. 2). The energy differences between proline cis/trans conformers are less pronounced than in other amino acids, which, in connection with a high energy barrier between the two isomers (~20 kcal/mol)58,59 results in slow cis/trans interconversion rates (10−3 s−1).56 Hence, on average, ordered proteins contain 5–10% cis-conformers of the Xaa-Pro peptide bonds, whereas the occurrence of cis-isoforms of usual amide bonds in proteins is typically below 0.5%.56,57 The cis-isomer content is influenced by the nature of the surrounding residues and by the types of surrounding secondary structure.60-62 Despite these similar energy levels in disordered peptides, prolines in natively folded proteins tend to display exclusive cis-, or trans-conformations, which are primarily established via the protein fold and the resulting specific interactions with residues close in space.63,64 Within protein Xaa-Pro motifs, Cα(Xaa)/Cα(Pro) distances of trans-proline conformations are on average 1.5 Å larger than for cis proline isomers;65,66 however, these effects are not systematic and strongly influenced by the nature of Xaa. In most folded proteins, isomer-specific structural changes are local, and vanish at a distance of 2–3 residues from the proline of interest. More extended conformational rearrangements have only been observed for a few cases.67 From a local point of view the effects that proline cis/trans isomers induce in polypeptide chains are important. Cis-isoforms result in turn-like structures, whereas trans-isoforms favor locally extended conformations (see Fig. 2). In protein folding cis/trans isomerization plays an important role and often functions as the rate limiting step in the overall folding process.64 Important cellular enzymes such as peptidyl-prolyl isomerases (PPIases) accelerate proline isomerization processes and thereby enhance the kinetic rates with which thermodynamic equilibrium states are reached. The relationships between PPIases and IDPs will be discussed in more detail, later in the article. One aspect that we want to stress is that proline cis-trans characteristics and behaviors of IDPs are similar to those of peptides. IDPs display cis population averages of ~5–10% and, therefore, IDPs with 10 or more prolines have high probabilities for multiple cis conformations. This creates substantial diversity in population conformers that sample a vast conformational space.

References 56,57 show that we can still find 5 to 10% cis conformations for X-Pro, even in ordered proteins. So, I believe this is rather an issue that is the concern of the person running the simulations.

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[j3mdamas]

X-Pro in cis naturally occur in PDB at a rate of 5%, i.e. it may not even be wrong.

Where and what the check should be in your opinion?

[giadefa]

it should have a warning if Proline is not in the conformation of 95% because you are not going to sample the 95% if you start from the 5% during your MD sim.

On Tue, 6 Nov 2018 at 17:57, João M. Damas notifications@github.com wrote:

X-Pro in cis naturally occur in PDB at a rate of 5%, i.e. it may not even be wrong.

Where and what the check should be in your opinion?

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[j3mdamas]

Gianni, I don't think we are understanding each other. Let's see if I can explain myself better. For example, in PDB 1NEP, Proline 81 is in cis conformation in the X-ray structure (no high temperature, no nothing). Do you want to warn the user and he should change it to trans? Why would I want to sample that Proline in trans if the X-ray already tells me that on average it is on cis?

[giadefa]

not that he needs to change, but that he needs to know what is doing because he is never going to see the other conformation even if in solution would be expected

On Tue, 6 Nov 2018 at 20:08, João M. Damas notifications@github.com wrote:

Gianni, I don't think we are understanding each other. Let's see if I can explain myself better. For example, in PDB 1NEP, Proline 81 is in cis conformation in the X-ray structure (no high temperature, no nothing). Do you want to warn the user and he should change it to trans? Why would I want to sample that Proline in trans if the X-ray already tells me that on average it is on cis?

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[j3mdamas]

I think this is rather a research subject, as it can be seen by a literature research. Namely, IDPs have higher percentages of Prolines and also higher percentages of cis conformations (i.e. it would be debatable that you would want all Prolines in trans). In folded proteins, the cis conformations have biological significance (there are even enzymes that catalyze the isomerization, and conformer population is shifted towards cis due to neighbouring conditions under tertiary structure). I mean, there are even papers coming out on ML prediction of Cis isomers (https://pubs.acs.org/doi/abs/10.1021/acs.jcim.8b00442).

That being said, let's talk about the check. Like @stefdoerr mentioned, where would we put it? proteinPrepare seems to me the most logical place, but do you have any other suggestion?

[stefdoerr]

It's useless in proteinPrepare as it's called before simulations and the flips only really happen in unfolding simulations (correct me if I'm wrong but I have not seen them happen in other cases) so I don't really think there is a point to this. If anything we might want to write an unfolding tutorial with all the warnings about flips etc.

[stefdoerr]

Or make an unfolding protocol?

[giadefa]

Joao just told you that the flip can be in the PDB as well. The problem is not the flip on its own, but the timescale of this process and the strong structural consequences when the proline flips.

g

On Tue, 6 Nov 2018 at 22:15, Stefan Doerr notifications@github.com wrote:

Or make an unfolding protocol?

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[stefdoerr]

Okay, after once again failing to notice a cis peptide bond in my molecule I added warnings to all builders if you build something with a cis bond https://github.com/Acellera/htmd/commit/8cc12fca6dcb84057b9d6e6a59ac399ad1e8a1b7

[stefdoerr]

I can add the check to the protocols as well but it can take many seconds to check the dihedrals for large systems, so it's up to you to decide if you want such a slow-down in our protocols.

[stefdoerr]

@giadefa @PabloHNieto opinions? Do you want the check default on protocols despite slow-down?

[PabloHNieto]

imho if the slowdown is very dramatic then with the warnings in the builders should be enough. However few seconds for warnings vs several days/weeks for noticing seems fair to me.

[stefdoerr]

Done, added to both equil_v2 and prod_v6 https://github.com/Acellera/htmd/commit/b0deebe7ad79d493a8cfd8ac98317791a4da3f75 Closing the issue