Structural difference between OR and CE chains in cellulose I-beta fibril module

[Adolfo Poma]

Dear developers,

I wonder if the final structure should take into account some information concerning  hydrogen bond between chains and if this structural motif should depend on the type of layer (made of  Origin /Center chains).
According to this work (http://www.sciencedirect.com/science/article/pii/S0008621505004660#). There is a sort of preference of the alcohol group -O6- in OR chain to be in TG (dihedral made by  C-4–C-5–C-6–O-6= 60) conformation and for the same group in CE chains to be in the GG (C-4–C-5–C-6–O-6=+60).
I wonder about the definition taken in consideration to define CE and OR by your nice builder.
It seems to me that all chains, independently of the type are setup in the TG conformation. If this is the case, can you let me know which is the argument (structural) to differentiate each type of sugar chain.

PS. enabling with VMD the hydrogen bond visualization for both type of chain it shows a large pattern of hydrogen bond (intra: O3-H- -O5,O2-H- -O6 and inter: O6-H- -O3) for CE chain, while just a few hbonds mainly the interchain: O2-H - -O6 for OR chains.


best
Regards

Adolfo Poma

[Thiago Gomes]

Dear Dr. Poma,

thank you for your interest in contacting us.

Indeed, all chains are setup by the builder in the TG conformation. The builder takes into account the atomic coordinates reported by Nishiyama et al. (http://pubs.acs.org/doi/full/10.1021/ja0257319). The first line (model A) in Table 3 in such work reports experimental determination of torsion angles Φ, Ψ, χ, χ‘ proposed by those authors. Hence, one can distinguish between origin and center chains by the numeric value of Φ and Ψ (defined by (O5−C1−O1−C4) and (C1−O1−C4−C5), respectively). They have found that Φ and Ψ are −98.5° and −142.3° for origin chains and −88.7° and −147.1° for center chains.

By performing MD simulations for a number of nanoseconds, one will obtain a distribution of gg, tg, gt conformations which is strongly dependent on the force field employed.

The VMD hydrogen bond visualization tool allows one to set geometric constraints to define what should be considered a hydrogen bond, therefore hydrogen bonds displayed will depend on such definitions.

I hope these informations help. Please feel free to contact us should you need any further.

Best Regards,

Thiago

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