Abstract
Significant strides have been recently made to fold peptides and small proteins in silico using MD simulations. However, facilities are currently lacking to include disulfide bonding in the MD models of protein folding. To address this problem, we have developed a simple empirical protocol to model formation of disulfides, which is perturbation-free, retains the same speed as conventional MD simulations and allows one to control the reaction rate. The new protocol has been tested on 15-aminoacid peptide guanylin containing four cysteine residues; the net simulation time using Amber ff14SB force field was 61 μs. The resulting isomer distribution is in qualitative agreement with experiment, suggesting that oxidative folding of guanylin in vitro occurs under kinetic control. The highly stable conformation of the so-called isomer 2(B) has been obtained for full-length guanylin, which is significantly different from the poorly ordered structure of the truncated peptide PDB ID 1GNB. In addition, we have simulated oxidative folding of guanylin within the 94-aminoacid prohormone proguanylin. The obtained structure is in good agreement with the NMR coordinates 1O8R. The proposed modeling strategy can help to explore certain fundamental aspects of protein folding and is potentially relevant for manufacturing of synthetic peptides and recombinant proteins.
Highlights
In silico folding of protein structures is a Holy Grail of computational modeling
It has been fully appreciated that disulfide bond formation, as normally occurs in the oxidative environment of the endoplasmic reticulum (ER), is one of the major
In many situations disulfide bonding can be viewed as a driver of protein folding[24, 25]
Summary
In silico folding of protein structures is a Holy Grail of computational modeling. Early efforts were focused on helical and β-hairpin peptides, as well as mini-proteins[1,2,3], and often relied on enhanced sampling schemes[4, 5]. The existing MD models of protein folding, do not have any facilities to include the effect of oxidative folding, i.e. primarily formation of disulfide bonds. Specialized coarse-grained force fields have been developed by Scheraga and others to address the problem of oxidative protein folding. These force fields were used in conjunction with simulated annealing algorithms[15, 16] and later employed in the context of bona fide MD simulations[17, 18]. The current situation is such that unbiased MD simulations can be used to successfully fold a (cysteine-free) 76-residue protein ubiquitin[6], but lack the facilities to attempt folding of another popular model protein, 58-residue BPTI, which contains three disulfide bridges[19].
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