Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2015-10, Vol.83 (10), p.1800-1812
• Main Authors: Varma, Sameer, Botlani, Mohsen, Hammond, Jeff R., Scott, H. Larry, Orgel, Joseph P. R. O., Schieber, Jay D.
• Format: Article
• Language: English
• Subjects: Algorithms; CCSD(T); collagen; Collagen Type I - chemistry; Collagen Type I - metabolism; Collagen Type I - ultrastructure; force fields; molecular dynamics; Molecular Dynamics Simulation; Pressure; quantum mechanics; Sodium Chloride; Temperature; Water
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.24864

ABSTRACT A signature feature of collagen is its axial periodicity visible in TEM as alternating dark and light bands. In mature, type I collagen, this repeating unit, D, is 67 nm long. This periodicity reflects an underlying packing of constituent triple‐helix polypeptide monomers wherein the dark bands represent gaps between axially adjacent monomers. This organization is visible distinctly in the microfibrillar model of collagen obtained from fiber diffraction. However, to date, no atomistic simulations of this diffraction model under zero‐stress conditions have reported a preservation of this structural feature. Such a demonstration is important as it provides the baseline to infer response functions of physiological stimuli. In contrast, simulations predict a considerable shrinkage of the D‐band (11–19%). Here we evaluate systemically the effect of several factors on D‐band shrinkage. Using force fields employed in previous studies we find that irrespective of the temperature/pressure coupling algorithms, assumed salt concentration or hydration level, and whether or not the monomers are cross‐linked, the D‐band shrinks considerably. This shrinkage is associated with the bending and widening of individual monomers, but employing a force field whose backbone dihedral energy landscape matches more closely with our computed CCSD(T) values produces a small D‐band shrinkage of < 3%. Since this force field also performs better against other experimental data, it appears that the large shrinkage observed in earlier simulations is a force‐field artifact. The residual shrinkage could be due to the absence of certain atomic‐level details, such as glycosylation sites, for which we do not yet have suitable data. Proteins 2015; 83:1800–1812. © 2015 Wiley Periodicals, Inc.