title: Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen.
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.
authors.affiliation: Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, 33620.
authors.forename: Sameer
authors.initials: S
authors.lastname: Varma
authors.affiliation: Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, 33620.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Botlani
authors.affiliation: Intel Corporation, Santa Clara, California, 95054-1537.
authors.forename: Jeff R
authors.initials: JR
authors.lastname: Hammond
authors.affiliation: Department of Physics, Illinois Institute of Technology, Chicago, Illinois, 60616.
authors.forename: H Larry
authors.initials: HL
authors.lastname: Scott
authors.affiliation: Department of Physics, Illinois Institute of Technology, Chicago, Illinois, 60616.|Department of Biology, Illinois Institute of Technology, Chicago, Illinois, 60616.|Department of Bioengineering, Illinois Institute of Technology, Chicago, Illinois, 60616.
authors.forename: Joseph P R O
authors.initials: JP
authors.lastname: Orgel
authors.affiliation: Department of Physics, Illinois Institute of Technology, Chicago, Illinois, 60616.|Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, Ilinois, 60616.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Schieber
mesh_terms: D000465:Algorithms; D016477:Artifacts; D024042:Collagen Type I / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*; D056004:Molecular Dynamics Simulation; D011312:Pressure; D012965:Sodium Chloride; D013696:Temperature; D014867:Water
chemical_list: D024042:Collagen Type I; D014867:Water; D012965:Sodium Chloride
keywords: CCSD(T); collagen; force fields; molecular dynamics; quantum mechanics