An energetic evaluation of a “Smith” collagen microfibril model

Abstract

An energy minimized three-dimensional structure of a collagen microfibril template was constructed based on the five-stranded model of Smith (1968), using molecular modeling methods and Kollman force fields (Weiner and Kollman, 1981). For this model, individual molecules were constructed with three identical polypeptide chains [Gly-Pro-Pro)n, (Gly-Prop-Hyp)n, or (Gly-Ala-Ala)n, where n = 4, 12, and 16) coiled into a right-handed triple-helical structure. The axial distance between adjacent amino acid residues is about 0.29 nm per polypeptide chain, and the pitch of each chain is approximately 3.3 residues. The microfibril model consists of five parallel triple helices packed so that a left-handed superhelical twist exists. The structural characteristics of the computed microfibril are consistent with those obtained for collagen by X-ray diffraction and electron microscopy. The energy minimized Smith microfibril model for (Gly-Pro-Pro)12 has an axial length of about 10.2 nm (for a 36 amino acid residue chain), which gives an estimated D-spacing (234 amino acids per chain) of approximately 66.2 nm. Studies of the microfibril models (Gly-Pro-Pro)12, (Gly-Pro-Hyp)12, and (Gly-Ala-Ala)12 show that nonbonded van der Waals interactions are important for microfibril formation, while electrostatic interactions contribute to the stability of the microfibril structure and determine the specificity by which collagen molecules pack within the microfibril.

Tale of two spikes in bacteriophage PRD1

“…First, the monomeric N-terminal homology model was trimerized (see Materials and Methods) (32). Second, the two linker regions not resolved in the x-ray maps, namely the collagen-like region and the eight-glycine stretch, were both modeled by using a collagen structure as a template (PDB ID code 1CLG) (33).…”

Development and utilization of a bovine type I collagen microfibril model

“…In the first stage of construction [20], (Gly-Pro-Hpr) 12 peptides were constructed as left-handed helices and visually docked into right-handed triple helices 3(Gly-Pro-Hpr) 12 , where individual chains were staggered by one residue with respect to each other. To produce a 36-residue long microfibril segment, four triple helical units 3(Gly-Pro-Hpr) 12 and one 3(Gly-Pro-Hpr) 10 , to simulate the start of a gap region, were packed into a left-handed superhelix [8].…”

“…The model would also be amenable to use by scientists whose modeling resources may be limited to publically available software such as the Swiss-PdbViewer at http://www.expasy.org/spdbv/ [19]. Over several years, a five-helix model of bovine type I collagen was developed [20][21][22][23], Table 1. Newer amino acid sequence data [24] and in situ conformations for telopeptides [25,26] are incorporated in the current model.…”

Template Synthesis into Gelatin-Immobilized Matrix as Perspective Method of Obtaining Supramolecular Macroheterocyclic Compounds

“…Gelatin has an extremely high surface area and an extensive system of micropores, so that when it comes into contact with any kind of aqueous solution, the permeation of both the solvent molecules and of the solute into polymer massif is a rule ensured comparatively readily. [5][6][7][8] In this connection, polymer layers on the basis of gelatin exhibits isotropic physical and mechanical parameters and is transparent, hydrophilic, and plastic.…”

“…Gelatin is stabilized by the formation of covalent crosslinks, both within the gelatin triple helix and between gelatin helices. [5] Such a structure is potentially very suitable for the formation of polymer-immobilized matrix materials; it permits the formation of no kind of rigid crystalline blocks and furthermore, contains a fairly large number of cells for the reception and subsequent fixation of the molecules of the immobilized substance. When filled with the molecules of corresponding compound, these cells retain a certain freedom of migration in space.…”