Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide

Abstract

In the canonical (G-X-Y)n sequence of the fibrillar collagen triple helix, stabilizing direct inter-chain hydrogen bonding connects neighboring chains. Mutations at G can disrupt these interactions and are linked to connective tissue diseases. Here we integrate computational approaches with NMR to obtain a dynamic view of hydrogen bonding distributions in the (POG)4-(POA)-(POG)5 peptide, showing that the solution conformation, dynamics and hydrogen bonding deviate from the reported x-ray crystal structure in many aspects. The simulations and NMR data provide clear evidence for inequivalent environments in the three chains. MD simulations indicate direct inter-chain hydrogen bonds in the leading chain, water-bridges in the middle chain, and non-bridging waters in the trailing chain at the G→A substitution site. Theoretical calculations of NMR chemical shifts using a quantum fragmentation procedure can account for the unusual downfield NMR chemical shifts at the substitution sites and are used to assign the resonances to the individual chains. The NMR and MD data highlight the sensitivity of amide shifts to changes in the acceptor group from peptide carbonyls to water. The results are used to interpret solution NMR data for a variety of glycine substitutions and other sequence triplet interruptions, to provide new connections between collagen sequences, their associated structures, dynamical behavior and ability to recognize collagen receptors.

Translational and Rotational Dynamics of Water Molecules in Aligned Collagenous Tissues: Implications for Assessing Collagen Organisation with Magnetic Resonance Imaging

“…Fullerton Again, it is noted that studies which seemingly agree with the notion of ice-like bonds [146,147,175,177] are carried out on fibres or fibrils, while those which disagree were concerned with a sole collagen molecule [64,65,148,181]. The key difference is the possible inclusion of intra-fibrillar water in the former.…”

“…These have included simulations of single collagen molecules [64,65,158,181,212,213], and collagen forming larger fibril structures [214][215][216][217][218]. The focus of these studies has primarily been the biomechanical properties [213,214,218] and stability [64,65] of the formed collagen structures, with only a few studies primarily focused on watercollagen interactions [64,158].…”

“…While some experimental evidence suggests hydrogen bonds between bridge water and the collagen backbone are ice-like [146,147], several studies [64,65,148,181] indicated that the life time of the water in the collagen hydration layer to be sub pico-second (see Section 2.2.6 for more detail). Additionally, when considering that the 2 H 2 O replacement in Tadimalla and Momot's study [175] took place over 12 to 24 hours, the ice-like bond hypothesis seems implausible; in order for the protons participating in the water bridges to remain unavailable for exchange, the hydrogen bond lifetime would have to be of the order of the 2 H 2 O replacement time.…”

“…Several studies have observed 1 water bridges in MD simulations of hydrated collagen [64,65,181]. Simulations by Ravikumar and Hwang [64] investigated lifetimes of single water bridges in a collagen peptide containing a segment of type III collagen with three potential single water bridges.…”

“…They defined a water bridge as a water molecule making two simultaneous hydrogen bonds with the collagen backbone (see Figure 9). They reported mean bridge lifetimes between 1 -2.5 ps with occupancies ranging from 10 to 70% across the different bridge sites at 300 K. Two other studies [65,181] report ~ 100 ps lifetimes for an entire water molecule near a bridge site, when no hydrogen bonding criteria were defined. None of these studies investigated the rotational motion of the water near the water bridge sites.…”