Dinosaur Peptides Suggest Mechanisms of Protein Survival

James D. San Antonio,Joseph P. R. O. Orgel,Shane T. Jensen,Mary H. Schweitzer,Raghu Kalluri,Michael Buckley,Hendrik W. van Veen

doi:10.1371/journal.pone.0020381

Abstract

Eleven collagen peptide sequences recovered from chemical extracts of dinosaur bones were mapped onto molecular models of the vertebrate collagen fibril derived from extant taxa. The dinosaur peptides localized to fibril regions protected by the close packing of collagen molecules, and contained few acidic amino acids. Four peptides mapped to collagen regions crucial for cell-collagen interactions and tissue development. Dinosaur peptides were not represented in more exposed parts of the collagen fibril or regions mediating intermolecular cross-linking. Thus functionally significant regions of collagen fibrils that are physically shielded within the fibril may be preferentially preserved in fossils. These results show empirically that structure-function relationships at the molecular level could contribute to selective preservation in fossilized vertebrate remains across geological time, suggest a ‘preservation motif’, and bolster current concepts linking collagen structure to biological function. This non-random distribution supports the hypothesis that the peptides are produced by the extinct organisms and suggests a chemical mechanism for survival.

Highlights

While it is widely accepted that proteins have the potential to survive significantly longer periods of time than DNA [1], persistence of original bone proteins in fossils at least 68 million years old is controversial [2,3], despite multiple lines of evidence supporting this hypothesis [4,5,6,7,8,9]
Technological improvements in recent years, including soft ionization mass spectrometry, allow increased detection of minute traces of biomolecules that may persist for extended periods of time via crystal encapsulation [17,18], even in the presence of exogenous contamination that precluded earlier forms of analysis such as amino acid composition analyses and stable isotope analyses [13]
The stability and unique function conferred by the triple-helical structure of collagen has been known for over forty years, but just how molecules assemble into microfibrils to form the massive cable-like fibrils in tissues has been less well understood

Summary

Introduction

While it is widely accepted that proteins have the potential to survive significantly longer periods of time than DNA [1], persistence of original bone proteins in fossils at least 68 million years old is controversial [2,3], despite multiple lines of evidence supporting this hypothesis [4,5,6,7,8,9]. We show here that molecular preservation is linked to protein function, and discuss how sequences of ancient peptides can test models of molecular function in extant organisms. The stability and unique function conferred by the triple-helical structure of collagen has been known for over forty years, but just how molecules assemble into microfibrils to form the massive cable-like fibrils in tissues has been less well understood.

Results

Conclusion