Date of Degree


Document Type


Degree Name





Yujia Xu

Committee Members

Hiroshi Matsui

Charles M. Drain

Dorthe Eisele

Vikas Nanda

Subject Categories

Chemistry | Materials Chemistry | Other Chemistry | Physical Sciences and Mathematics


protein self-assembly, peptide design, peptide interactions, d-periodicity, collagen triple helix, collagen fibrils


Collagen is the major component of the extracellular matrix and is involved in a wide range of cellular functions during tissue development and action. At the core of the diverse functions of this versatile protein is its remarkable ability to form supramolecular structures through self-assembly and/or through interactions with other biomolecules. One typical example of such supramolecular structure is the fibrils of collagen types I, II and III of the connective tissues. These fibrils have staggered arrangement of the laterally associated collagen triple helices – the structural unit of collagen – to form long, smooth fibrils with a characteristic 67 nm axial structural feature known as the D-periodicity.

The fibrillogenesis of collagen in tissues is a complex process involving other macromolecules; the fibril formation itself, however, is a self-assembly process proceeding from the self-association of the triple helix. While many of the structural details of both the triple helix and the collagen fibrils have been elucidated, the molecular recognition mechanisms of the self-assembly process remain poorly understood. Efforts of producing collagen-like, self-assembled fibrils through protein design have not been successful.

In this work, we describe the self-assembly of a collagen-like periodic mini-fibril from a recombinant collagen triple helix. The triple helix, designated Col108, is expressed in E. coli using an artificial gene and consists of a 378–residue triple helix domain organized into three pseudo-repeating sequence units. The Col108 peptide forms a stable triple helix with a melting temperature of 41°C. Upon increases of pH and temperature, The Col108 peptide self-assembles in solution into smooth mini-fibrils with the cross-striated banding pattern typical of fibrillar collagens. The banding pattern is characterized by an axially repeating feature of ~ 35 nm as observed by TEM and AFM. Both the negatively stained and the positively stained. TEM patterns of the Col108 fibrils are consistent with a staggered arrangement of triple helices with a staggering value of 123 residues, a value closely connected to the size of one repeating sequence unit.

A mechanism is proposed for the fibril formation of Col108 with axial periodicity, which is stabilized by the optimized interactions between the triple helices in a 1-unit staggered arrangement, pointing towards the similar underlying molecular mechanisms i.e. inherent sequence periodicity at play in guiding the self-assembly of collagen. Col108 establishes itself as a system comparable to native collagen to establish a connection in the self-assembly mechanisms as it is significantly larger than other collagen-like peptides which are only 30-45 residues long.

Col108 TEM.rar (364180 kB)
COl108 fibrils AFM.rar (1321 kB)