Yujia Xu

E-mail: Yujia.xu@hunter.cuny.edu

Office: Room 1304C HN

Phone: (212) 772-4310 (office)

             (212) 772-5614 (Lab)

Research Interest

Biological functions often depend on the assembling of macromolecules into well-defined networks and complexes. Our research is to use recombinant collagen triple helix as a model system to explore the determining factors that govern the higher level molecular assembly. About twenty different types of collagen molecules have been identified in humans, occurring in almost every tissue. Different types of collagen share the same basic structure unit – the triple helix, consisting of three poly-peptide chains with the characteristic (Gly-X-Y)_n repeating (amino acid) sequence. The triple helix further assembles into different supramolecular structures that confer the diverse biological properties of different tissues.  Understanding of the mechanism of molecular assembly of collagen will be essential for our understanding of the molecular basis of tissue functions, the mechanism of macromolecular organizations and how mutations in collagens cause diseases.

THE SCOPE OF RESEARCH

1. The Molecular Mechanisms of the Organization of Collagen
   
   One of the major challenges of collagen research is the large size of the molecules, often containing more than 1000 amino acids.  Consequently, many of the presently available research tools are difficult and cumbersome to adapt for use.  Our approach is to use recombinant collagen fragments expressed in E Coli and/or yeast, with the size ranging from 100 to 500 amino acid residues.  Special effort will be made to generate fragments that model the regions of triple helix crucial to the supera-molecular assembly. It has been shown that the information of assembly of collagens, especially that of fibrillogenesis of fibril forming collagens in connective tissues, is encoded exclusively in the amino acid sequence of the triple helix. A battery of biochemical and biophysical techniques, combined with the mutagenesis approach will be, then, used to elucidate the structural properties of the collagen fragments and to investigate the determinant factors of collagen assemblies.
2. The Mechanisms of Protein folding
   
   As one of the major protein structural motifs, the collagen triple helix represents a unique system for structural and biophysical studies of proteins.  Extensive work in this area using short triple helical peptides has revealed many features of molecular interactions, complementing studies of globular proteins. The structure features of triple helix have much in common with that of the ‘secondary structures’ of protein, such as the a -helix and b-sheets. The further association of triple helix to fibrils or other higher order molecular assemblies is driven by hydrophobic interactions of side chains in an analogous fashion to the packing of secondary structures in a globular protein.  Since peptides with certain length and the Gly-X-Y sequence pattern can form stable triple helix in solution, study of the further association of the triple helix offers a special opportunity to investigate the subtle balances and interplay of the localized ‘secondary structure’ and the long-range tertiary interactions.  Such knowledge is at the core to our understanding of the folding and the 3-dimensional molecular organization of proteins.
3. Molecular Etiology of Collagen Related Heritable Connective Tissue Diseases
   
   More than 300 collagen mutations have been identified that lead to inheritable connective tissue diseases of varying severity. The most intriguing feature of these diseases is the strong dependence of the severity of the disease on the location of the mutation site.  We hypothesize that that the severity of the disease correlates with the ‘subdomains’ along the rod shaped collagen triple helix with distinct local properties. The structural and dynamic properties of collagen fragments mimicking the regions of mutation ‘hot-spot’ will be investigated using NMR, CD spectroscopy and HX techniques. 

1. Xu, Y., Baum, J.and Brodsky, B. "Effects of Trimethylamine-N-Oxide (TMAO) on Collagen triple-helix conformation", in preparation for FEBS Letters
2. Persikov, A., Xu, Y., Brodsky, B. ‘The two-state reversible folding and unfolding reaction of collagen triple helical peptides’, accepted Protein Sciences.
3. Xu, Y. (2004) "Characterization of heterogeneity of self-associating systems using equilibrium sedimentation techniques”, in press Biophysical Chemistry
4. Chien, C., Xu, Y.,Xiao, Rong., Aramini, J. M., Sahasrabudhe, P. V., Krug, R. M., and Montelione, G. T. (2004) “Biophysical Characterization of the Complex Between Double-Stranded RNA and the N-terminal Domain of the NS1 Protein from Influenza A Virus: Evidence for a Novel RNA-Binding Mode”,  Biochemistry 43:1950-1962
5. Xu, Y., Hyde T.,Bhate, M., Lu, X., Broadsky, B., and Baum. (2003) ‘NMR and CD Spectroscopy Show that Imino Acid Restriction of the Unfolded State Leads to Efficient Folding’. Biochemistry 42:8696-8703
6. Xu, Y., M. Bhate and Brodsky, B. (2002) Characterization of the Nucleation Step and Folding of a Collagen Triple Helix Peptide, Biochemistry 41:8143-51
7. Milne, J. S., Xu, Y., Mayne, L. & Englander, S. W. (1999) Experimental Study of the Protein Folding Landscape: Unfolding Reactions in Cytochrome C. J. Mol. Biol. 209:811-822
8. Xu, Y., Mayne, L. & Englander, S. W. (1998) Evidence of a Sequential Folding Pathway. Nature Struc. Biol. 5:774-778