Averaged NMR solution structure of Ca(II) loaded Ca.CD2 (1T6W.pdb).

Designing Calcium and Metal Binding Sites

The objectives of this project are 1) to develop a general methodology to design metal binding sites with high coordination numbers such as calcium and lanthanides, 2) understand the mechanism of calcium-regulated biological process such as ligand-induced conformational changes in cell adhesion, 3) monitor calcium signaling in vivo, and 4) characterize large protein complexes using residue dipolar coupling and lanthanide binding. Based on graph theory and statistical analysis, several computational algorithms for designing metal binding sites have been developed in collaboration with experts in biostatistics and computer sciences. Various biophysical and chemical tools, including high resolution methods, are used to characterize the Ca(II) binding sites and optimize our methods for the design of calcium/lanthanide binding proteins.   We have also applied our design approach to develop calcium sensors and MRI contrast agents.

Our publications in regard to de novo design calcium binding protein are shown below:

Anna Wilkins Maniccia, Wei Yang, Shunyi Li, Julian A. Johnson, Jenny J Yang. using Protein design to dissect the effect of charged residues on metal binding and protein stability. Biochemistry (2006), 45, 5848-5856.

Wei Yang, Anna L. Wilkins, Shunyi Li, Yiming Ye, Jenny J. Yang. The effects of Ca2+ binding on the dynamic properties of a designed Ca2+-binding protein. Biochemistry (2005), 44, 8267-8273.

Yang W, Wilkins AL, Ye YM, Liu ZR, Li SY, Urbauer JL, Hellinga HW, Kearney A, van der Merwe PA and Yang JJ, Design of a calcium-binding protein with desired structure in a cell adhesion molecule. Journal of the American Chemical Society (2005), 127, 2085-2093.

Wei Yang, Lisa Jones, Leanne Isley , Yiming Ye, Hsiau-Wei Lee, Anna Wilkins, Zhi-ren Liu, Homme W. Hellinga , Russell Malchow , Mohammed Ghazi and Jenny J. Yang. De Novo Design of a Calcium Binding Protein. Journal of the American Chemical Society , (2003), 125 (20), 6165-71.

Anna Wilkins and Jenny J. Yang, Structural Biology of the Cell Adhesion Protein CD2: From Protein Folding and Design to Molecular Recognition Current Protein and Peptide Science (2003 ), 4 , 367-73.

Anna L. Wilkins, Yiming Ye, Wei Yang, Zhi-ren Liu, Sarah Shealy , Hsiau-wei Lee, and Jenny J. Yang. Calcium-binding Affinity of a de novo designed protein. Protein Engineering (2002) , 15, 571-4.

Wei Yang, Hsiau-wei Lee, Homme Hellinga and Jenny J. Yang. Identification and Design of Metal-Binding Proteins. Proteins (2002), 47 , 344-356.

Wei Yang, Hsiauwei Lee, Homme Hellinga , Michelle Pu and Jenny Jie Yang. Design Calcium Binding Sites by Computer Algorithm. Computational Studies, Nanotechnology , and Solution Thermodynamics of Polymer Systems . Kluwer Academic/Plenum Publishers (2000) ,127-138.