Quantitative analysis of the effects of photoswitchable distance constraints on the structure of a globular protein.
Photoswitchable distance constraints in the form of photoisomerizable chemical cross-links offer a general approach to the design of reversibly photocontrolled proteins. To apply these effectively, however, one must have guidelines for the choice of cross-linker structure and cross-linker attachment sites. Here we investigate the effects of varying cross-linker structure on the photocontrol of folding of the Fyn SH3 domain, a well-studied model protein. We develop a theoretical framework based on an explicit-chain model of protein folding, modified to include detailed model linkers, that allows prediction of the effect of a given linker on the free energy of folding of a protein. Using this framework, we were able to quantitatively explain the experimental result that a longer, but somewhat flexible, cross-linker is less destabilizing to the folded state than a shorter more rigid cross-linker. The models also suggest how misfolded states may be generated by cross-linking, providing a rationale for altered dynamics seen in nuclear magnetic resonance analyses of these proteins. The theoretical framework is readily portable to any protein of known folded state structure and thus can be used to guide the design of photoswitchable proteins generally.
Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada.
Andrew A
AA
Beharry
Tao
T
Chen
M Sameer
MS
Al-Abdul-Wahid
Subhas
S
Samanta
Kirill
K
Davidov
Oleg
O
Sadovski
Ahmed M
AM
Ali
Simon B
SB
Chen
R Scott
RS
Prosser
Hue Sun
HS
Chan
G Andrew
GA
Woolley
D000480:Alkynes / Q000138:chemical synthesis / Q000737:chemistry; D001391:Azo Compounds / Q000138:chemical synthesis / Q000737:chemistry; D003432:Cross-Linking Reagents / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008958:Models, Molecular; D010782:Photolysis; D011487:Protein Conformation; D017510:Protein Folding; D051076:Proto-Oncogene Proteins c-fyn / Q000737:chemistry*; D013425:Sulfanilic Acids / Q000138:chemical synthesis / Q000737:chemistry; D018909:src Homology Domains
C575877:3,3'-bis(sulfonato)-4,4'-bis(chloroacetamide)azobenzene; D000480:Alkynes; D001391:Azo Compounds; D003432:Cross-Linking Reagents; D013425:Sulfanilic Acids; D051076:Proto-Oncogene Proteins c-fyn