Protein phase diagrams II: Non-ideal behavior of
biochemical reactions in the presence of osmolytes
Allan C Ferreon 1, Josephine C Ferreon 1, David Bolen 2 and Jorg Rosgen 3*
1 Scripps
2 Univ. of Texas Medical Branch
3 UTMB
* To whom correspondence should be addressed. E-mail: jorosgen{at}utmb.edu.
Submitted on June 27, 2006
Revised on July 26, 2006
Accepted on 20 September 2006
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Abstract |
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In the age of biochemical systems biology, proteomics and high throughput methods the thermodynamic quantification of cytoplasmatic reaction networks comes into reach of the current generation of scientists. What is needed to efficiently extract the relevant information from the raw data is a robust tool for evaluating the number and stoichiometry of all observed reactions while providing a good estimate of the thermodynamic parameters that determine the molecular behavior. The recently developed phase diagram method (Rösgen & Hinz, 2003, JMB 328, 255-271), strictly speaking a graphical representation of linkage or Maxwell Relations, offers such capabilities. Here, we extend the phase diagram method to non-ideal conditions. For the sake of simplicity we choose as an example a reaction system involving the protein RNase A, its inhibitor CMP, the osmolyte urea, and water. We investigate this system as a function of the concentrations of inhibitor and osmolyte at different temperatures ranging from 280K to 340K. The most interesting finding is that the protein-inhibitor binding equilibrium depends strongly on the urea concentration - by orders of magnitude more than expected from urea-protein interaction alone. Moreover, the m-value of ligand binding is strongly concentration dependent, which is highly unusual. It is concluded that the interaction between small molecules like urea and CMP can significantly contribute to cytoplasmic non-ideality. Such finding is highly significant because of its impact on renal tissue where high concentrations of co-solutes occur regularly.
Key Words:
ligand binding, non-ideal, nucleotides, osmolytes, protein folding
