Structure and dynamics of a detergent-solubilized membrane protein: measurement of amide hydrogen exchange rates in M13 coat protein by proton NMR spectroscopy

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Abstract
The coat protein of bacteriophage M13 is inserted into the inner membrane of Escherichia coli where it exists as an integral membrane protein during the reproductive cycle of the phage. The protein sequence consists of a highly hydrophobic 19-residue central segment flanked by an acidic 20-residue N-terminus and a basic 11-residue C-terminus. We have measured backbone amide hydrogen exchange of the protein solubilized in perdeuteriated sodium dodecyl sulfate using 1H nuclear magnetic resonance (NMR) spectroscopy. Direct proton exchange-out measurements in D2O at 24.degree. C were used to follow the exchange of the slowest amides in the protein. Multiple exponential fitting of the exchange data showed that these amides (29 .+-. 3 at pH 4.5) exchanged in two kinetic sets with exchange rates [(1.2 .+-. 0.4) .times. 10-4 s-1 and (4.1 .+-. 1.2) .times. 10-7 s-1] that differed by more than 100-fold, the slower kinetic set being retarded 105-fold relative to poly(DL-alanine). The exchange rate constant for the slowest set of amides exhibited an unusual pD dependence, being proportional to [OD-]1/2. It is shown that this is an artifact of the multiple exponential fitting of the data, and a new method of presentation of exchange data as a function of pD is introduced. Steady-state saturation-transfer techniques were also used to measure exchange. These methods showed that 15-20 amides in the protein are very stable at 55.degree. C and that about 30 amides have exchange rates retarded by at least 105-fold at 24.degree. C. Saturation-transfer studies also showed that the pH dependence of exchange in the hydrophilic termini was unusual. This is explained as being due to long-range electrostatic effects arising both from the protein itself and also from the anionic detergent molecules. Hydrogen exchange studies on the products of proteinase K digestion of the protein localized the slowly exchanging amides to the hydrophobic core of the protein. Relaxation [Henry, G. D., Weiner, J. H., and Sykes, B. D. (1986) Biochemistry 25, 590-598] and solid-state NMR experiments [Leo, G. C., Colnago, L. A., Valentine, K. G., and Opella, S. J. (1987) Biochemistry 26, 854-862] have previously shown that the majority of the protein backbone is rigid on the picosecond to microsecond time scale, except for the extreme ends of the molecule which are mobile. The hydrogen exchange results, which are sensitive to a much longer time scale (> 10-4 s), suggest a stable core with a progressive increase in amplitude or frequency of motions as the ends of the protein are approached.