We demonstrate the utility of a new empirical function to represent the degree of solvent exposure of an individual residue in a protein. This new term was designed based on the location of neighboring atoms or “crowding” around the residue, which is directly related to the solvent accessibility (Supplemental Figure 1
). The ability to distinguish “inside” and “outside” residues in principle should assist in determining a global fold of the protein. We illustrated the feasibility of this approach using both experimentally acquired water to protein magnetization transfer data and solvent PRE data. These data correlated well with the values calculated from the known protein structures using the new empirical term (&). The addition of this new potential to a limited number of NMR-based restraints can significantly improve structure convergence to the correct conformation as evidenced for protein Bax () and ubiquitin (Supplemental Table 1
). Furthermore, these types of solvent accessibility restraints were used in determining the protein complex structures as illustrated with the Qua1 homodimer (). These restraints are very useful in this case since the interaction surfaces of the complex have different solvent accessibility profiles than the free proteins. During the calculation the proper slope and offset in Eq. 2
, or 5
can be searched by a coarse grid method and further optimized using an iterative operation by fitting to the experimental data to the calculated structures. From the calculations tested using proteins Bax, ubiquitin and Qua1 homodimer, we demonstrated that access to this type of solvent accessibility information could substantially expedite the initial stage of the NMR structure determination.
The water to protein magnetization transfer experiment used to illustrate our method probes very complicated interactions between the protein and the water molecules. This measurement alone will not differentiate the water to a protein-proton NOE rate from the solvent exchange rate. In experimental conditions used here, the chemical exchange rates between bulk water and exchangeable NH protons are generally faster than the inefficient NOE rates between the two due to the short residence time [33
]. For those amide hydrogen’s protected by hydrogen-bonds, most of the amide hydrogen-water NOE correlations seen in bulk solution are also likely dominated by exchange-relayed NOE interactions with labile side chain hydrogen, not by direct protein-water NOEs [30
]. Nevertheless, it is important to point out that an increase in both NOE and solvent exchange rates still indicates that the residue is solvent exposed. In addition to the above issue, long lived bound water or buried water molecule, Cα
protons that resonate close to water frequency, as well as rapidly exchanging hydroxyl protons can result in measured intensity ratios that will not follow the relationship described here. Some of these contributions can be distinguished by carrying out a complementary ROE experiment as previously suggested [36
]. Interestingly, the intensity ratios for Bax and Bid that we measured were not screened for any of these possible effects and still resulted in an acceptable outcome. We did, however, use a deuterated ubiquitin sample in our water to protein magnetization transfer experiment to try to overcome the problem due to some Hα
resonances that are close to the frequency of water. Alternatively, any intensity ratios that do not follow the empirical relationship can be identified during the structure refinement process and treated accordingly, since they most likely will not agree with the distance restraints of the protein. This is similar to the PRE refinement when there is contribution from minor, previously unknown, conformation that would result in a deviation from the predicted PRE values [48
The results presented here provide some evidence that the SAcc metric can be of general use in quantitatively interpreting various observations that primarily depend on solvent accessibility. The inclusion of this type of structural information that differentiates surface exposed from buried residues can significantly improve convergence and accuracy in structure calculations.