The input for this program can either be a sequence of residue names or PDB format. If the input is in PDB format and it contains more than one monomer, the number of residues needs to be given. If the input in PDB format contains a hetero-complex, the peptide to be predicted needs to be the first. Missing residues in a PDB file will be replaced by alanines.
If exchange is in D2O, 0.4 is added to the pH meter reading in order to correct for the glass electrode solvent isotope artifact. It is recommended that you do not change this, since this will keep it consistent with the correction factors in references 2 and 3. Actual data points should be plotted without making the correction (i.e., using the uncorrected pH meter reading).
The activation energy for base catalyzed rate is defaulted to 2.6, instead of 17 in ref. 2, because the act. enthalpy (~14.3) for water ionization as a function of temperature is calculated separately. The activation energy for general catalyzed rate is defaulted to 13 to match the experimental data at high temperature for BPTI (ref. 7) and Ribonuclase A (ref. 8).
The program outputs the following values:
"AA pair" - the residue number, the preceding amino acid, and the amino
acid for which exchange is being predicted.
"kex (sec-1)" - the predicted intrinsic exchange rate for that residue.
"Time Const. (min.)" - the time constant in minutes = 1/(60*kex)
"HalfLife (min.)" - the half life in minutes = time constant * ln(2)
"kexmin (sec-1)" - the minimum exchange rate (at pHmin)
"T.C.max (min.)" - the maximum time constant (at pHmin)
"H.L.max (min.)" - the maximum half life (at pHmin)
"pHmin" - the pH at which exchange is slowest, where the acid and base-catalyzed rates intersect. The pHmin given is actually pDmincorrected.
"log(kH)" - log kH
"log(kOH)" - log kOH
"log(kH2O)" - log kH2O
Testing of the program with BPTI and RNase A was done by YZ. Zhang
and H. Roder.
1. Yu-Zhu Zhang, Protein and peptide structure and interactions studied by hydrogen exchange and NMR. Ph.D. Thesis, Structural Biology and Molecular Biophysics, University of Pennsylvania, PA, USA.
2. Bai, Milne, Mayne & Englander, Proteins 17: 75-86 (1993).
3. Connelly, Bai, Jeng & Englander, Proteins 17: 87-92 (1993).
4. Englander & Poulsen, Biopolymers 7: 379-93 (1969).
5. Molday, et al. Biochemistry 11: 150-8 (1972).
6. Englander, et al. Anal. Biochem. 92: 517-24 (1979).
7. Roder, et al. Biochemistry 24: 7407-11 (1985).
8. Robertson & Baldwin, Biochemistry 30: 9907-14 (1991).
9. Cantor & Schimmel, Biophysical Chemistry. WH Freeman and Company, New York, (1979).
10. Covingtion, et al. J. Chem. Phys. 70: 3820-4 (1966).
Credits: The GWBasic programs HXPRED4-6 first by Andy Robertson and later modified by Paul Laub, Yu-Zhu Zhang and Heinrich Roder were referenced.
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