Supplementary material for Alonso and Daggett (2000) Proc. Natl. Acad. Sci. USA 97 (1), 133-138.
Table 2. Properties of protein A transition states
Simulation | Time*, ps | <Rg>, Å | <SASA>, Å2 | <Cont>§ Nat, % | <Cont>§ Tot, % | H1 | H2 | H3 | |||
% a (f, y) | HB | % a (f, y) | HB | % a (f, y) | HB | ||||||
E1(498) | 240 | 11.1 | 4,800 | 76 | 85 | 95 | 8/9 | 91 | 11/11 | 82 | 11/12 |
E2(498) | 660 | 12.0 | 5,200 | 70 | 80 | 83 | 7/9 | 84 | 10/11 | 84 | 10/12 |
B1(498) | 240 | 12.4 | 5,700 | 64 | 81 | 6 | 2/8 | 72 | 6/8 | 86 | 11/12 |
B2(498) | 1200 | 12.4 | 5,500 | 63 | 78 | 80 | 7/8 | 45 | 2/8 | 76 | 11/12 |
*The transition state ensembles span the 5 ps before the given time.
Radius of gyration, see Table 1.
Solvent-accessible surface area [Hubbard, S. J. & Thornton, J. M. (1993) NACCESS (Dept. Biochem. and Mol. Biol., University College, London)].§
Percentage of native and total extent of native heavy atom contacts (distances less than 5.4 Å for aliphatic carbons and 4.6 Å for all others) with respect to NMR structure.¶
Helix properties for H1, H2, and H3 relative to the secondary structure in the starting structures (see Fig. 1). %a(f, y) is the percentage of helix based on repeating (f, y) angles [Daggett, V., Kuntz, I. D. & Kollman, P. A. (1991) Biopolymers 31, 1115-1134]. HB is the number of intact helical hydrogen bonds (rdonor-acceptor £ 2.6 Å more than 25% of the time). The number of native hydrogen bonds is given after the slash.