Kinetic analysis of the acid and the alkaline unfolded states of staphylococcal nuclease

Structural and Mechanistic Exploration of Acid Resistance: Kinetic Stability Facilitates Evolution of Extremophilic Behavior

“…Structural alignments, used for Supplemental Figure 1 and the sequence alignment in Figure 1, were performed using the Combinatorial Extension method. 76 Figures 5 and 9 were produced with Pymol 77 and Figure 6 with CCP4-MG. 7,79 The NAPase structure shown in Figure 6 includes two arginine side-chains that could not be accurately fit into the final model. For the purposes of Figure 6, these side-chains were placed into the most favorable rotamer.…”

“…Acidophilic proteins must have mechanisms in place to counter the buildup of large net positive charge due to neutralization of carboxylates, 6 the loss of carboxylate mediated salt-bridges, 7,8 and, at moderately acidic pH, the protonation of buried histidines. [9][10][11][12] Many acidophilic proteins, such as pepsin, 13 xylanase from Aspergillus kawachii, 14 the soxF protein from Sulfolobus acidocaldarius, 15 and the acid-tolerant killer toxin from Pichia farinosa, 16 have actually evolved an overabundance of acidic surface residues, thus reducing their overall pI and their net positive charge at any pH.…”

The Dependence of Membrane Permeability by the Antibacterial Peptide Cecropin B and Its Analogs, CB-1 and CB-3, on Liposomes of Different Composition

“…A i and i are the normalized amplitude and the time constant (or relaxation time) for the ith reaction. The best fit to the number of the exponential terms was determined from the chi square error (44). Measurements were repeated three times at a given condition to ensure reproducibility.…”

Significance of Local Electrostatic Interactions in Staphylococcal Nuclease Studied by Site-directed Mutagenesis

“…With rigorous investigation, however, both the kinetics and thermodynamics of protein folding may yield answers to this major biological question. From the kinetic point of view, a protein can be refolded in vitro to its active three-dimensional conformation on a millisecond time scale, as we have shown for staphylococcal nuclease (SNase) 1 (2)(3)(4). The sequence of equilibrium reactions among three denatured states and one native state has been established (5): D 3 u D 2 u D 1 u N 0 , where D i (i ϭ 1, 2, or 3) denotes the protein in its unfolded state and N 0 is the protein in its native state.…”